User Guide to

MODDE

By Umetrics

Version 9
© 1992-2009 MKS Umetrics AB, all rights reserved
Information in this document is subject to change without notice and does not
represent a commitment on part of Umetrics. The software, which includes
information contained in any databases, described in this document is
furnished under license agreement or nondisclosure agreement and may be
used or copied only in accordance with the terms of the agreement. It is
against the law to copy the software except as specifically allowed in the
license or nondisclosure agreement. No part of this user guide may be
reproduced or transmitted in any form or by any means, electronic or
mechanical, including photocopying and recording, for any purpose, without
the express written permission of Umetrics.
Umetrics patents and trade marks:
OPLS/O2PLS®, SWE-9802229-6, USA-6754543,
OSC®, SWE-0000563-7, USA-6853923
PLS-TREE®, Pending
SEQUENTIAL MODELING, Pending
DESIGN SPACE, Pending
MODDE®, RED - MUP®, VALUE FROM DATA®, OPLS®, O2PLS®, O2-
PLS®, OPLS-DA®, O2PLS-DA™
PLS-TREE™, S-PLOT™, EZinfo®, SBOL®, FABSTAT®, BATCH
FINGERPRINT®, SIMCA®.

ID # 2038

MKS Umetrics AB
Stortorget 21
SE-211 34 Malmö
Sweden
Phone: +46 (0)40 664 2580
Email: info@umetrics.com
Welcome

Welcome to the user guide for MODDE 9. This is your guide to MODDE and
its capabilities.
Assumed prior knowledge
We assume that you are already familiar with Windows. You should be
familiar with the topics discussed in your Microsoft Windows User's Guide,
including how to use the mouse select, click, shift-click, control-click, press,
drag, and choose from a menu. You should also know how to search through
directories to find files.
Content
This user guide is divided into 21 chapters. Chapter 1 gives a short
introduction of how to use MODDE. Chapter 2 presents an introduction to
experimental design. Chapter 3 is an overview of the program. Chapters 4 - 20
provide step-by-step procedures for creating and using experimental designs
with MODDE. Chapter 21 describes how the Help function works.
Appendix A, "Statistical notes" presents short explanations of statistical
methods used by MODDE.
Appendix B, “Designs” presents short descriptions of the designs available in
MODDE.
Appendix C: "Optimizer" describes the optimizer feature and the properties of
the different optimizer objectives.
Appendix D: "Design Space" describes the design space estimation feature.
References are available on the references page.
User guide edition Tuesday, September 22, 2009.
Table of Contents
How to get started with MODDE 1 
Installation ..................................................................................................................... 1 
Starting MODDE ........................................................................................................... 1 
Experimental cycle ........................................................................................................ 1 
Design phase .................................................................................................................. 2 
Defining factors................................................................................................................... 2 
Defining responses .............................................................................................................. 2 
Defining objective ............................................................................................................... 2 
Analysis phase ............................................................................................................... 2 
Explore the data (Worksheet menu) .................................................................................... 2 
Evaluate the design ............................................................................................................. 3 
Fit ........................................................................................................................................ 3 
Review the fit using plots and lists ...................................................................................... 3 
Diagnostics .......................................................................................................................... 3 
Interpret the model .............................................................................................................. 3 
Refine the model ................................................................................................................. 4 
Prediction phase (using the model) ................................................................................ 4 
Introduction to MODDE and experimental design 5 
General description ........................................................................................................ 5 
What is modeling and experimental design? ................................................................. 5 
Objectives of modeling and experimental design .......................................................... 5 
Screening models and designs ....................................................................................... 5 
Number of factors in screening designs .............................................................................. 6 
Number of factors with split objective ................................................................................ 6 
Response surface modeling (RSM) designs................................................................... 6 
Number of factors in RSM designs ..................................................................................... 6 
Number of factors in Split objective ................................................................................... 7 
Fit methods .................................................................................................................... 7 
Multiple Linear Regression (MLR) ..................................................................................... 7 
Partial Least Squares (PLS)................................................................................................. 7 
Results ................................................................................................................................. 8 
Analysis phase ............................................................................................................... 9 
Review the model fit ........................................................................................................... 9 
Assess model adequacy ....................................................................................................... 9 
Prediction - using the fitted model ................................................................................. 9 
Convention................................................................................................................... 10 
Limitations in investigation names.................................................................................... 10 
Limitations in factor and response names ......................................................................... 10 
Case sensitivity ................................................................................................................. 10 
Menu reference syntax ...................................................................................................... 10 
Suggestions for further reading on experimental designs ............................................ 10 
Overview 11 
Application icon and symbol ....................................................................................... 11 

i
User Guide to MODDE

Investigation ................................................................................................................ 11 

Managing investigations ................................................................................................... 11 
Compatibility with older MODDE versions ...................................................................... 12 
Organization ................................................................................................................ 12 
Command menu bar ..................................................................................................... 13 
File menu .......................................................................................................................... 13 
Edit menu .......................................................................................................................... 14 
View menu ........................................................................................................................ 14 
Design menu ..................................................................................................................... 14 
Worksheet menu ............................................................................................................... 15 
Analysis menu ................................................................................................................... 15 
Prediction menu ................................................................................................................ 15 
Show menu........................................................................................................................ 16 
Window menu ................................................................................................................... 16 
Toolbars ....................................................................................................................... 16 
Plots and lists ............................................................................................................... 16 
File 17 
Introduction.................................................................................................................. 17 
New.............................................................................................................................. 17 
Traditional designs ............................................................................................................ 18 
Advanced designs.............................................................................................................. 18 
Import design from file ..................................................................................................... 21 
Open............................................................................................................................. 21 
Save and save as .......................................................................................................... 21 
Delete investigation ..................................................................................................... 21 
Save plot/list as ............................................................................................................ 21 
Revert........................................................................................................................... 22 
Send by E-Mail ............................................................................................................ 22 
Generate HTML report ................................................................................................ 22 
Complement design ..................................................................................................... 23 
Available complementing methods ................................................................................... 24 
Fold over ........................................................................................................................... 24 
Estimate squares of selected factors in factorial designs ................................................... 24 
D-Optimal ......................................................................................................................... 25 
Complement Doehlert ....................................................................................................... 27 
Screening to RSM Rechtschaffner .................................................................................... 28 
Plackett Burman Super-Saturated to Plackett Burman ...................................................... 28 
Protect investigation .................................................................................................... 29 
Encrypt/password protect an investigation ........................................................................ 29 
Lock investigation ............................................................................................................. 29 
Print Setup ................................................................................................................... 30 
Print Preview ............................................................................................................... 30 
Print ............................................................................................................................. 30 
Print format for plots ......................................................................................................... 30 
Exit............................................................................................................................... 30 
Edit 31 
Introduction.................................................................................................................. 31 
Undo ............................................................................................................................ 31 
Cut, copy, paste, delete, select all ................................................................................ 31 

ii
 Table of Contents

Add factor, add response, add experiment, insert rows ............................................... 32 
Sort............................................................................................................................... 32 
Sorting the candidate set ................................................................................................... 33 
Model / reference mixture............................................................................................ 34 
Model ................................................................................................................................ 34 
Reference mixture ............................................................................................................. 36 
Generators .................................................................................................................... 37 
Edit the model and/or generators before creating the worksheet ................................. 38 
View 39 
Introduction.................................................................................................................. 39 
Toolbars ....................................................................................................................... 39 
Standard toolbar ................................................................................................................ 39 
Spreadsheet toolbar ........................................................................................................... 41 
Plot toolbar ........................................................................................................................ 41 
Model toolbar .................................................................................................................... 44 
Window toolbar................................................................................................................. 44 
Status bar........................................................................................................................... 44 
Dockable windows....................................................................................................... 44 
Analysis advisor ................................................................................................................ 45 
Audit trail .......................................................................................................................... 45 
Favorites............................................................................................................................ 45 
Output ............................................................................................................................... 50 
Notes ................................................................................................................................. 50 
Add to Favorites .......................................................................................................... 51 
Add to Report .............................................................................................................. 51 
Full Screen ................................................................................................................... 51 
Changing the default options using Investigation Options .......................................... 52 
Plot labels .......................................................................................................................... 52 
Number format .................................................................................................................. 52 
Audit trail .......................................................................................................................... 53 
Alpha level ........................................................................................................................ 54 
Coefficients ....................................................................................................................... 55 
Blocking ............................................................................................................................ 56 
Confidence level ............................................................................................................... 56 
List presentation ................................................................................................................ 57 
R2 in plots ......................................................................................................................... 57 
Residuals ........................................................................................................................... 58 
Select Factor...................................................................................................................... 58 
General Options ........................................................................................................... 58 
General page ..................................................................................................................... 59 
List Options ....................................................................................................................... 60 
Restore .............................................................................................................................. 61 
Customize .................................................................................................................... 61 
Customize toolbars ............................................................................................................ 61 
Customize commands ....................................................................................................... 61 
Customize options ............................................................................................................. 62 
Customize options ............................................................................................................. 62 

Design 63 
Introduction.................................................................................................................. 63 

iii
User Guide to MODDE

Factors ......................................................................................................................... 63 

Responses .................................................................................................................... 63 
Constraints ................................................................................................................... 63 
Inclusions ..................................................................................................................... 64 
Objective ...................................................................................................................... 64 
D-Optimal .................................................................................................................... 64 
Design wizard .............................................................................................................. 64 
Factors 65 
Introduction.................................................................................................................. 65 
Factor definition dialog ................................................................................................ 65 
Factor name ....................................................................................................................... 66 
Abbreviation...................................................................................................................... 66 
Units .................................................................................................................................. 66 
General page ..................................................................................................................... 66 
Advanced .......................................................................................................................... 69 
Factor definition spreadsheet ....................................................................................... 72 
Printing the factor spreadsheet .......................................................................................... 72 
Factor manipulations in short....................................................................................... 73 
Opening the factor definition spreadsheet ......................................................................... 73 
Adding a factor.................................................................................................................. 73 
Modifying a factor............................................................................................................. 73 
Updating the worksheet..................................................................................................... 73 
Copying a factor ................................................................................................................ 73 
Deleting a factor ................................................................................................................ 74 

Responses 75 
Introduction.................................................................................................................. 75 
Response definition dialog........................................................................................... 75 
Response name .................................................................................................................. 76 
Abbreviation...................................................................................................................... 76 
Units .................................................................................................................................. 76 
Selecting type of response ................................................................................................. 76 
Limits ................................................................................................................................ 76 
Regular responses ........................................................................................................ 77 
Transformation .................................................................................................................. 77 
MLR scaling...................................................................................................................... 77 
PLS scaling ....................................................................................................................... 77 
Derived responses ........................................................................................................ 78 
Defining derived responses ............................................................................................... 79 
Modifying a derived response ........................................................................................... 80 
Copying or deleting a derived response ............................................................................ 80 
Using sets of variables in derived responses ..................................................................... 80 
Syntax for derived responses............................................................................................. 81 
Operators and functions in derived responses ................................................................... 81 
Qualitative factors in derived responses ............................................................................ 82 
Linked responses ......................................................................................................... 82 
Response definition spreadsheet .................................................................................. 83 
Printing the response definition spreadsheet ..................................................................... 83 
Response manipulations in short ................................................................................. 84 
Opening the responses spreadsheet ................................................................................... 84 

iv
 Table of Contents

Adding a response ............................................................................................................. 84 

Modifying a response ........................................................................................................ 84 
Deleting a response ........................................................................................................... 84 
Copying and pasting a response ........................................................................................ 84 

Constraints and inclusions 85 

Constraints ................................................................................................................... 85 
Specifying constraints ....................................................................................................... 85 
Constraints supported ........................................................................................................ 86 
Defining constraints in the spreadsheet ............................................................................. 86 
Defining a constraint graphically ...................................................................................... 87 
Modifying a constraint graphically ................................................................................... 88 
Candidate set with a constraint.......................................................................................... 89 
Constraints in qualitative or quantitative multilevel factors .............................................. 89 
Inclusions ..................................................................................................................... 90 
Inclusions vs. complement design ..................................................................................... 90 
Inclusions added to the worksheet..................................................................................... 90 
Inclusions as part of the design ......................................................................................... 91 
Generating inclusions ........................................................................................................ 92 
Modifying inclusions ........................................................................................................ 92 

Objective, model and design 93 

Introduction.................................................................................................................. 93 
Selecting the objective ................................................................................................. 94 
Screening objective ........................................................................................................... 94 
RSM objective................................................................................................................... 94 
Split Objective................................................................................................................... 94 
Paste Data.......................................................................................................................... 95 
Selecting model and design ......................................................................................... 95 
Designs in MODDE .......................................................................................................... 95 
Recommended designs ...................................................................................................... 96 
Runs in design ................................................................................................................... 96 
Model ................................................................................................................................ 96 
Screening models .............................................................................................................. 96 
RSM models...................................................................................................................... 96 
Split models ...................................................................................................................... 96 
Pseudo resolution for blocked designs .............................................................................. 97 
Design runs ....................................................................................................................... 97 
Center points ..................................................................................................................... 98 
Replicates .......................................................................................................................... 98 
Total runs .......................................................................................................................... 98 
Settings.............................................................................................................................. 99 
Description ...................................................................................................................... 101 
Blocks ............................................................................................................................. 102 

D-Optimal 103 
What are D-Optimal designs? .................................................................................... 103 
When do I use D-Optimal designs? ........................................................................... 103 
D-Optimal pages in the design wizard ....................................................................... 104 
Design generation criteria section ................................................................................... 104 
Design alternatives section .............................................................................................. 106 
Candidate set section ....................................................................................................... 107 

v
User Guide to MODDE

D-Optimal results ............................................................................................................ 108 

D-Optimal on the Design menu ................................................................................. 109 
Generate .......................................................................................................................... 109 
Candidate set ................................................................................................................... 109 
Evaluate........................................................................................................................... 110 
Onion plot, onion 3D scatter ........................................................................................... 110 
Design plot ...................................................................................................................... 110 
D-Optimal onion design............................................................................................. 111 
Candidate set ................................................................................................................... 111 
Generating the design ...................................................................................................... 112 
D-Optimal on the Design menu with Onion .................................................................... 113 
Evaluate........................................................................................................................... 114 
Onion plots ...................................................................................................................... 115 

Design Wizard 117 

Introduction................................................................................................................ 117 
Defining factors ......................................................................................................... 117 
Defining responses..................................................................................................... 119 
Selecting the objective ............................................................................................... 120 
Selecting model and design ....................................................................................... 121 
D-Optimal pages in the design wizard ....................................................................... 122 
Worksheet 123 
Introduction................................................................................................................ 123 
Worksheet menu ........................................................................................................ 123 
Opening the worksheet spreadsheet ................................................................................ 123 
Setting run order.............................................................................................................. 124 
Curvature diagnostic plot ................................................................................................ 125 
2D and 3D scatter plots ................................................................................................... 126 
Histogram ........................................................................................................................ 127 
Descriptive statistics........................................................................................................ 128 
Correlation ...................................................................................................................... 129 
Replicate plot .................................................................................................................. 130 
Worksheet spreadsheet .............................................................................................. 131 
Description of the worksheet........................................................................................... 131 
Missing values in the worksheet ..................................................................................... 131 
Deleting the worksheet .................................................................................................... 131 
Displaying the worksheet ................................................................................................ 131 
Adding experiments in the worksheet ............................................................................. 132 
Sorting the worksheet ...................................................................................................... 132 
Colors in the worksheet ................................................................................................... 132 

Analysis 133 
Introduction................................................................................................................ 133 
Organization of the Analysis menu............................................................................ 133 
Evaluate ..................................................................................................................... 134 
Condition number ........................................................................................................... 134 
Runs, terms and degrees of freedom ............................................................................... 134 
Analysis Wizard......................................................................................................... 135 
Open the Analysis Wizard............................................................................................... 135 
Analysis Wizard content ................................................................................................. 136 

vi
 Table of Contents

Customize the Analysis Wizard text ............................................................................... 136 

Fitting the model to the data ...................................................................................... 136 
Selecting fit method ........................................................................................................ 137 
Fitting the model ............................................................................................................. 137 
Next component (only PLS) ............................................................................................ 138 
Displaying the summary of fit ................................................................................... 139 
Summary of fit plot ......................................................................................................... 139 
Summary of fit list .......................................................................................................... 141 
PLS summary plot (only PLS) ........................................................................................ 141 
PLS response plot (only PLS) ......................................................................................... 142 
PLS summary list ............................................................................................................ 142 
Saturated models ............................................................................................................. 142 
Investigating diagnostics............................................................................................ 143 
Normal probability plot of residuals................................................................................ 143 
Residuals ......................................................................................................................... 144 
Distance to the model in the Y space – DModY (only PLS) ........................................... 146 
Box Cox Plot (MLR only) ............................................................................................... 147 
Observed vs. predicted .................................................................................................... 148 
Lack of fit plot................................................................................................................. 149 
Analysis of Variance (ANOVA) ..................................................................................... 150 
Reviewing and interpreting the fit ............................................................................. 152 
Coefficient plots and lists ................................................................................................ 152 
Effects plots and list ........................................................................................................ 155 
Variable importance in the projection – VIP (only PLS) ................................................ 161 
PLS score and loading plots....................................................................................... 162 
Score plots (only PLS) .................................................................................................... 162 
Score plot examples (only PLS) ...................................................................................... 163 
Loading plots (only PLS) ................................................................................................ 163 
Loading plot example (only PLS) ................................................................................... 164 

Prediction 165 
Introduction................................................................................................................ 165 
Contour plot wizard ................................................................................................... 166 
Inner plot type ................................................................................................................. 166 
Selecting responses ......................................................................................................... 166 
Using constraints ............................................................................................................. 166 
Plot options ..................................................................................................................... 167 
2D contour ...................................................................................................................... 167 
4D contour ...................................................................................................................... 169 
Response Surface ............................................................................................................ 172 
Prediction plot wizard ................................................................................................ 173 
Prediction plot wizard first page selections ..................................................................... 173 
Axes and constants .......................................................................................................... 174 
Overlay prediction plot ................................................................................................... 174 
Response prediction plot ............................................................................................ 175 
Factor type ...................................................................................................................... 175 
Prediction list ............................................................................................................. 176 
Scatter plot ................................................................................................................. 176 
Sweet spot plot ........................................................................................................... 177 
Creating a sweet spot plot ............................................................................................... 177 
Optimizer ................................................................................................................... 180 
Factor spreadsheet in the Optimizer ................................................................................ 181 

vii
User Guide to MODDE

Response spreadsheet ...................................................................................................... 181 

Run list ............................................................................................................................ 183 
Optimizer context menu .................................................................................................. 184 
Optimizer buttons ............................................................................................................ 185 
Design Space Validation ............................................................................................ 190 
Design Space 191 
Introduction................................................................................................................ 191 
Design Space Estimation around the selected setpoint .............................................. 191 
Design Space Validation for robustness testing ......................................................... 192 
Design Space window ................................................................................................ 192 
Factor spreadsheet ........................................................................................................... 193 
Response spreadsheet ...................................................................................................... 194 
Design Space buttons ...................................................................................................... 194 
Design Space Properties .................................................................................................. 195 
Factor histogram ........................................................................................................ 196 
Response histogram ................................................................................................... 197 
Design Space Statistics list ........................................................................................ 197 
Final factor adjustments ............................................................................................. 198 
Show 199 
Introduction................................................................................................................ 199 
Objective .................................................................................................................... 199 
Design matrix............................................................................................................. 200 
Design region ............................................................................................................. 201 
Design region properties ................................................................................................. 201 
Design region for mixture designs ............................................................................. 202 
Confoundings............................................................................................................. 202 
Summary D-Optimal.................................................................................................. 203 
Model ......................................................................................................................... 204 
Reference mixture ...................................................................................................... 204 
Plots and lists 205 
Introduction................................................................................................................ 205 
Properties page........................................................................................................... 205 
Opening property page by right-clicking......................................................................... 205 
Making a change in the property page ............................................................................ 205 
Automatic update of plots and lists ............................................................................ 205 
Saving plots and lists ................................................................................................. 205 
Generating multiple plots or lists ............................................................................... 206 
Plot settings................................................................................................................ 206 
Axis ................................................................................................................................. 207 
Header and Footer ........................................................................................................... 209 
Plot Area ......................................................................................................................... 210 
Saving plot settings ......................................................................................................... 212 
Customizing contour plots using the property page ................................................... 213 
Resolution ....................................................................................................................... 213 
Scale subplots equally ..................................................................................................... 213 
Lock contour levels ......................................................................................................... 213 
Use color ......................................................................................................................... 213 

viii
 Table of Contents

Show contour level labels ............................................................................................... 214 

Plot settings for contour plots .................................................................................... 214 
Axis ................................................................................................................................. 214 
Header ............................................................................................................................. 214 
Regions ........................................................................................................................... 214 
Labels .............................................................................................................................. 214 
Contour ........................................................................................................................... 214 
Plot settings for sweet spot plots ................................................................................ 215 
Axis ................................................................................................................................. 215 
Header ............................................................................................................................. 215 
Contour ........................................................................................................................... 215 
Plot settings for 3D scatter plots ................................................................................ 216 
Cube ................................................................................................................................ 216 
Axis ................................................................................................................................. 217 
Header ............................................................................................................................. 218 
Legend ............................................................................................................................ 218 
Footer .............................................................................................................................. 218 
Symbols........................................................................................................................... 219 
Labels .............................................................................................................................. 219 
Colors .............................................................................................................................. 219 
Zoom and rotate ......................................................................................................... 220 
Report generator 221 
Introduction................................................................................................................ 221 
Starting the report generator ...................................................................................... 221 
Report generator window........................................................................................... 222 
Command menu bar ................................................................................................... 222 
File menu ........................................................................................................................ 222 
Edit menu ........................................................................................................................ 224 
View menu ...................................................................................................................... 224 
Insert menu...................................................................................................................... 224 
Format menu ................................................................................................................... 225 
Tools menu...................................................................................................................... 225 
Help menu ....................................................................................................................... 226 
Generate report toolbar .............................................................................................. 226 
New ................................................................................................................................. 226 
Generate report specific buttons ...................................................................................... 226 
Format toolbar ........................................................................................................... 226 
Placeholder window................................................................................................... 227 
Properties window ..................................................................................................... 228 
Adding plots and lists to the report ............................................................................ 228 
Help 229 
Introduction................................................................................................................ 229 
HTML help ................................................................................................................ 229 
Registration and activation ........................................................................................ 229 
Manage Licenses ....................................................................................................... 229 
Umetrics on the Web ................................................................................................. 230 
About MODDE .......................................................................................................... 230 

ix
User Guide to MODDE

Appendix A: Statistical notes 231 

Fit methods ................................................................................................................ 231 
Multiple Linear Regression (MLR) ................................................................................. 231 
Partial Least Squares (PLS)............................................................................................. 232 
Model ......................................................................................................................... 234 
Hierarchy......................................................................................................................... 234 
Scaling ....................................................................................................................... 235 
Scaling X ......................................................................................................................... 235 
Scaling Y ......................................................................................................................... 235 
Condition number ...................................................................................................... 236 
Condition number definition ........................................................................................... 236 
Condition number with mixture factors........................................................................... 236 
PLS and Cox reference mixture model ........................................................................... 236 
MLR (regression) and the Cox model ............................................................................. 236 
MLR (regression) and Scheffé model ............................................................................. 237 
Missing data ............................................................................................................... 237 
Missing data in X ............................................................................................................ 237 
Missing data in Y with Multiple Linear Regression ........................................................ 237 
Missing data in Y with PLS ............................................................................................ 237 
N-value ...................................................................................................................... 237 
Residual Standard Deviation (RSD) .......................................................................... 237 
ANOVA ..................................................................................................................... 238 
Measures of goodness of fit ....................................................................................... 239 
Q2.................................................................................................................................... 239 
R2 .................................................................................................................................... 239 
Degrees of freedom ......................................................................................................... 239 
Coefficients ................................................................................................................ 240 
Scaled and centered coefficients ..................................................................................... 240 
Normalized coefficients .................................................................................................. 240 
PLS orthogonal coefficients ............................................................................................ 240 
Confidence intervals........................................................................................................ 240 
Coding qualitative factors at more than 2 levels ........................................................ 241 
Residuals .................................................................................................................... 241 
Raw residuals .................................................................................................................. 241 
Standardized residuals ..................................................................................................... 241 
Deleted studentized residuals .......................................................................................... 241 
Predictions ................................................................................................................. 242 
PLS plots.................................................................................................................... 242 
Plot loadings.................................................................................................................... 242 
Plot scores ....................................................................................................................... 242 
PLS coefficients ......................................................................................................... 242 
Box-Cox plot (only MLR) ......................................................................................... 243 
Mixture data in MODDE ........................................................................................... 243 
Mixture factors only ........................................................................................................ 243 
Process and mixture factors............................................................................................. 247 
Optimizer ................................................................................................................... 248 
Desirability ...................................................................................................................... 248 
Overall desirability .......................................................................................................... 249 
Overall Distance to Target .............................................................................................. 249 
Starting simplexes ........................................................................................................... 249 
Sensitivity Analysis......................................................................................................... 250 

x
 Table of Contents

Orthogonal blocking .................................................................................................. 250 

Block interaction ............................................................................................................. 250 
Recoding the blocking factors ......................................................................................... 251 
Inclusions and blocks ...................................................................................................... 251 
Blocking screening designs ............................................................................................. 251 
Blocking RSM designs .................................................................................................... 252 
Blocking D-Optimal designs ........................................................................................... 252 
Random versus fixed block factor ................................................................................... 253 
Design Space statistics ............................................................................................... 254 
Monte Carlo simulations ................................................................................................. 254 
DPMO and Cpk ............................................................................................................... 255 
Predictions including model error ................................................................................... 256 

Appendix B: Designs 257 

Designs for process factors ........................................................................................ 257 
Screening designs ............................................................................................................ 257 
RSM designs ................................................................................................................... 260 
Designs for mixture factors........................................................................................ 263 
Mixture and process factors ............................................................................................ 263 
Mixture factors definition................................................................................................ 263 
Mixture constraint ........................................................................................................... 264 
Mixture experimental region ........................................................................................... 264 
Classical mixture designs ................................................................................................ 265 
D-Optimal designs ..................................................................................................... 268 
What are D-Optimal designs? ......................................................................................... 268 
Candidate set ................................................................................................................... 268 
D-Optimal algorithm ....................................................................................................... 269 
Implementation of the D-Optimal algorithm in MODDE ............................................... 269 
Potential terms................................................................................................................. 269 
Design evaluation ............................................................................................................ 271 
Inclusions and design augmentation ................................................................................ 271 
Irregular region ............................................................................................................... 272 
D-Optimal Onion designs .......................................................................................... 274 
Screening onion designs .................................................................................................. 274 
RSM onion designs ......................................................................................................... 274 

Appendix C: Optimizer 275 

Introduction................................................................................................................ 275 
Search function .......................................................................................................... 275 
Optimizer objectives .................................................................................................. 276 
Limit optimization........................................................................................................... 276 
Target optimization ......................................................................................................... 277 
Focus optimization .......................................................................................................... 277 
Define optimizer specifications ................................................................................. 277 
Response specification example in the optimizer ............................................................ 278 
Optimizer result ......................................................................................................... 279 
Appendix D: Design Space 281 
Introduction................................................................................................................ 281 
Predictive Design Space Estimation .......................................................................... 281 
Monte Carlo simulations ................................................................................................. 282 
Evaluate the results and make necessary adjustments. .................................................... 283 

xi
User Guide to MODDE

How to find the best Design Space.................................................................................. 283 

Design Space Validation for robustness testing ......................................................... 284 
Design Space Validation example ................................................................................... 284 
Evaluation ....................................................................................................................... 285 
Factor spreadsheet ........................................................................................................... 285 
Response spreadsheet ...................................................................................................... 285 
Final adjustments ............................................................................................................ 286 
Result statistics for k2 ..................................................................................................... 288 

References 289 
Index 291 

xii
How to get started with MODDE

Installation
You can install MODDE under Windows Vista, XP, and 2000.

Note: You must have administrative privileges to be able to install the

software.
To install and activate MODDE follow the steps described below:
1. Download the password protected installation file from the Umetrics web
page www.umetrics.com, click Downloads. The password is available in the
delivery letter.
2. Open the file and when prompted enter personal information as well as
product information found in the delivery letter.
3. After completing the installation, MODDE needs to be activated with a
license file. Activation is done either (a) from an internal license server or (b)
from Umetrics. See the delivery letter, sent to the license administrator at
your company, for instructions.

Starting MODDE
Start MODDE by double-clicking its icon.
• To read about the MODDE software look in Help (contains the same
information as the user guide).
• To run tutorial examples, find them at www.umetrics.com (Downloads),
select an example, open the investigation used in the tutorial (.mip-file
included with the installation in the Investigation folder) and follow the
analysis steps.
• To start a new investigation, on the File menu click New.

Experimental cycle
The experimental cycle consists of three phases:
1. The design phase where you define your factors and within which ranges
they should be varied, your responses, objective, design and model.
2. The analysis phase where you explore your data, review the raw data and the
fit, review diagnostics in plots and lists, refine and interpret the model.

1
User Guide to MODDE

3. The prediction phase where you use the model to predict the optimum area
for operability.

Design phase
Once you have clicked New on the File menu the design wizard is then opened. Enter
the name and location of the new investigation in the appropriate fields.
For details on the design wizard, see the Design Wizard chapter.

Defining factors
On the second page of the design wizard, enter factor names, ranges, etc.
For details on defining factors see the Factors chapter.

Defining responses
On the third page of the design wizard, enter response name(s), etc.
For details on defining responses see the Responses chapter.

Defining objective
On the next page of the design wizard, click your objective Screening, RSM, or Split
Objective. Clicking Paste Data disables Next; clicking Finish opens the worksheet
for pasting.
Given your objective, the type of factors (formulation or process) and the number of
factors, MODDE recommends a design, a model, and a number of center points. The
total required number of runs for this design is displayed. Other choices compatible
with your objective type and number of factors are listed with the required number of
runs.
After clicking Finish, the Worksheet is automatically generated for all classical
designs. With D-Optimal designs, clicking Next opens a dialog for the selection and
generation of the D-Optimal design and worksheet.
After making the experiments, fill in the response values and actual factor values in the
worksheet.
For details on the objective pages, see the Objective, model and design chapter. For
details on the worksheet, see the section Worksheet spreadsheet in the Worksheet
chapter.

Analysis phase
After the response values have been entered in the worksheet you can review the raw
data, fit the model, review the fitted model, interpret the model, and refine the model.

Explore the data (Worksheet menu)

To explore the unfitted data use the Worksheet menu. The plots and lists available are:
the curvature diagnostic plot, scatter plot, histogram plot, descriptive statistics plot and
list, correlation plot and matrix, and the replicate plot.
For details on the worksheet menu plots and lists, see the Worksheet Menu section in
the Worksheet chapter.

2
 How to get started with MODDE

Evaluate the design

The condition number is used to evaluate the goodness of the design. As a rule of
thumb the condition number for screening designs should not exceed 3. For RSM
designs it should not exceed 10.
The condition number is listed in the Evaluate table, found on the Analysis menu. The
evaluate table also lists the number of runs and model terms, and the degrees of
freedom of the residuals.

Fit
When you are ready to fit a model to your design you click Fit on the Analysis menu.
MODDE automatically fits using MLR when the condition number is low and there are
no mixture factors. The fit methods available are MLR, PLS and for mixtures several
variants.
For PLS models you can choose to extract more components than the MODDE default.
To extract more components click Next Component on the Analysis menu. Next
Component is unavailable when MLR is used as fit method.

Review the fit using plots and lists

After fitting the model the Summary of Fit plot is displayed summarizing the fit in four
columns:
• Percent of the variation of the response explained by the model, R2. R2
overestimates the goodness of fit.
• Percent of the variation of the response predicted by the model according to
cross validation, Q2, and expressed in the same units as R2. Q2
underestimates the goodness of fit.
• Model Validity: A Measure of the validity of the model. When the Model
Validity column is larger than 0.25, there is no Lack of Fit of the model (the
model error is in the same range as the pure error).
• Reproducibility: The variation of the response under the same conditions
(pure error), often at the center points, compared to the total variation of the
response.

Diagnostics
MODDE has a number of diagnostic plots:
• Residual plots to find outliers, drifts, trends etc.
• Box Cox Plot to select the best transformation of Y.
• ANOVA: ANalysis Of VAriance, in particular review the Lack of Fit. The
estimation of lack of fit is only available when there are replicated points as
it compares the pure error and the model error.

Interpret the model

To interpret the influence of terms on the model use the Coefficient and Effect plots
and lists. The interaction plot is particularly useful if your model has strong interaction
terms. To display the interaction plot, click Effects on the Analysis menu, then click
Interaction plot.

3
User Guide to MODDE

When PLS is used for regression, scores and loadings can be plotted. These plots
provide an overview of the data. On the Analysis menu, click PLS Plots to select the
score or loading plot you want to display.

Refine the model

If you discover bad outliers or want to remove or add a term to the model you can
refine your model.

To remove outliers or insignificant model terms use the interactive exclude tool .
Click the button and then click/mark the outlier/term the in a plot. You can also
exclude it in the worksheet, by right-clicking the specific cell and clicking Exclude
value(s). The model is automatically refitted.

Note: When excluding an outlier or model term in a plot, the outlier or model
terms is only excluded for the displayed response.
Remove/Add terms from/to the model that are insignificant/significant for all
responses. Use Edit | Model or the interactive tool with the coefficient plot.
After refining your model you should once more review the fit and diagnostics as
described above.

Note: You can have a different model for each response in the same
investigation.

Prediction phase (using the model)

When you are content with the models (fit, predictivity, lack of fit etc.) you can use the
model to make predictions and find the “best conditions” area. The plots and lists to
use for this are found under the Predictions menu.
Under Predictions you find the Contour plots, Prediction plots and list, Sweet Spot
plot, Optimizer and the Design Space feature.
For more see the Prediction chapter.

4
Introduction to MODDE and
experimental design

General description
MODDE - (MODeling and DEsign) is a Windows program for the generation and
evaluation of statistical experimental designs.
Methods of statistical experimental designs have evolved since the pioneering work of
Fisher in 1926. These methods, further refined by Box, Hunter, Scheffé, Tagushi and
others, provides the users with a powerful methodology for efficient experimentation.

The application icon for MODDE is a pink circle with a gray M inside.

What is modeling and experimental design?

Experimental design is how to conduct and plan experiments in order to extract the
maximum amount of information from the collected data in the presence of noise. The
basic idea is to vary all relevant factors simultaneously, over a set of planned
experiments, and then connect the results by means of a mathematical model. This
model is then used for interpretation, predictions and optimization.

Objectives of modeling and experimental design

During an investigation one needs answers to the following questions:
• Which factors have a real influence on the responses (results)?
• Which factors have significant interactions (synergies or antagonism)?
• What are the best settings of the factors to achieve optimal conditions for
best performance of a process, a system or a product?
• What are the predicted values of the responses (results) for given settings of
the factors?
An experimental design can be set up to answer all of these questions.

Screening models and designs

Screening is the first stage of an investigation where the goal is just to identify the
important factors. An important factor is a factor that causes substantial changes
(effects) in the response when it varies.

5
User Guide to MODDE

In the screening stage one uses simple models (linear or linear with interactions), and
experimental designs that allows the identification of the factors with the largest effects
in the fewest possible number of experimental runs.
MODDE supports: Full Factorial, Fractional factorial, L-designs, Plackett Burman,
Rechtschaffner, Onion, and D-optimal designs for screening experiments.
With mixture factors, MODDE supports the classical axial design when the region is a
simplex.

Number of factors in screening designs

Process factors: MODDE supports up to 32 factors in problems involving process
factors only.
Mixture factors: Up to 20 mixture factors are allowed in problems involving mixture
factors only.
Process and mixture factors: In problems involving both mixture and process
factors, up to 12 factors are supported.

Number of factors with split objective

Split objective is available only when there are both process and mixture factors
defined. Up to 12 factors are supported.
For more, see the Selecting model and design section in the Objective, model and
design chapter.

Response surface modeling (RSM) designs

After screening, the goal of an investigation is usually to approximate the response by
a quadratic polynomial (model) in order to:
• Understand in more detail HOW the factors influence the response; get a
map of the system.
• Make predictions, optimize or find a region of operability.
MODDE supports: Three-level full factorial, central composite, (CCC and CCF), Box
Behnken, Rechtschaffner, Doehlert, Onion, and D-optimal designs for RSM
investigations.
With mixture factors, MODDE supports the modified simplex centroid when the
experimental region is a simplex.
For investigations with only qualitative terms no square or cubic terms can be
estimated. Creating RSM-designs for such investigations is therefore impossible.

Number of factors in RSM designs

Process factors: RSM designs are supported for up to 20 process factors
Mixture factors: Up to 15 mixture factors are allowed in problems involving mixture
factors only.
Special Cubic Model is supported for up to 8 mixture factors, and the full cubic for up
to 5 mixture factors.
Process and mixture factors: In problems involving both mixture and process
factors, up to 12 factors are supported.

6
 Introduction to MODDE and experimental design

Number of factors in Split objective

Split objective is available only when there are both process and mixture factors
defined. Up to 12 factors are supported.
For more, see the Selecting model and design section in the Objective, model and
design chapter.

Fit methods
The data collected by the experimental design is used to estimate the coefficients of the
model. The model represents the relationship between the response Y and the factors
X1, X2, etc.
MODDE uses multiple linear regression (MLR) or Partial Least Squares (PLS) to
estimate the coefficients of the terms in the model. MODDE recommends PLS when
the investigation has a high condition number.

Multiple Linear Regression (MLR)

With Multiple Linear Regression the coefficients of the model are computed to
minimize the sum of squares of the residuals, i.e. the sum of squared deviations
between the observed and fitted values of each response. The least squares regression
method yields small variances for the coefficients and small prediction errors. It is
important to note that MLR separately fits one response at a time and hence assumes
them to be independent.

Partial Least Squares (PLS)

PLS deals with many responses simultaneously, taking their covariances into account.
This provides you with an overview of how all the factors affect all the responses.
• PLS contains the multiple regression solution as a special case, i.e. with a
single response or different models, and a given number of PLS dimensions,
the PLS regression coefficients are identical to those obtained by multiple
regression.
• PLS has been extensively described in the literature and only a brief
description is given here. PLS finds the relationship between a matrix Y
(response variables) and a matrix X (model terms).
• The PLS model consists of a simultaneous projection of both the X and Y
spaces on a low dimensional hyper plane with new coordinates T
(summarizing X) and U (summarizing Y), and then relating U to T.

7
User Guide to MODDE

This analysis has the following two objectives:

1. To well approximate the X and Y.
2. To maximize the correlation between X and Y in the projected space
(between u and t).

The dimensionality, number of significant PLS components, is determined by cross

validation (CV), where PRESS (Predictive Residual Sum of Squares) is computed for
each model dimension. MODDE selects automatically the number of PLS dimensions
that give the smallest PRESS.
PRESS is then re expressed as Q2 = (1 - PRESS/SSY), where SSY is the sum of squares
of Y.

Results
Both MLR and PLS computes regression coefficients for each response. Thus Y is
expressed as a function of the X's according to the selected model (i.e. linear, linear
plus interactions, or quadratic).

8
 Introduction to MODDE and experimental design

Analysis phase
All results of model fitting, by MLR or PLS are displayed, in the same way,
graphically and in lists.

Review the model fit

Review the model fit by examining the following plots and lists:
• Summary of the fit, R2, Q2, Model validity, and Reproducibility for every
response.
• Coefficients and their 95% confidence intervals.
• ANOVA table.
• Effect plots for screening designs.

Assess model adequacy

Assess the model adequacy further by reviewing the following plots:
• Normal probability plot of residuals
• Plot of residuals against fitted values, run order or other factors.
• Box-Cox plot to check for the optimal transformation of the response.
For PLS, summary of the fit by component and PLS score and loading plots are
available.

Prediction - using the fitted model

Use the fitted model to make predictions in the form of:
• Contour and rotatable 3D plots.
• Optimizer to find the “best conditions” for a desired profile of the responses.
This helps in the interpretation of the results and to find a region of
operability.
• Sweet Spot plot to draw a plot highlighting areas were the responses are
within the specified ranges.
• Design Space to estimate the area of operability or robustness.

9
User Guide to MODDE

Convention
Limitations in investigation names
The following characters cannot be used: = \ / : * “ ? < > |.
The length (including path) cannot be larger than 260 characters.

Limitations in factor and response names

The following characters cannot be used: ~ * ? \ = [ ] and $.
The length cannot be larger than 50 characters.

Case sensitivity
MODDE is case insensitive. Lower or upper case in names will be displayed as
entered, but for all comparisons lower or upper case are considered the same.

Menu reference syntax

In this manual we use the following syntax when referring to a command menu:
• Menu | Menu item. An example: File | New
• On the Menu menu, click Menu item. An example: On the File menu, click
New.
• Click Menu item on the Menu menu. An example: Click New on the File
menu.

Suggestions for further reading on experimental

designs
1. Box, W.G. Hunter and J.S. Hunter, “Statistics for Experimenters”, John
Wiley & Sons, Inc., New York (1978).
2. Box and N.R. Draper, “Empirical model-building and Response Surfaces”,
John Wiley & Sons, Inc., New York (1987).
3. C.K Bayne and I.B. Rubin, “Practical Experimental Designs and
Optimization Methods for Chemists”, VCH Publishers, Inc., Deerfield
Beach, Florida (1986).
4. Haaland, “Experimental Design in Biotechnology”, Marcel Dekker, Inc.,
New York (1989).
5. J.A. Cornell, “Experiments with Mixtures”, John Wiley & Sons, Inc., New
York (1981).
6. D.C. Montgomery, “Design and Analysis of Experiments, John Wiley &
Sons, Inc., New York (1997).

10
Overview

Application icon and symbol

The symbol for MODDE is a gray cube with a pink M (above). The application icon is
a pink circle with a grey M inside (below).

Investigation
Experimental plans in MODDE are organized into investigations. You can think of an
investigation as a file folder containing all of the information related to a particular
experiment. When you select or open a given investigation you can access, display and
use all of its information. This information is organized in the following components:
factors, responses, constraints, inclusions, candidate set, model, design, worksheet,
analysis and predictions.

Managing investigations
Investigations are binary files saved by MODDE with the extension *.mip. When you
start a new investigation you select its name and destination directory.
You can open, save, save as, and delete investigations.
You can generate the fold over of investigations with fractional factorial designs or
Plackett Burman.
You can double-click a MODDE investigation (a *.mip file), in Microsoft Explorer, to
open that investigation.

11
User Guide to MODDE

MODDE does not save the fitted model. In order to review the results of the analysis
and use make predictions, you need to fit the model by clicking Analysis | Fit or
having Automatic fit turned on (default) in View | General Options tab General
when the investigation is opened. After the model has been fitted, you can use the
Analysis menu to create plots and list to review the model and fit and use the
Prediction menu to create prediction plots and lists.

Compatibility with older MODDE versions

All investigations from MODDE 3.0 and upwards can be opened in MODDE 9.0 (the
reverse is not true).

Organization
The MODDE window consists of a command menu bar and toolbars.

12
 Overview

Command menu bar

With the command menu bar you define or edit your factors and responses, specify
your objective and generate your model, design, and worksheet. After you enter the
results of the experimental plan (the response values) in the worksheet, you analyze
your data, display the results graphically and use the prediction menu.
Each component of the investigation i.e. factors, responses, objective, constraints,
inclusions, candidate set, model, design, worksheet, analysis and predictions is
displayed as a plot or list.
A detailed description of the command menu bar follows.
The command menu bar is located just beneath the title bar.

The menu bar consists of the menus File, Edit, View, Design, Worksheet, Analysis,
Prediction, Show, Window, and Help.

File menu
Under the File menu the following is available:
• New: Start a new investigation.
• Open: Open a MODDE investigation.
• Close: Close a MODDE investigation.
• Save: Saves the current investigation.
• Save As: Saves the current investigation under a specified path and name.
• Delete Investigation: Deletes the current investigation.
• Save Plot/List A : Saves the active plot or list.
• Revert: Reverts to the last saved copy of the investigation.
• Send by email: Sends the current Investigation by e-mail.
• Generate HTML report: Automatic report generator in HTML format.
• Complement Design: Select to complement your design by:
1. Fold over: Complements screening designs of resolution III or IV
by adding the fold over.
2. Estimate square terms in a screening design: complements the
design to support a quadratic model for a selection of factors.
3. Complement the design with D-Optimal to support a specified
model.
4. Screening to RSM Rechtschaffner: Complements the
Rechtschaffner screening design to the RSM Rechtschaffner.
5. Complement the Doehlert design.
6. Plackett Burman Super-Saturated to Plackett Burman:
Complements PBSS to the regular PB.
• Protect Investigation: Allows for a password protected investigation and
locking of investigation.

13
User Guide to MODDE

• Print, Print setup and Print Preview.

• Exit.

Edit menu
From the Edit menu you can:
• Undo
• Cut/Copy/Paste and Delete
• Select All
• Row insertion, addition
• Sort
• Edit the Model
• Edit the Reference Mixture
• Edit the Generators of fractional factorial designs

View menu
The following is available from the View menu:
• Toolbars: View/Hide Toolbars.
• Dockable windows: Show or hide dockable windows.
• Add to Favorites: Add the current plot or list to the Favorites dockable
window.
• Add to Report: Add the current plot or list to the current report generated by
MODDE.
• Full screen: Maximize the plot area.
• Investigation Options: Change the default plot and list options.
• General Options: Change the default options.
• Customize: Customize the toolbars.

Design menu
Use the Design menu for the following:
• Factors and Responses: Define and modify factors and responses
• Constraints and Inclusions: Define constraints and inclusions
• Objective: Specify and modify objective, model and design
• D-Optimal: Generate and evaluate D-Optimal designs, open the candidate
set for viewing or editing, evaluate onion plots.
• Design wizard: Open the design wizard

14
 Overview

Worksheet menu
Use the Worksheet menu to:
• Edit the Worksheet.
• Set Run Order.
• Open the Curvature Diagnostic Plot.
• Create the Scatter plot.
• Open the Histogram plot.
• Open the Descriptive statistics plot and list.
• Open the Correlation plot or matrix.
• Open the Replicate plot.

Analysis menu
Use the Analysis menu to:
• Evaluate the design
• Analyze each response in the Analysis Wizard
• Select Fit Method (MLR, PLS etc)
• Fit model by MLR or PLS
• Extract the Next Component: Add a PLS component
Review the fit
Results displayed as tables, lists, or graphs
• Summary of the fit
• PLS Summary
• PLS Plots
• Coefficients and Effects
• VIP Plot (PLS only)
Investigate diagnostics
• Residuals Plots
• Box-Cox Plot (MLR only)
• ANOVA

Prediction menu
With the fitted model you can click the Prediction menu and:
• Display contour plot from the Contour plot wizard including mixture
contour plots and response surface plots (3D).
• Create prediction plots.
• Make predictions in the Prediction spreadsheet.

15
User Guide to MODDE

• Create the Sweet Spot Plot.

• Use the Optimizer.
• Estimate the Design Space.

Show menu
Use the Show menu to display the following: objective, design matrix, design
region, confounding, model, D-Optimal summary, and reference mixture.

Window menu
Use the Windows menu to access the standard window commands.

Toolbars
Click Toolbars from the View menu to display or hide the following:
1. The Standard toolbar consist of command buttons for immediate action and
menu commands.
2. The Spreadsheet toolbar displays all spreadsheets.
3. The Plot toolbar is for zooming in and out on plots, reading plot values and
coordinates, and drawing regression lines.
4. The Model toolbar (model information) summarizes the investigation. The
summary consists of the number of factors and responses, the number of
runs, the Objective, Design and model and the Fit method.
5. The Window toolbar displays buttons for arranging the open windows and
Full Screen.
6. The Status bar displays an explanation to the button that the mouse points to.
These toolbars are described in detail in the View chapter.

Plots and lists

All plot and lists in MODDE have a context sensitive menu that appears when you
right-click the plot or list. This menu includes commands such as Copy, Print, Save,
Add to Favorites, Properties etc.
All plots can be customized by double-clicking the plot or right-clicking the plot and
then clicking Plot Settings.
For more on customizing plots and lists, see the Plots and lists chapter.

16
File

Introduction
Use the File menu to create, open, close, save, and delete investigations, save active
plot or list, revert to last saved investigation, send the current investigation by e-mail,
generate a HTML report, complement the design, lock or password protect the
investigation, for print purposes and to close MODDE.

New
To create a new investigation click File | New.
This first page allows you to:
• Enter the name of the new investigation.
• Select the location where to save.
• Select the design type: Traditional Designs or Advanced Designs including
RED-MUP and D-Optimal designs from an imported candidate set or scores
from a SIMCA-P model.
• Select to import a design from file.
• Enable the audit trail by selecting the Enable the Audit trail check box.

17
User Guide to MODDE

Click Next to open the design wizard. The design wizard guides you through the
design phase, from factor and response definition, objective, design and model
selection, up to the generation of the worksheet.
For a detail description of the design wizard see the Design Wizard chapter.

Traditional designs
When you create a new design Traditional Designs is by default selected. The
traditional designs include classical designs such as factorial, Plackett Burman, L-
designs, Rechtschaffner, and also D-Optimal and onion designs. For details, see the
Design appendix.

Advanced designs
When you select Advanced Designs and click Next the Advanced Designs box is
opened with the available designs:
• RED-MUP.
• Onion or D-Optimal designs from imported candidate set.
• Multivariate onion or D-Optimal designs from scores.

18
 File

RED-MUP
RED-MUPs are designs available for 96 (8x12), 384 (16x24), and 1536 (32x48) runs.
The designs are built from sub-designs.
To create a RED-MUP:
1. In the first page of the design wizard click Advanced Designs and then
Next.
2. Click RED-MUP and then Next.
3. Define all factors for the two sub-designs and then click Next.
4. Define the responses and then click Next.
5. Select the objective for both the vertical and the horizontal designs:
Screening or RSM.
6. Leave the factors that should be included in the vertical design with fewer
runs to the left.
7. Move the factors that should be included in the horizontal design to the right.
8. In this page you can also select the number of plates used, and if applicable
the plate factor(s) that contain plate information.
9. Select the desired plate size in the Plate-Size box and optionally select the
Plate/Block factor interactions check box.
10. Click Next to select the vertical design then click Next again to select the
horizontal design. MODDE adds center points when the selected design does
not fill up the plate size.

Note: Some special RED-MUP designs, that aim to aim to make better use of
the plate, are available for the 96 well plates (8 x 12).

For more see the Design appendix and the Tutorial.

19
User Guide to MODDE

Onion design in regular factors with imported candidate set

To create an onion design from an imported candidate set other than from SIMCA-P:
1. Click Onion or D-Optimal designs from imported candidate set on the
Advanced Designs page.
2. Click the Browse button to find the file holding the candidate set. Many file
types are supported.
3. Click Next to open the Import Candidate Set dialog for defining the correct
factor names, experiment names, and data.
4. Click OK to open the factor definition page in the design wizard. Note that
when the candidate set has been imported in this way you cannot modify or
add factors in the Define factors page.
5. If you want to place constraints on the factors, select the Place constraints
on the experimental region check box and click Next to open the Define
constraints... page.

Note: Only regular factors are imported here. If your candidate set contains
qualitative or formulation factors you have to enter the factors and settings in
the Factor Definition and import the candidate set from the D-Optimal page.
The designs available here are Onion and D-Optimal designs. Onion is only available
when there are enough experiments in comparison with the number of factors. For
more on Onion designs, see the D-Optimal Onion designs section in the Design
appendix and the Tutorial.

Multivariate designs
To create a design using the scores from a SIMCA-P project as factors:
1. On the Advanced Designs page click Multivariate onion or D-Optimal
designs from scores.
2. Click the Browse button under Import scores (factors) from a .usp created
in SIMCA-P 9 or higher to select the SIMCA-P project.
3. SIMCA-P opens automatically. Return to MODDE without closing SIMCA-
P.
4. Select the model from the Model box and click Next to import the factors
from SIMCA-P. The scores are then automatically loaded from the SIMCA-
P .usp-file, and the candidate set for the onion design comprised of all
objects (rows) in the workset of the SIMCA-P model is selected as the basis
of the onion design.

Note: To be able to import scores from the SIMCA-P project, SIMCA-P 10 or

later needs to be installed.
When importing the scores of a SIMCA-P project as factors in MODDE, the only
designs available are the D-Optimal and the Onion designs.

Note: 'SIMCA-P' above includes both SIMCA-P and SIMCA-P+ when

available. For the functionality described here the type of SIMCA-P is not
relevant.
For more on Onion designs, see the D-Optimal Onion designs section in the Design
appendix and the Tutorial.

20
 File

Import design from file

If you have already done experiments and want to import them into MODDE for
analysis:
1. Click File | New.
2. Select the Import design from file check box.
3. Click Browse and select the file to import.
4. Click Next and specify what is what in the Data Specification dialog.

Note: This dialog recognizes regular quantitative and qualitative factors. If

there are formulation factors in the imported design, you have to manually
alter the factor type (starting with formulation factor you want to end up last)
in the factor definition page.

Open
To open a MODDE investigation, click Open on the File menu. In the Open-dialog
select the directory and you get a list of all the MODDE Investigation Projects (*.mip)
present in that directory. Double-click the desired investigation to open it or mark it
and click Open.
To open investigations created in MODDE version 4 and earlier, switch to Old
MODDE Files (*. ini) in Files of type to view them, mark the .ini and click Open to
convert it to the current format.

Save and save as

To save the current investigation, click Save on the File menu.
To save the current investigation at a different location or with a different name, click
Save As. In the Save As dialog that opens, enter the new name and location of your
investigation. MODDE switches to the "new" investigation.

Delete investigation
To delete the current investigation click Delete Investigation on the File menu. It is
not possible to delete any other investigations than the current from MODDE.
For read-only investigations Delete Investigation is unavailable.

Save plot/list as
Plots can be saved as Enhanced Meta Files (*.emf), Bitmap files (*.bmp), Jpeg files
(*.jpg) or PNG files (*.png). Lists can be saved as Text files (*.txt) or Web Pages
(*.htm, html).

21
User Guide to MODDE

To save a plot, display it, make sure it is active and then click File | Save Plot As. The
Save Format dialog is displayed.

In the dialog check the Keep aspect ratio box to keep the proportions of the plot as on
the screen or according to a predefined plot size.
In the Plot size box you can choose between Custom, 640x480(VGA),
800x600(SVGA), 1024x768, Original size.

The predefined formats are useful primarily when displaying MODDE plots on a small
screen.
To save a list, display it, make sure it is active and then click File | Save List As. The
Save dialog is then displayed.
In the Save as type box, select file type .txt or .htm/html.

Revert
To revert to the investigation as when it was last saved, click Revert on the File menu.

Send by E-Mail
To send an investigation by e-mail click Send by E-Mail on the File menu. Note that
the investigation sent is the current investigation as it was last saved.

Generate HTML report

MODDE has an automatic report generator. Create a new report by clicking Generate
HTML Report on the File menu or right-click a plot or list and then click Add to
Report.
The report generator can use the MODDE default template or any template previously
saved. All formatting functionality is available for writing the text. Plots and lists can
be added to the report at any time, as placeholders or actual plots and lists.

22
 File

A placeholder tells MODDE the desired item to fill from the current investigation
when you click Update Report. If you add plots and lists as placeholders and save the
template, you can generate a report in the desired format, for any investigation, by
selecting the saved template and clicking Update Report.
For details, see the Report Generator chapter.

Complement design
To complement a design is to make a new investigation consisting of the design, or a
part of the design, of the current investigation plus its complement. See also the section
Inclusions vs. complement design in the chapter Constraints and Inclusions.
Use Complement Design when you want to:
• Estimate separately a set of terms (interactions, or main terms and
interactions) that were confounded in a Resolution III or IV fractional
factorial design.
• Complement a screening design to an RSM design supporting the full
quadratic model.
• Complement a screening design to estimate selective curvature effects.
• Add additional experimental runs to improve the quality (i.e. the condition
number or G-efficiency) of an existing set of experiments.
• Use already performed experiments in a Doehlert design to set up a new
Doehlert moving the center of the design or add a factor. For more on the
Doehlert designs see the Design appendix.
• Use already performed experiments in a Super-Saturated Plackett Burman
design to add experiments resulting in a regular Plackett Burman design.
To complement the current design, click Complement Design on the File menu and
the Complement Design Wizard is opened. Click the desired complementing method
and click Next.

23
User Guide to MODDE

Available complementing methods

You can complement your design using the following complementing methods:
Fold over: With screening fractional factorial designs of resolution III and N (number
of runs) equal to 8 or 16, it is usually recommended to complement by fold over.
Estimate squares of selected factors in factorial designs: If the screening design
indicates the presence of curvature, you may want to estimate the square terms in
selected factors or you may want to upgrade your design to a full RSM in these
selected factors.
D-Optimal: If you want to upgrade the design to support a customized model, or if
your investigation contains mixture factors, select D-Optimal.

Design specific complementing methods

Doehlert: When you have performed a Doehlert design and want to move the design
center or add a factor.
Screening to RSM Rechtschaffner: When you have performed a screening
Rechtschaffner design.
Plackett Burman Super-Saturated to Plackett Burman: When you have performed
a PBSS.

Fold over
When you choose to complement your design with fold over MODDE makes a new
investigation consisting of the design of the current investigation plus its fold over
(complement). The fold over design has as many experimental runs as the original
design.
Fold over designs are available for fractional factorial design of resolution III or IV
and Plackett Burman designs.
With the complete design (original + fold over), all main effects are clear from 2
factors interactions. With resolution III and IV designs MODDE automatically adds a
block factor. You may remove the block factor from the model in the menu Edit |
Model.
To fold over your design:
1. Click File | Complement Design.
2. Click Fold over and then click Next.
3. Enter the name and location of the new investigation. It is recommended to
add an additional center point to detect a shift in the mean.
4. Click Finish and the new investigation opens.

Estimate squares of selected factors in factorial designs

To complement your design with Estimate square terms in a screening design, select
the factors to include in the quadratic model. The unselected factors are excluded from
the model and set in the worksheet on their averages.
For this complementing method to work well the original design has to be of resolution
V or the collapsed design in the selected factors has to be a full factorial (as in the case
above). The design is complemented to a CCF by adding the face center runs, or to
CCC when entering a star distance > 1.

24
 File

After clicking File | Complement Design:

1. Click Estimate square terms... and click Next.
2. Mark the factors for which to estimate the square terms.
3. Optionally change the star distance. Click Next.
4. Enter the name, location of the new investigation and number of
additional center points.
5. The model has been updated with the squares of the selected factors.

D-Optimal
Complementing a design d-optimally is the most flexible way of complementing a
design.

Process factors only

After clicking File | Complement Design:
1. Click D-Optimal and click Next.
2. Click Edit Model and specify the new model. MODDE recommends the
number of additional new runs based on the specified model, to ensure the
proper degrees of freedom.
3. Enter the name and location of the new investigation and click Finish. The
D-Optimal wizard guides you in generating the new investigation. Here the
original design runs in the selected factors are used as inclusions and the
displayed Design Runs in the D-Optimal page includes the inclusions. The
additional new runs are selected D-Optimally to support the selected model.

25
User Guide to MODDE

Mixture factors
Complementing the design d-optimally with mixture factors, after giving the name and
location of the new investigation, the D-Optimal wizard opens. Select the new model.

The displayed number of runs includes the original design runs. Click Next, the wizard
guides you in generating the new investigation.

Mixture and process factors

Complementing a design d-optimally with mixture and process factors, after giving the
name and location of the new investigation, the D-Optimal wizard opens. The
objective is set to Split Objective. Click Settings | Model and select a new model for
both the process and mixture factors, and if you want interactions between them.

The displayed number of runs includes the original design runs as inclusions. Click
Next; the wizard guides you in generating the new investigation.

26
 File

Complement Doehlert
Doehlert designs can be complemented by expanding the design region or adding a
factor.
To complement a Doehlert design, click Doehlert in the Complement Design Wizard
and click Next.

As the dialog suggests you can complement by:

• Leaving the default Select new center selected and selecting one of the
experiments of the design as the center of a new Doehlert design.
• Selecting Add factor and typing the name of the new factor and typing the
Center and Range in the respective boxes. The value you type in Center is
the value that will be entered in the design for the already performed
experiments, for the new factor.

27
User Guide to MODDE

Select how to complement, click Next, enter the name, location of the new
investigation and number of additional center points, and then click Finish to generate
the new investigation.

Screening to RSM Rechtschaffner

The design is complemented by adding the star points resulting in a 3-level
Rechtschaffner design.
To complement your screening Rechtschaffner design to an RSM Rechtschaffner
design:
1. Click File | Complement Design.
2. Click Screening to RSM Rechtschaffner and then click Next.
3. Enter the name, location of the new investigation and number of additional
center points, and then click Finish to generate the new investigation.
This option is only available for screening Rechtschaffner designs.

Plackett Burman Super-Saturated to Plackett Burman

The design is complemented with runs adding up to a regular Plackett Burman design.
To complement your PBSS to regular Plackett Burman:
1. Click Plackett Burman Super-Saturated to Plackett Burman in the
Complement Design wizard.
2. Click Next.
3. Enter the name, location of the new investigation and number of additional
center points and click Finish to generate the new investigation.
This option is only available for Plackett Burman Super-Saturated designs.

28
 File

Protect investigation
When you click File | Protect Investigation you can select to Encrypt/Password
protect or Lock the investigation.

Encrypt/password protect an investigation

Enter a password and the investigation is encrypted and password protected. This
investigation can now be opened only with the selected password.
To remove the encryption, click File | Protect Investigation | Remove Encryption
and enter the password.

Lock investigation
Click File | Protect Investigation | Lock to lock the investigation. Locked
investigations are automatically fitted when opened. Any plot or list can be displayed,
but you cannot make any changes in the investigation. The investigation becomes
'Read only' with the exception of the prediction spreadsheet. If you click Permanently,
unlock on Save As, a copy of the investigation can be unlocked by using File | Save
as. When Permanently is selected the investigation cannot be unlocked.

It is possible to also encrypt and password protect the investigation by selecting the
Encrypt / Password Protect investigation check box. The investigation is then
encrypted. This check box is optional; select it only if you want the investigation to be
password protected.

Note: The lock cannot be removed.

29
User Guide to MODDE

Print Setup
Change the page orientation, printer, and printer settings by clicking Print Setup on
the File menu.
Plots are preferably printed with Orientation Landscape.
The print menu is only valid for an active list or plot.

Print Preview
On File, click Print Preview and the current window can be view as it will be printed.
Print Preview is only available when there is an open plot or list.

Print
Print is only available for the active plot or list. With the plot or list active, use one of
the following manners to print:
• On File menu click Print.
• Right-click the plot or list and click Print.

• Click the Print-button in the Standard toolbar.

• Press CTRL+P.
When printing plots, the plot is by default scaled to look exactly as on the screen.
The lists and plots in MODDE can also be printed from another Windows application
after first being copied through the clipboard to that application.

Print format for plots

When clicking Print with a plot active, the Print Format dialog opens. For more on
the dialog, see the Save plot/list as section in this chapter.

Exit
Click Exit from the File menu to close the MODDE program.

30
Edit

Introduction
Use the Edit menu to undo, cut, copy, paste, delete, select all, add experiment/insert
rows/add factor/add response, sort, edit model, edit reference mixture, and edit the
generators.

Undo
Click Edit | Undo or press CTRL+Z to undo changes in MODDE. Such changes can
be changing values or text (factor name for instance), cutting, copying, pasting,
deleting, sorting in spreadsheets, or editing the model.
Undo is activated after changes in:
• The spreadsheets Worksheet, Factors, Responses, Constraints, Inclusions,
Prediction, and Optimizer.
• The model terms in the Model Properties dialog (Edit | Model) or by
clicking the Exclude-button and marking model terms to exclude in a plot.
• Plots displaying experiments (observations) by clicking the Exclude-button
and marking model terms to exclude in a plot.
Undo remembers the ten last actions in the worksheet, in the edit model dialog, and in
plots displaying experiments (observations) or model terms.
Undo works on the active plot or spreadsheet.

Note: After editing the values in worksheet the undo feature of plots
displaying experiments stops working as manual changes in the worksheet
empty the undo-memory for such plots.

Cut, copy, paste, delete, select all

Cut (CTRL+X), Copy (CTRL+C), Paste (CTRL+V), Delete (pressing the Delete-key
on the keyboard), and Select All (CTRL+A) are standard Windows commands. They
can all be used in all MODDE spreadsheets. Copy and Select All can be used in all
MODDE lists and tables.

31
User Guide to MODDE

Add factor, add response, add experiment, insert rows

The menu item Add Factor, Add Response, Add Experiment, Insert Rows on the
Edit menu is context sensitive and available for all spreadsheets although in slightly
different forms.
When the factor spreadsheet is active Add Factor is available as the menu item, when
the response spreadsheet is active Add Response is available, when the worksheet is
active Add Experiment is available, and when any other spreadsheet is active Insert
Rows is available. The shortcut menu, displayed after right-clicking a spreadsheet, also
includes this command.
When adding a factor or response the respective dialog is opened.
When selecting Add Experiment or Insert Rows the number of rows marked are
inserted shifting all rows after down, except for in the Worksheet where new rows are
always added last.

Sort
Sorting is available for the worksheet, constraints, inclusions, candidate set, and
predictions list.
To sort a list, right-click and click Sort or click Edit | Sort.

In the dialog, select the column to sort the list by from the Select the column to sort
box and click the Add Column button. The column appears in the list with the default
sort type. Click the sort order you want under Sort selected, Ascending or
Descending.
If a column of the spreadsheet is marked when sort is activated it becomes, by default,
the primary column to sort by.
Add more columns to select secondary and tertiary etc., columns to sort by. Specify for
each column the sort order. Use the Remove button to remove a column from the sort
list or drag the item outside the list.
The sorting starts when OK is clicked.

32
 Edit

Sorting the candidate set

Sorting the candidate set is useful if you want to exclude some rows that correspond to
undesirable runs.
A candidate set imported to create an onion design cannot be sorted.
To sort the candidate set, click Edit | Sort or right-click and click Sort.

33
User Guide to MODDE

Model / reference mixture

In the Model Properties page you can add or delete model terms such as linear,
interaction, square, and cubic terms. Use Edit | Model to add uncontrolled factors.
Uncontrolled factors are by default not included.

Model

Click Edit | Model or the Edit Model button to modify the model. The Model
Properties dialog opens on the Model Terms page and you can edit the model by
adding or deleting terms.
Use the For Response box to specify for which response you want to alter the design,
if not for all.
A quadratic term is represented by factor1*factor1 and a cross term (interaction) by
factor1*factor2. A cubic term is represented by factor1*factor1*factor1 and a three
factor interaction is represented by factor1*factor2*factor3.

34
 Edit

Add terms
To add terms in the Model Properties dialog use one of the following methods:
1. Mark the factors to the left and click the relevant buttons Factors,
Interactions, Squares, or Int. & Sq. (interactions and squares)
2. Double-click a factor or mark it and click the left arrow =>; note that it is
added in the New term field. Continue until the new term is fully defined
and click the second arrow => adding the term to the right side.
3. Position the cursor in the New term field and type the abbreviation of the
factors to include using ‘*’ to separate them.
4. To add three factor interactions, mark the three factors, click the left arrow
and then on the right =>. Or type the abbreviations in the New term field.

Remove terms
To remove terms in the Model Properties dialog, mark the term(s) and click the
Remove button in the dialog.

Undo
The Undo button becomes active after making a change in the model. Clicking Undo
only reverses the last change in the Model Properties dialog.

Reset
Click the Reset button to reset the model to the default model.

Enforce mixture hierarchy

The Enforce the mixture model hierarchy check box is available in the Model
Properties dialog, and by default selected when there are formulation factors in the
model. This means that a group of terms are treated as a unit, and terms cannot be
removed individually. If the Enforce the mixture model hierarchy check box is
cleared, the terms can be removed individually but the model can only be fitted with
PLS.

35
User Guide to MODDE

Reference mixture
In Model Properties, click the Reference Mixture tab to switch to the reference
mixture page.

Use this dialog to change the default reference mixture of a Cox model. The reference
mixture is used to impose constraints on the coefficients of the Cox mixture model.
The default reference mixture is the centroid of the experimental region. If the region is
a regular simplex with q mixture factors, the centroid is the point with coordinates 1/ q,
1/ q,....1/ q. If the experimental region is irregular, the centroid is the constrained
centroid of the irregular constrained region.
Click the Reset button to restore the reference mixture to the default values.

36
 Edit

Generators
Click Generators on the Edit menu to open the Generators dialog.

A generator is a column of signs in the extended design table of the basic factors that is
used to introduce additional factors in the fractional factorial designs.
For example, let us assume that 5 factors are to be investigated in 8 runs. The extended
design table is the table of the full factorial in three factors (basic factors), symbolically
named a, b and c plus the additional columns for all the interactions. Any
interaction column can be used to introduce additional factors. Let us say that to
introduce the 2 additional factors, d, and e, the column of signs of a*b and a*c are
selected. Then d = ab and e = ac are the generators of the fractional factorial design 25-2
(see Box, Hunter and Hunter for further information).
When MODDE generates fractional factorial designs the default generators used are
those published in Box, Hunter and Hunter.
Editing and/or changing the default generators of a design is done in order to estimate
selected interactions in a fractional factorial design of resolution III or IV instead of the
default.
MODDE supports the choice of positive or negative generators.
To edit a generator, click in the generator column of the desired row, and enter a new
generator. The confounding, in the confounding column, is updated.
When you click OK, your design and worksheet are deleted and new ones are
generated.

37
User Guide to MODDE

Edit the model and/or generators before creating the

worksheet
For fractional factorial designs of resolution III, IV, and V it is possible to edit the
model and/or generators before creating the worksheet by clicking Settings | Edit
Model in the page entitled Select the model and design in the Objective page or
Design wizard.
See the chapter Objective, model and design for more.

38
View

Introduction
Using the View menu you can show/hide the toolbars, show/hide the dockable
windows Analysis Advisor, Audit trail, Favorites, Output, and Notes, and execute the
commands: Add to Favorites, Add to Report, make window Full screen, change the
default investigation options, change the general options, and customize toolbars,
commands and options.

Toolbars
On the View menu, click Toolbars to view the available toolbars. Click the name of
the toolbar to show or hide it. All toolbars can be floating or docked beneath the menu
bar.
Clicking a button on a toolbar will perform a certain task. As a guide to what happens
when a button is clicked, a short text will appear when you hold the pointer over a
button. Text will also appear in the Status bar at the bottom of the screen.
You can customize all toolbars according to your wishes. For more, see Customize
later in this chapter.

Standard toolbar

The Standard toolbar consists of a number of command buttons and the response box.
The buttons listed below are available.

39
User Guide to MODDE

Standard windows buttons

The buttons for File | New, Open, Save, Print, Print Preview, Edit | Cut,
Copy, Paste, and Undo are all standard Windows buttons and work as in other
Windows applications.

Open the design wizard

Click the Objective button to open the design wizard. If none or too few factors
are defined the design wizard opens on the factor page, otherwise it opens on the
objective page where you select the objective of the design.

Open the worksheet

Click the Worksheet button to open the worksheet for editing or viewing.

Edit model

Click the Edit model button to edit the model or reference mixture when
applicable. Model Terms is the default page opened. To edit the reference mixture,
click the Reference Mixture tab.

Open MODDE table, plots, and Analysis Wizard

The MODDE ANOVA table, the coefficient plot, normal probability of residuals plot,
observed vs. predicted plot, and the Analysis Wizard can be opened by clicking the
appropriate buttons.

Response box
Use the Response box to change responses in the active plot or list.

Select All Responses to generate multiplots with all responses.

40
 View

The last response check box cannot be cleared. To get single selection when switching
between responses using the response combo box, hold down the CTRL-button for
single selection functionality.

Show or hide favorites

To open or close the favorites window use one of the following methods:

• Click the Favorites button on the Standard toolbar.

• Click Dockable Windows on the View menu, and then click Favorites.
• Press CTRL+T.

Show or hide analysis advisor

Show or hide the Analysis Advisor window is available by clicking View | Dockable

Windows | Analysis Advisor or by clicking the ? - button .

Spreadsheet toolbar
The Spreadsheet toolbar contains buttons for all MODDE spreadsheets. In the order of
the toolbar: the factor, response, worksheet, prediction, and optimizer spreadsheets.

Plot toolbar
The Plot toolbar holds buttons that enable you to select type of marking to be used
when marking areas in plots, insert labels or text in plots, zoom in and out, read
positions in graphs, do linear regression in scatter plots, get information about
observations (experiments) or variables (model terms or responses), or exclude
experiments and model terms.
The tools are activated when you click them.

41
User Guide to MODDE

Arrow
The arrow button is used to select which type of marking to use.
Click the small arrow to the right of the arrow and click the type of marker from the
menu.
• Free Mark: Allows marking to take any shape.
• Block Mark: Marks in a rectangular shape.
• X Mark: Vertical bar.
• Y Mark: Horizontal bar.
• No Mark: The arrow works as a data reader displaying the number, name,
and value of plotted data points when hovering near the data point symbol.

Text

Click the T-button to insert a text-field in a plot. The field can contain text or a
value and be inserted in all plots but the contour, response surface, sweet spot, and 3D
scatter plots.
Open the plot, click the T-button, click where you want to position the text-field, type
the text or numbers, and then press ENTER or click somewhere else in the plot.
MODDE will continue to open a new text-field each time you click until the T-button
is pressed again. This label can be removed by clicking it again and emptying the cell.

Zoom in

Click the arrow near the Zoom in button , and select the type of zoom from the
drop down menu:
• Scale xy: Magnifies a rectangular region
• Scale x: Expands the x direction
• Scale y: Expands the y direction
• Subplot: Magnifies a subplot in a multiplot.
And then mark the desired region of the plot to zoom.
Zooming in a scatter 3D plot is described in the Zoom and rotate section in the Plots
and lists chapter.

Zoom out

Click the Zoom out button to revert zoom to original scale in the steps taken
when zooming.

Coordinate Reader
The coordinate reader displays the coordinate values of any point of the plot area.

Click the Read coordinate values button and mark the point of interest and the
coordinate reader will display the coordinates at that point.

42
 View

Regression line
The regression line and equation can be displayed for any 2D scatter plot in MODDE.
Open a scatter plot, for instance the Observed vs. predicted plot, and click the

Show/Hide regression line button .

Rotate
For rotating a scatter 3D or response surface plot see the Zoom and rotate section in
the Plots and lists chapter.

Interactive exclude button

To interactively exclude model terms or experiments:
1. Open a plot displaying model terms or experiments.

2. Click the Exclude button .

3. In the plot mark the term(s)/experiment(s) you want to exclude from the
model.

4. Optionally click the Undo-button to reverse these exclusions.

MODDE removes the terms/experiments from the model of the currently displayed
response ONLY and automatically refits the model.

43
User Guide to MODDE

Model toolbar
The Model toolbar displays the summary of the current investigation.
1. Factors: The total number of factors (the number of uncontrolled).
2. Responses: The number of responses.
3. Runs: The number of runs included in the design (not counting rows set as
'Excl' in the worksheet).
4. Objective: The objective, Screening, RSM or Split Objective.
5. Design: The selected design and model.
6. Method of Fit: MLR, PLS etc.

Window toolbar
The Window toolbar commands are general Windows commands and work
accordingly. Click the Window toolbar commands Full screen (press the F9 key to get
back to regular), Cascade Windows, Tile Windows horizontally or Tile Windows
vertically to arrange the windows.

Status bar
The Status bar displays the explanation to the command button that the mouse points
to.

Dockable windows
MODDE has five dockable windows: analysis advisor, audit trail, favorites, output,
and notes.

Open the dockable windows by clicking Dockable Windows on the View menu and
then clicking the desired dockable window.
When you click the Auto Hide button the window will hide away. If you then
hover with the mouse over the dockable window name, it slides out and becomes
visible. If you want your window to stay visible after it has slid out, just click the pin
button again .

44
 View

Analysis advisor
The Analysis Advisor is automatically activated after fitting an investigation. The
advisor explains the analysis plots and results.
Show or hide the Analysis Advisor window is available by clicking View | Dockable

Windows | Analysis Advisor or by clicking the ? - button .

Audit trail
When turned on, the audit trail logs changes done to the investigation.
To open or close the audit trail, click Dockable Windows on the View menu, and then
click Audit Trail.
For more, see the Audit trail subsection in the Changing the default options using
Investigation Options section.

Favorites
To open or close the favorites window use one of the following methods:

• Click the Favorites button on the Standard toolbar.

• Click Dockable Windows on the View menu, and then click Favorites.
• Press CTRL+T.

The Favorites window by default includes a few default commands, spreadsheets,

lists, and plots and can be extended and modified as desired.
Execute a command, or open a plot or list by clicking it. When settings must be
selected, a dialog window opens, select the settings and click OK. Plots and lists are
displayed with its selected settings.
Not all plots in MODDE are available to be added to the favorites as plots. Generally
plots that are displayed for the first response by default, and do not require a dialog for
the selection of settings, can be added to the favorites as plots. Other plots requiring the
selection of settings from a dialog can preferably be added to the favorites as
commands. For instance, if the Contour plot wizard is added as a command, selecting it
from the favorites opens the dialog and settings can be selected.

45
User Guide to MODDE

Adding favorites
To add an open plot or list to favorites, right-click it and click Add to Favorites or
select it from the View menu. Note that this adds the plot with the selected settings to
the favorites.
You can also right-click in the Favorites window and select Add Command to
Favorites.

Favorites window
Right-clicking the Favorites window opens the menu below. A description of the
menu items follows.

Adding favorites
To add an open plot or list to favorites, right-click it and click Add to Favorites or
select it from the View menu. Note that this adds the plot with the selected settings to
the favorites.
You can also right-click in the Favorites window and select Add Command to
Favorites.

46
 View

Open all items in folder – Executing a folder

To execute all commands in a folder, right click the folder and select Open All Items
in Folder.
For example with the Analysis folder:

Opening all items in the folder displays the coefficient plot and observed vs. predicted
plot for the first response tiled.

Treat folder as item

Click Treat Folder as Item to treat the folder as an item. The folder is then displayed
as an item:

Click it to open all the items. This gives the same result as Open All Items in Folder
but with a single click.

47
User Guide to MODDE

Rename
All folders, commands, plots, spreadsheets, and lists can be renamed according to your
wishes by right-clicking it and clicking Rename.
Delete
All items in Favorites can be deleted by right-clicking the item and clicking Delete, or
marking it and pressing the DELETE-key on your keyboard.
Add command to favorites
A number of commands can be added to favorites. The commands from the menu and
toolbars are displayed on the left, under Categories, and the items available under that
command are displayed to the right.
For example, if you click Prediction under Categories, all the commands on the
Prediction menu are displayed to the right.

Click a command, for example Prediction Plot Wizard, and click Add. The command
is added to the Favorites window. You may continue adding commands, and when
done, click Close.

48
 View

When a command has a submenu, double-click it to view the submenu items. For
example Analysis | Residuals, double-click Residuals and the submenu of four items
it displayed. Select the desired one and click the Add button.

Create a new folder

It is convenient to group commands in folders, and automatically execute all the
commands in the folder in sequence. To create a folder in Favorites, right-click and
click New Folder.
The created folder is default named 'New Folder'; change the name as desired, for
example to 'Residuals Plots'.
To move favorites to the Residuals Plots folder, use the drag-and-drop feature.

49
User Guide to MODDE

Importing and exporting Favorites configuration

The Favorites window configuration can be saved as an .xml-file.

Note: When importing a favorites file, the new favorites will replace the
current favorites. If you want to keep you current configuration and switch
back to it later, export to file before importing.
To save the current favorites configuration to file:
1. Right-click the Favorites window.
2. Click Export.
3. Enter the name and location in the Save As dialog,
4. Click Save.
To import favorites from .xml-file:
1. Right-click the Favorites window.
2. Click Import.
3. Browse for the file in the Open dialog.
4. Click Open.
Restoring favorites
To restore Favorites to the MODDE default, click General Options on the View
menu, click the Restore tab and click the Restore button after Restore favorites.

Output
The output window is a log book of the session. All MODDE messages and actions are
recorded in the Logbook.
Open the output window by clicking Dockable windows on the View menu and
clicking Output.

To make this window smaller, pull the top and it will remember its size. Double-click
the window caption to make it floating or make it dock.

Hint: While dragging the window hold down the CTRL key. It won't dock if
you are close to the frame of the main frame window.

Notes
In Notes you can record your own notes concerning the investigation. You can
paste MODDE plots and lists, and embed objects such as Microsoft Excel
spreadsheet, word, etc. All these commands are available by right-clicking the window.
This file can then be saved as .rft (Rich Text Format) and read directly by a word
processor with all plots.
Open the notes window by clicking Dockable windows on the View menu and
clicking Notes.

50
 View

Add to Favorites
Plots and lists can be added to the Favorites dockable window. For more, see the
Favorites section earlier in this chapter.

Add to Report
Plots and lists can be added to the HTML report generator. For more, see the Report
Generator chapter.

Full Screen
You can use the Full screen command to maximize the plot area. Full screen can be
toggled on and off using F9 and is available from the Window toolbar as well as from
the View menu. When Full Screen is selected from the menu, the Window toolbar is
automatically opened as a floating toolbar.

51
User Guide to MODDE

Changing the default options using Investigation

Options
All plots and lists in MODDE have a context sensitive menu, most of them with the
menu item Properties. The settings of the property page are inherited from the
Investigation Options.
To change the options of the active plot or list, see the chapter Plots and Lists.
To change the default options for the current investigation click View | Investigation
Options and select the option to change.

Plot labels
Select the plot label to display as default on plots displaying the experiments, for
example residual plots, by clicking None, Experiment Number, Experiment Name,
or Run Order taken from the worksheet.

Number format
Click the number of decimals 2 - 5 or the scientific (E) format in lists by clicking
Auto, .00, .000, .0000, .00000, or Scientific.
When exporting unscaled coefficients to use in other applications, use the scientific
format to get maximum precision in the coefficients.

52
 View

Audit trail
When the Audit Trail is turned on each investigation in MODDE has a separate audit
trail. Each audit trail consists of one or more sessions that in turn consist of events. A
new session is started and appended to the audit trail when an investigation is opened,
and ends when the investigation is saved.
In addition to logging events, MODDE logs information about the user, and date and
time of the events.
To view the audit trail, click the Audit Trail tab in the Output / Notes / Audit trail
dockable window. If this tab is not shown, display it by clicking View | Dockable
Windows | Audit Trail.

Enable and disable the Audit Trail

By default the audit trail is disabled. To turn it on, select the Log events in the Audit
Trail check box in Investigation Options, tab Audit Trail or select Enable the Audit
Trail on the first page of the design wizard when creating a new investigation.
To empty the audit trail, use the Clear Audit Trail button.
Click the Prompt new users to edit the extended user information box to demand
new users to enter more information than just the user name.
Click the Edit button to change the extended user information.
Click the Save button to save the current version of the audit trail separate from the
investigation, in XML format.
Administrators can disable the entire audit trail page in general options and control the
behavior of the audit trail, i.e., always have it on or off and strict audit trail (forced
saving of the audit trail). For instructions on how to disable the audit trail options, see
the knowledge base at www.umetrics.com.

Audit trail and internet explorer

MODDE uses Internet Explorer 5 functionality to display the audit trail.

53
User Guide to MODDE

Logged in the audit trail

Specific actions the MODDE audit trail logs are:
* Factors (adding, modifying, deleting), displaying all details about the factor after the
change
* Responses (adding, modifying, deleting), displaying all details about the response
after the change
* Constraints (modifying, deleting)
* Reference Mixture
* Objective
* Generators
* Design
* Model
* Worksheet, every change of every cell
* Registers when a digital signature in the Audit trail is incorrect.
* Clearing of the Audit trail (View | Investigation Options, Clear Audit trail).
* Activation and deactivation of the Audit Trail.
* Changes in the Audit Trail extended user information.
Strict Audit Trail also logs:
* Open and Close of Investigations
* Printing of plots and lists
* Saving of plots and lists to disk

Alpha level
Select the significance level by clicking 1%, 5%, or 10% to be used in the Lack of
fit (LoF) plot. The default is 5%.

54
 View

Coefficients
In MODDE you can select the type of coefficients you want to display. The default is
Scaled and centered coefficients.

Scaled and centered

With multiple linear regression, MLR, the scaled and centered coefficients are the
coefficients of the fitted model, with the factors centered and scaled. The default
scaling in MLR is orthogonal scaling. With PLS these coefficients are for the factors
centered and scaled to unit variance.

PLS orthogonal
The PLS orthogonal coefficients are available only when fitting the model with PLS.
The PLS orthogonal coefficients are the PLS model coefficients re-expressed to
correspond to factors centered and scaled using orthogonal scaling (coded as -1 to 1).
PLS orthogonal coefficients are not available in investigations with formulation factors
only.
With process and mixture factors, the PLS orthogonal coefficients refer to process
factors scaled orthogonally, and mixture factors unscaled (original units).

Note: The PLS orthogonal coefficients are meant for comparison with
MLR only. They are incorrect when the design is not balanced and the mean is
not equal to the mid-range.

Normalized
To make the coefficients comparable when responses (Y's) have different ranges, you
can select to display the coefficients in Normalized form that is, the coefficients are
divided by the standard deviation of their respective response. The normalized mode is
the system default for the Coefficient Overview Plot.

55
User Guide to MODDE

Unscaled
The unscaled coefficients are the coefficients corresponding to unscaled, uncentered
data. When exporting unscaled coefficients to use in other applications, be sure to use
the E-format to get maximum precision in the coefficients.

Extended or compact format

For qualitative factors at p levels (p > 2), MODDE generates p - 1 dummy variables
numbered from 2 to p.
Click Extended format to display coefficients for all the p levels of the qualitative
factor or Regular to display coefficients for p - 1 levels of the qualitative factor.

Blocking
You can select to have the block factor treated as a fixed or random effect and the
predictions computed accordingly.
Select the block factor as Fixed effect when the external variability can be set at will
and the primary objective for blocking is to eliminate that source of variability
Select the block factor as Random effect when the external variability cannot be
controlled and set at will, and the primary objective is to make prediction without
specifying the block level, and taking into account the external variability.
See the Statistical Appendix for more information.

Confidence level
Select the confidence level 90%, 95%, or 99% for computation of the confidence
interval on the model coefficients, effects, and predictions. The system default is 95%.

56
 View

List presentation
By default lists are displayed using the Regular - shows all orthogonal settings
option, when there are qualitative factors. And the design matrix by default displays
The current Worksheet scaled and centered.

Qualitative factors - Extended or compact format in the model list

and design matrix
For qualitative factors at p levels (p > 2), MODDE generates p - 1 dummy variables
numbered from 2 to p.
Click Extended – shows all settings to display all the p levels of the qualitative
factor or Regular – shows all orthogonal settings to display only p - 1 levels of the
qualitative factor.

Modified factor settings in worksheet - Original or modified

design matrix
When you have changed the factor settings of worksheet from the default suggested by
MODDE you can select to display the design matrix as the current worksheet scaled
and centered, or as the original design generated by MODDE.
The default is to display The current Worksheet scaled and centered. If you want to
display the original design matrix, click The design as generated by MODDE.

R2 in plots
Click R2 or R2 adjusted to display in the Summary plot and PLS Summary plot. The
default is to display R2.

57
User Guide to MODDE

Residuals
Select the type of residuals to be used in the residual plots.

Raw residuals
The raw residual is the difference between the observed and the fitted (predicted)
value.

Standardized residuals
The standardized residual is the raw residual divided by the residual standard deviation
(RSD).

Deleted Studentized residuals

The deleted studentized residual is the raw residual ei divided by its standard deviation
(si) where the standard deviation (si) is computed with observation (i) left out of the
analysis, and corrected for leverage. Deleted studentized residuals require at least two
degrees of freedom.
Deleted Studentized residuals are not available for PLS.

Default
With MLR and 2 or more degrees of freedom, deleted studentized residuals are the
MODDE default when plotting residuals.
With PLS and models with less than 2 degrees of freedom, MODDE uses as default the
Standardized residuals.

Select Factor
Select the factor to display as default in the Residuals | vs. Variable plot and Effects |
Main Effect plot.

General Options
The General Options has three pages with settings that are used for all investigations.
• General with general settings such as automatic fit.
• List Options like coloring and grid styles.
• Restore with buttons to restore plot settings, favorites, and ‘don’t show
again’-messages.
Click General Options on the View menu to access the options.
Click the Show Details button to display a short description of the marked option.

58
 View

General page
The General page is divided into the parts General, Investigation Settings, Program
Limits, and Audit Trail.

General
Under General you can change the following options:
• With Automatic fit = Yes, each investigation opened is automatically fitted.
This is MODDE's default. If you set Automatic Fit = No MODDE will not
fit when you open, nor when you make changes in the worksheet, but will
still fit when you make changes using the interactive exclude tool.
• With Automatically display log = Yes, the Output window is automatically
opened when opening an investigation. This is MODDE's default.
• In Most recent file list you can enter the number of investigations you want
to see in the recent file list under the menu File. MODDE's default is 6.
• When Show expanded design factors in RED-MUP worksheet = No, the
expanded design factors will be hidden. This is MODDE's default. For more
see the section on RED-MUP in the Design appendix.
• In Theme you can change the look of MODDE. The default is Office 2003
Classic Theme. Available are also Office 2000, Office XP Classic Theme,
Windows XP, and Whidbey.
• OpenGL plots = No is the default and recommended for the Contour and
Sweet Spot Plots. In 3D scatter plots, OpenGL is always used.

59
User Guide to MODDE

Investigation settings
The available investigation settings are:
• Max number of layers in Onion Design to limit how many layers that will
be possible to make. MODDE's default is 10.
• Replicate tolerance is the number used when MODDE decides whether
experiments can be considered to be replicates or not. MODDE's default is
0.1, that is, 10% of the range for each factor.
• Show units in worksheet = Yes results displaying the specified factor and
response units in parenthesis after the factor resp. response names.

Program limits
Under Program Limits you can set the Maximum candidate set size.
The size of the candidate set in MODDE is by default limited to 512 000 rows when
MODDE creates the candidate set for you. You can change this limit.
The maximum size of the candidate set that you can create and generate a design from
is limited by the RAM in your computer.

Audit trail
Prompt for extended user info, found under Audit Trail, is by default No. If you
want MODDE to prompt the user to enter extended user information, change this
setting to Yes.

List Options
Use this page to change the default colors on lists. Other options available in tab list
options are:
• Default number format
• Print lists in color
• Headers in bold
• Threshold for the correlation matrix

60
 View

Restore
Use the Restore page to restore Umetrics defaults for Plot Settings, Favorites, and
'don’t show again'-messages.

Customize
Use Customize to customize toolbars and menus as in Office 2003 and later.
Click Customize on the View menu to open the dialog.
With the Customize dialog open you can interactively customize all available toolbars
and menus by dragging an item to a new location.

Customize toolbars
On the Toolbars page you can:
• Select which toolbars to display by clearing or selecting the available
toolbars.
• Create new toolbars by clicking New.
• Rename toolbars you have created
• Delete toolbars you have created.
• Reset MODDE toolbars to their default content and position.

Customize commands
On the Commands page you can customize available menus and create new menus.

61
User Guide to MODDE

Customize options
On the Options page you can select:
• To Always show full menus.
• To display Large icons.
• To Show ScreenTips on toolbars.
• To Show shortcut keys in ScreenTips.
• Menu animations among: (System default), Random, Unfold, Slide,
Fade, None.

Customize keyboard
On the Keyboard page you can select to assign and reassign shortcut keys to new and
old commands.

62
Design

Introduction
When you create or modify a design, some or all items on the Design menu are used.
The available items are:
• Factors and Responses: Define and modify factors and responses.
• Constraints and Inclusions: Define constraints and inclusions.
• Objective: Specify and modify objective, model and design
• D-Optimal: Generate and evaluate D-optimal designs, open the candidate set
for viewing or editing, view onion plots.
• Design wizard: Open the design wizard.

Factors
Click Factors on the Design menu to open the factor spreadsheet.
To modify one of the factors listed, mark it and press the ENTER key on your
keyboard or right-click the factor and click Edit.
To add a new factor, double-click the last line or right-click the spreadsheet and click
Add Factor.
For details, see the Factors chapter.

Responses
Click Responses on the Design menu to open the response spreadsheet.
To modify one of the responses listed, mark it and press the ENTER key on your
keyboard or right-click the response and click Edit.
To add a new response, double-click the last line or right-click the spreadsheet and
click Add Response.
For details, see the Responses chapter.

Constraints
Click Constraints on the Design menu to open the Constraints dialog.
To add a constraint, use the spreadsheet part or the graphical part of the dialog.
For details, see the Constraints section in the Constraints and inclusions chapter.

63
User Guide to MODDE

Inclusions
Click Inclusions on the Design menu to open the inclusions dialog.
In this dialog you can do the following:
• Import runs from a text file or another investigation to inclusions.
• Import the current worksheet.
• Add the current inclusion runs to the current worksheet.
• Open the D-Optimal page in the design wizard.
For details, see the Inclusions section in the Constraints and inclusions chapter.

Objective
Click Objective on the Design menu to open the objective pages.
In the objective pages you define the purpose of the design by selecting Screening,
Response Surface Modeling (RSM), Split Objective, or Paste Data. Click Next to
select which design you want MODDE to create. When selecting Paste Data, clicking
Finish opens the worksheet allowing you to paste the data.
For details, see the Objective, model and design chapter.

D-Optimal
When you have created a D-Optimal design a number of items are available under D-
Optimal on the Design menu. For all D-Optimal designs you can click:
• Generate to regenerate the design.
• Candidate set to view the current candidate set and which design runs that
are included in the current design.
• Evaluate to view the D-Optimal results and select another one of the
generated designs.
• Design Plot to create the D-Optimal design plot.
For Onion designs you can additionally create onion plots by clicking Onion plot and
Onion 3D Scatter. These plots display the current candidate set colored according to
layer and the experiments currently included colored black.
For details, see the D-Optimal chapter.

Design wizard
The design wizard is automatically opened when starting a new investigation from File
| New. It can also be opened after creating an investigation by clicking Design Wizard
on the Design menu or by pressing CTRL+W.
The design wizard includes pages for creating/modifying factors, creating/modifying
responses, defining/modifying a constraint numerically, objective and design selection,
and when applicable the D-Optimal pages with the possibility to define inclusions.
For details, see the Design Wizard chapter.

64
Factors

Introduction
Factors are variables that can be varied, or vary, during an experiment. A typical
example of a factor is amount of raw material or temperature.
Open the Factor spreadsheet by clicking Design | Factors or File | New, and then
Next.
In the Factors spreadsheet (window), you define (enter), modify, and delete factors.
MODDE supports quantitative, qualitative, and mixture factors.
Quantitative factors may be used in a transformed metric. When factors are
transformed, the design is made in the transformed units, but the worksheet is
expressed in original units.

Factor definition dialog

When you start a new investigation from File | New, the factor definition page is the
second page of the Design Wizard. Click New or double-click the last row in the
factor definition spreadsheet to open the factor definition dialog.
From outside the design wizard, the factor definition dialog can be opened by clicking
Design | Factors and then:
• Double-clicking the last line of the spreadsheet or
• Right-clicking the spreadsheet and clicking Add Factor.

65
User Guide to MODDE

The Factor Definition dialog is divided in an upper part and a lower part. The upper
part displays Factor name, Abbreviation, and Units and is available independently of
what is displayed in the lower part of the dialog. The lower part has two pages:
General, which is the default page when opening the dialog, and Advanced.

Factor name
Enter the Factor name with up to 50 alphanumeric characters.

Abbreviation
The Abbreviation is automatically filled with the first 3 characters of the factor name.
You can change the abbreviation as desired using up to 5 characters.
The abbreviation is used as plot label in plots, in the Model and Confoundings lists
found under the Show menu, in Worksheet | Correlation | Matrix, and in Edit |
Generators.

Units
Enter the unit of the factor (optional). The units are displayed in the factor spreadsheet
and can optionally be displayed in the worksheet, see the General page section in the
View chapter for more.

General page
On the General page of the factor definition dialog you select which type of factor you
are defining in Type of factor, the factor settings in Low and High or Settings, and
how it is used in Use.

66
 Factors

Factor types and settings

Process factors are regular factors (i.e. temp, pH, etc.) that are not part of a mixture or
formulation. They are expressed as amounts or levels, and can be varied independently
of each other. Quantitative, quantitative multilevel, and qualitative factors are
process factors.
Mixture factors are expressed as the fraction of the total amount of the formulation.
Their experimental ranges lie between 0 and 1.
Mixture factors can be defined as Formulation or Filler.
For quantitative and formulation factors the Low and High fields should be filled with
the desired values.

Note: MODDE is limited in the precision of the factor values. Factors ranging
over a larger range than that, for instance. low at 0.0001 and high at 10000,
cannot be treated as a factor.
For quantitative multilevel and qualitative factors the levels planned to be used should
be entered. For a qualitative factor each entry in Settings has to be text, optionally
including numbers, while for quantitative multilevel each entry has to be a number.

Note: In the same experiment you can have both mixture factors and regular
process factors defined as quantitative or qualitative. Up to 12 factors are
allowed when both process and formulation factors are defined in the design.
Quantitative (default)
Quantitative factors are continuous factors defined at two levels, Low and High. To
define more than two levels, see Quantitative multilevel.
Up to 32 factors are allowed for screening designs and up to 20 for RSM designs.
Quantitative multilevel
To specify more than two levels for a quantitative factor click Quantitative multilevel
under Type of Factor.
MODDE supports up to 24 levels for quantitative multilevel factors. Constraints are
not allowed with this type of factor, and the available designs are D-Optimal, Mixed
full factorial, and three level designs when applicable.
Up to 32 factors are allowed for screening designs and up to 20 for RSM designs.
Qualitative
To specify a qualitative factor, click Qualitative under Type of Factor.
Qualitative factors are discrete. For a qualitative factor, the levels should not stand in
relation to each other. If the levels are a range although discrete then the factors should
be defined as quantitative multilevel.
MODDE supports up to 24 levels for qualitative factors.
RSM designs cannot be created with only qualitative terms. With one or more
quantitative terms present up to 20 extended qualitative terms are allowed for RSM
designs.

67
User Guide to MODDE

Formulation
To specify a mixture factor, click Formulation under Type of Factor.
Define a mixture factor as Formulation, when it is not an inert filler. Define the
experimental range of the mixture formulation factor by entering its Low and High
values.
Up to 20 formulation factors are allowed in screening designs and up to 16 in RSM
designs.
Filler
Specify a mixture factor as filler, by clicking Filler under Type of Factor, when:
• It is always present in the mixture. That is, the sum of the High of the other
mixture factors does not exceed 1.
• It accounts for a large percentage of the mixture.
• There are no restrictions on its range. Rather that factor is added at the end to
bring the mixture total to the desired amount, 1 (100%).
• You are NOT interested in estimating the effect of the filler per se.
For a filler factor, the experimental range Low and High values are grayed out as it
will be calculated as 1 minus the sum of the other mixture factors.

Note: Only one mixture factor can be defined as Filler.

A typical example of a filler factor is the solvent in a synthesis.
When you specify a filler factor, MODDE checks that the above conditions are met,
and generates:
1. A slack variable model i.e. a model with the filler factor left out.
2. Classical or D-Optimal process design.
If the conditions are not met, MODDE issues a message, and changes the filler factor
to formulation.
See the Statistical appendix for more details on mixture factors.

Use
Under Use you can select how the factor will be used in the design. A factor can be
Controlled, Uncontrolled, or Constant.
Controlled (default)
When you can control the settings of the factor, leave the default under Use
(Controlled).
These factors can be regular process factors (i.e. pH, Temp, etc.) defined as
quantitative, quantitative multilevel or qualitative, or mixture factors, defined as
formulation or filler.
A Filler factor can only be defined as Controlled. Uncontrolled and Constant are
unavailable for a filler factor.

68
 Factors

Uncontrolled
Define a factor as Uncontrolled (under Use) if you cannot control it but want to
measure and record its value. Examples of such factors are ambient temperature or
humidity.
Mixture factors (defined as Formulation or Filler) cannot be uncontrolled and the
option Uncontrolled is therefore unavailable.
Constant
Define a factor as Constant (under Use) when you want the worksheet to display a
setting of a factor that is not changed.
Quantitative, qualitative, and formulation factors can be defined as Constant factors.
Quantitative and qualitative constant factors are displayed in the worksheet and
counted in the model toolbar.
When mixture factors are constant, the mixture total T for the controlled mixture
factors is equal to: T = 1 - Σ[constant mixture factors].
Multilevel quantitative and filler factors cannot be defined as Constant.

Advanced
For quantitative and quantitative multilevel factors the Advanced tab offers the
possibility to transform and change the MLR scaling. For regular quantitative factors it
is also possible to define number of decimals to be used for the factor from this page.

69
User Guide to MODDE

Transformation
To transform a factor, click the Advanced tab, and in the Transform box click the
transformation of your choice.
When you transform a factor, the design is created in the transformed units, but the
worksheet is expressed in original units. Hence transformation of a factor will change
the center point and the star point values in the worksheet.
All transformed factors are displayed with a “~” (tilde) near the name in lists and plots.
The following transformations are available:
Transformation Description

None Default

Lin C1 * Y + C2

Log Log10(C1 * Y + C2)

Negative Log -Log10(C2 - C1 * Y)

Exp e(C1 * Y + C2)

Logit Log10((Y - C1)/(C2 - Y))

(C1 * Y + C2)C3
Power
where C3 can be any value from -2 to 2.

When a transformation is selected (except None), the relevant constant fields are
displayed.
The field C3 is only displayed for the power transformation.

Scaling options for MLR scaling

When fitting with MLR the factors can be scaled using orthogonal, mid-range, or unit
variance scaling in the Advanced page of the factor definition dialog box.
Orthogonal (default)
The factors are centered and scaled using the mid-range and Low and High values
from the factor definition. This is the system default.
Mid-range
When you select to scale a factor using mid-range it is centered only using the mid-
range of the factor. Mid-range is calculated as (High-Low)/2 where High and Low are
the values defined in the factor definition.
Unit variance
When you select to scale a factor to unit variance the worksheet columns are scaled
and centered to unit variance in the calculations.

70
 Factors

Mixture factors
When fitting the model with MLR, the mixture factors are not scaled.
You can select to fit the model in pseudo components. This is recommended when the
mixture region is regular.
For investigations containing both process and mixture factors, by default process
factors are orthogonally scaled and the mixture factors are unscaled. The coefficients
displayed as scaled and centered correspond to this default scaling of the variables i.e.
mixture unscaled and process orthogonally scaled. If you select to display the unscaled
coefficients, they correspond to all factors unscaled, including the process factors.

Note: You should select the same scaling for all the factors, the system default
is recommended.

PLS scaling
When fitting the model with PLS, all factors including mixture factors are always
scaled and centered to unit variance.
For mixture factors, when you select pseudo components, the mixture factors are first
transformed to pseudo components and then scaled to unit variance (pseudo
components can be switched on/off).

Number of decimals
In the Advanced page of the factor definition dialog you can select Number of
decimals.
The values for number of decimals are: Free, 0, 1, 2, 3, 4 and represent the number of
digits displayed after the decimal point.
The Number of decimals-value should correspond to the precision with which the
factor can be set in your equipment. It is important that it is not set too low since after
setting this value all values for that factor will be rounded accordingly in the
worksheet. If you do not know the precision of the instrument, leave No. of decimals
'Free'. 'Free' means that no rounding off of the results and values corresponding to this
factor will take place.
For example, the settings of a factor in a CCC design, is its high value (in
orthogonal scaled units) multiplied by the 4th root of the number of runs in the factorial
part of the design. If the precision of this factor is set to 0 all decimal digits are
removed from this factor setting in the worksheet and computation will take place
using the values in the worksheet.

71
User Guide to MODDE

Factor definition spreadsheet

When a factor has been defined, the Factors definition spreadsheet provides an
overview of the factor definitions, with one factor in each row. The factor properties
are listed in the form of name, abbreviation, unit, type (quantitative, quantitative
multilevel, qualitative, formulation, or filler), use (controlled, uncontrolled, or
constant), settings (high and low vales displayed except for quantitative multilevel and
qualitative where all levels are displayed), transformation, precision, MLR scaling, and
PLS scaling.
In the factor definition spreadsheet, the fields Name, Abbr, Units, and Settings can be
modified directly. To modify any of the other fields, double-click one of them and the
Factor Definition dialog box opens.

Factors can be added by double-clicking the last row of the factor definition
spreadsheet or right-clicking the spreadsheet and clicking Add Factor.
To copy factors, mark the factors to copy, click Edit | Copy or press CTRL+C, and
click Edit | Paste or press CTRL+V. MODDE copies the factors and adds a digit after
the name when pasting to make it unique.

Printing the factor spreadsheet

Use the menu File | Print or right-click the spreadsheet and click Print to output the
factor definition spreadsheet to a printer.

72
 Factors

Factor manipulations in short

Opening the factor definition spreadsheet
Click Design | Factors to activate the factor definition spreadsheet and display the list
of defined factors.

Adding a factor
To add a factor through the factor definition dialog use one of the following methods:
• Double-click the last line of the factor definition spreadsheet.
• Right-click the spreadsheet and click Add Factor.
• Open View | Design Wizard and click New in the Define factors page.
Quantitative factors can be added by typing on the last (empty) row starting with
entering the factor name, see the example:

Modifying a factor
It is possible to edit the fields Name, Abbr., Units, and Settings directly in the
spreadsheet.
To modify any of the other fields, double-click that factor in the factors spreadsheet.
The Factor Definition dialog opens with the attributes of the factor to modify.
The Factor Definition dialog can also be opened by clicking View | Design
Wizard and clicking Edit in the Define factors page.

Updating the worksheet

When performing the experiments according to your experimental plan, the worksheet,
you also take note of deviances of the factor settings. When you enter the response
values you must also enter the actual value of the factors in the worksheet.

Copying a factor
Factors can be copied and pasted in the factor spreadsheet by clicking Edit | Copy and
then Edit | Paste or pressing CTRL+C and then CTRL+V.

73
User Guide to MODDE

Deleting a factor
To delete a factor, mark it in the factor definition spreadsheet and use one of the
following methods:
• Press the DELETE key on the keyboard.
• Right-click and click Delete.
• Click Edit | Delete.
You are warned of the possible consequences. Click Yes/No in the confirmation box.

74
Responses

Introduction
A response is the result from an experiment. A typical example of a response is yield.
Open the response definition spreadsheet from Design | Responses or File | New,
Next, Next.
In the response definition spreadsheet, you define (enter), modify, delete, copy, print,
and list responses. MODDE supports only quantitative responses.
Responses may be transformed, and MODDE supports several transformations. For
transformed responses, predictions, contour plots and 3D plots, are back transformed to
original units.

Response definition dialog

When you start a new investigation from File | New, the response definition page is the
third page of the Design Wizard. Click New or double-click the last line of the
spreadsheet in the Define responses window to open the response definition dialog.
From outside the Design Wizard, the response definition dialog can be opened by:
• Clicking Design | Responses and double-clicking the last line of the
spreadsheet or
• Right-clicking the spreadsheet and clicking Add Response.

75
User Guide to MODDE

Response name
Enter the response name with up to 50 alphanumeric characters in the Response name
box.

Abbreviation
The Abbreviation is automatically filled with the first 3 characters of the response
name. You can change the abbreviation as desired using up to 5 characters.
The abbreviation is used as plot label in plots and in Worksheet | Correlation |
Matrix.

Units
Optionally enter the unit of the response in the Units box. The units are displayed in
the response definition spreadsheet and can optionally be displayed in the worksheet,
see the General page subsection in the View chapter for more.

Selecting type of response

There are two types of responses: Regular and Derived. After defining the response
and exiting the response definition dialog it is not possible to change the type.

Limits
Fill in the Min, Target, and Max fields when that information is available to you.
These values are then automatically used in the Design Space, Sweet Spot, and
Optimizer windows.

76
 Responses

Regular responses
Regular responses are the standard responses measured and fitted in the current
investigation. Regular responses can be transformed and it is also possible to change
the modifier for PLS scaling.

Transformation
The following transformations are available:
Transformation Description

None Default

Lin C1 * Y + C2

Log Log10(C1 * Y + C2)

Negative Log -Log10(C2 - C1 * Y)

Exp e(C1 * Y + C2)

Logit Log10((Y - C1)/(C2 - Y))

(C1 * Y + C2)C3
Power
where C3 can be any value from -2 to 2.

When a transformation is selected (except None), the constants in the formula are
entered in the fields displayed after selecting a transformation. The C3 field is only
displayed for the power transformation.
Specifying a transformation for a response is done to get the best mathematical fit of
the estimated function.

Note: You can specify or modify the current transformation by right-clicking

the Histogram plot and clicking Transform.

MLR scaling
When fitting the model with MLR no scaling of responses is available.

PLS scaling
When fitting the model with PLS it is possible to scale to unit variance with or without
a modifier.
With the default scaling option, the responses are centered and scaled to unit variance
when fitting.

Unit variance (default)

With the default scaling option, the responses are centered and scaled to unit variance
when fitting.

77
User Guide to MODDE

Autoscale modifier
In the PLS Scaling box, click Autoscale Modifier to change the modifier. Leaving the
modifier at the default=1 gives the same result as when selecting Unit Variance. Enter
a different value of the modifier and the response will be scaled to unit variance
multiplied by the value of the modifier.

Note: To keep a response out of the analysis set its autoscale modifier to zero
(i.e., enter 0 in the edit field).

Derived responses
A Derived response is a computed response as function of the factors and/or fitted
regular responses. When you add a derived response, you enter its formula. Derived
responses can be edited and deleted.
Derived responses are displayed in the responses spreadsheet. The values of the
derived responses are entered automatically in the worksheet when the model is fitted.
The derived responses are also available for all plots and list under the Worksheet and
Prediction menus and can be used as regular responses under these menus.

Note: Derived response values are only available after fitting (clicking Fit on
the Analysis menu) the model. When responses are included in the formula,
MODDE uses the fitted (predicted by the model) values of the responses in the
computation.

78
 Responses

Defining derived responses

To create derived responses open the Response Definition dialog, enter the name,
abbreviation and units of the response.
Under Select type of response, click Derived, and then click the Edit button.

When clicking the Edit button, the Derived Response Wizard opens. The first page
contains information about derived responses. Select the Don’t show this page again
check box if you do not want to see this information again.

79
User Guide to MODDE

Clicking Next opens the next page in which you Enter the formula for the derived
response.

When you click Finish, MODDE parses the formula for correctness, and only
computes and displays the derived response in the worksheet, when you fit the model.
The derived response is added to the responses spreadsheet and the worksheet.

Modifying a derived response

To modify a derived response, you must edit its formula in the Response Definition
dialog. You cannot edit the values in the worksheet.

Copying or deleting a derived response

Derived responses can be copied and deleted as regular responses.

Note: Derived responses are deleted when regular factors are deleted, or
changed and when responses that are part of the derived response are deleted.

Using sets of variables in derived responses

In MODDE you generate one derived response at a time.
Hence you can only use sets of variables with the operators avg, stdev, and sum that
return one variable.
Examples using sets of variables
Avg(v[1,3,4] + v[6,8,9])
Results in the average of 3 variables, v1+v6, v3+v8, v4+v9.
Avg(v5 + v[1:6]) is an illegal syntax, the two operands are not of the same size.
Sum(v[1,3,4] +v9)
Results in the sum of 3 variables, v1+v9, v3+v9, v4+v9.
Stdev(v[3:5]*v1)
Results in the standard deviation of the 3 variables v3*v1, v4*v1 and v5*v1
avg(v[1:5]*v8/v7)
Results in the average of 5 variables, i.e. the average of variables 1 to 5 each multiplied
by the ratio v8/v7.
Sum(v8/v7 * v[1:5]) is an illegal syntax.

80
 Responses

Syntax for derived responses

MODDE recognizes the following syntax:
• Integer, Variables (factors or responses), List of Integers and Sets of
Variables
• Integer constant and floating points
• Operator ‘:’ denotes a sequence, i.e., from: to, for example 6:8 means 6,7,8
• List of integers, such as 1,3,5:8 is the same as 1,3,5,6,7,8
• Variables (factors or responses) are denoted by vint, where int refers to the
variable number in the worksheet (i.e. v5, v15, for variables 5 and 15)
• A set of variables (matrix) is denoted by v[int1,int2, int3:int4,int6] with
square brackets. Int refers to the variable number in the worksheet. For
example v[1,5,7:10] refers to the set of variables v1, v5, v7, v8, v9, and v10.

Note: To denote a set of variables you have to use the square brackets [ ], and
not regular parenthesis ( )

Operators and functions in derived responses

The operators and functions listed below are recognized and can be used with a single
variable or a set of variables. Operators have the usual precedence, i.e. ^ > * and / > +
and -. Parenthesis can be used to group expressions in the usual way.

Functions
The functions available are Log10, Ln (natural log), and Exp (exponential).

Addition and subtraction

Addition/subtraction (+, −) can be applied to:
• A set of variables with a constant
• A set of variables with a single variable
• A set of variables with another set of variables of the same size (they are
added pair wise).
• A single variable with a constant or a single variable

Power, multiplication, and division

Power, multiplication, and division (^,*, /) can be applied to:
• A set of variables with a constant
• A set of variables with a single variable.

Note: Power, multiplication and division cannot be applied to a set of

variables and another set of variables. The first operand can be a constant, a
variable or a set of variables, but the second and following operands must be
a single variable or a constant.

81
User Guide to MODDE

Additional operators
The following additional operators apply to variables or sets of variables:
Avg(v[int1:int2]) Average of variables vint1... to vint2

Stdev(v[int1:int2]) Standard deviation of variables vint1... to vint2

Sum(v[int1:int2]) Sum of variables vint1... to vint2

Note: The parser is not case sensitive (t and T mean the same thing).

Qualitative factors in derived responses

When you use a qualitative factor in the formula for a derived response, enter the
values (weights), to be used when computing the derived response, for each qualitative
level setting. If no settings are entered, '0' is used as value for all settings of the
qualitative factor.

Linked responses
A Linked response is a response available in one investigation but fitted in another.
Linked responses are no longer available in MODDE.
Investigations containing linked responses are converted in MODDE 9 to instead hold
different models and/or worksheets. MODDE supports as many models in one
investigation as there are responses.

82
 Responses

Response definition spreadsheet

When the responses are defined, the response definition spreadsheet provides an
overview of response definitions, with one response in each row. The response
properties are listed in the form of name, abbreviation, unit, transformation, MLR
Scale, PLS Scale, and type of response (regular or derived). A response is selected by
clicking when pointing to it or by using the keyboard arrow keys to move in the
spreadsheet.
The fields Name, Abbr, Min, Target, and Max can be edited directly in the
spreadsheet. To modify any other fields double-click one of them, or mark the response
and press ENTER, to open the Response Definition dialog. Type cannot be modified
after a response has been defined.
Responses can be added by double-clicking the last row of the Responses definition
spreadsheet or by right-clicking the spreadsheet and then clicking Add Response.
To copy responses, mark the responses to copy, click Edit | Copy or press CTRL+C,
and then click Edit | Paste or press CTRL+V. MODDE copies the responses and adds
a digit after the name when pasting to make it unique.

Printing the response definition spreadsheet

To print the Responses definition spreadsheet, click Print on the File menu or right-
click the spreadsheet and click Print.

83
User Guide to MODDE

Response manipulations in short

Opening the responses spreadsheet
On the Design menu, click Responses to open or activate the Responses spreadsheet
(window) displaying the list of the defined responses.

Adding a response
To add responses, double-click the last entry in the Responses spreadsheet window.
Enter the responses name, abbreviation etc, in the Response Definition dialog.

Modifying a response
The fields Name and Abbr. can be edited directly in the Responses spreadsheet.
To modify other fields for regular or derived responses, mark the desired response in
the responses spreadsheet and:
• Double-click it or
• Press ENTER.
The Response Definition dialog opens with the attributes of the response to modify.

Deleting a response
To delete one or more responses, mark the response(s) in the responses spreadsheet
and press the DELETE key on the keyboard or click Edit | Delete.
A dialog is displayed to confirm the deletion.

Copying and pasting a response

Regular and derived responses can be copied and pasted by marking them and then
clicking Edit | Copy and Edit | Paste or pressing CTRL+C and CTRL+V.

84
Constraints and inclusions

Constraints
A common problem is that experimentation may not be possible in some region of the
experimental space. For example it may not be possible, in an experiment, to have high
temperature and simultaneously low pH, and you want to cut-off the corner High temp,
Low pH. In MODDE this is solved by adding a Constraint using Design | Constraint.
A linear constraint is a function of the factors that specify a part of the experimental
region to be included or excluded.
The resulting experimental region is an irregular polyhedron. The corners of this region
are called the extreme vertices; they constitute part of the candidate set, i.e. a
discrete set of potentially good runs.
D-optimal designs are the only designs available when the experimental region is
constrained to an irregular polyhedron.
Constraints can be defined for quantitative or formulation factors.

Specifying constraints
Enter your constraints in the Constraints spreadsheet. The Constraints window is
opened by clicking Constraints on the Design menu.
In the upper part, the spreadsheet, you define each constraint (one per row) as a
mathematical relation. In the lower part, the graphical view, you can define constraints,
to be added to the upper part, geometrically. Such constraints may include two factors
only and are shown in the upper part after clicking the Add button.

85
User Guide to MODDE

Constraints supported
MODDE supports linear constraints, specified as exclusions, for quantitative process
factors or mixture factors Xk of the form

ΣAkXk < Limit

or

ΣAkXk > Limit

A constraint cannot be defined to include both quantitative and formulation factors.
Constraints cannot be defined in quantitative multilevel, qualitative, filler,
uncontrolled, or constant factors.
MODDE supports up to 50 linear constraints.

Defining constraints in the spreadsheet

To define a constraint in the spreadsheet, enter the coefficients Ak of every factor in the
constraint. Select “<“ or “>“ and enter the Limit of the constraint.

An example of entering a constraint in the spreadsheet

For example, in an experiment with three mixture factors:
X1 qualitative 3 levels: A, B, C
X2 qualitative 2 levels: K, L
X3 mixture
X4 mixture
X5 mixture
X6 mixture
A set of constraints may be entered as follows:

The first constraint specifies to exclude experimental runs where the sum of X3, X4,
and X5 is < 0.6
The second constraint specifies to exclude experimental runs where the sum of X4 and
X5 < 0.3

86
 Constraints and inclusions

Defining a constraint graphically

The graphical interface in MODDE helps you define the constraints to exclude a region
of the experimental space defined by the intersection of a line with the experimental
region. Only two factor constraints can be defined graphically.
1. In the Factor on the X-axis and Factor on the Y-axis boxes select the name
of the two factors defining the constraint.
2. Define the coordinates of the extreme vertices (intersection of the line with
the experimental region) or pull the end of the line along the side to select the
region to cut off. When pulling, MODDE enters the current extreme vertices
in Low and High of the selected X and Y-axis factors.
3. Under Exclude area click Above line or Below line to exclude the correct
area.
4. Clicking the Add button. MODDE computes the equation of the line and
enters the coefficients Ak of the two factors in the constraints spreadsheet in
the upper part of the constraints window.

87
User Guide to MODDE

An example of entering a constraint graphically

For example in an experiment with temperature and pH, temperature varies between
120 and 160C and pH between 1 and 5. You may want to exclude the corner
Temperature =160 and pH =1. Define the extreme acceptable conditions, that is the
lowest pH when temperature is 160, for example pH=3, and the highest temperature
when pH =1 for example temperature = 140.
These are the coordinates of the extreme vertices, the intersection of the line that cuts
off the undesirable corner.
Enter these in the Low and High boxes, and the coefficients of the intersecting line are
computed when you click the Add button.

Modifying a constraint graphically

To modify a constraint graphically, mark the row showing the constraint in the
spreadsheet, change the constraint by pulling the end points of the line, or by
modifying the values in Low and/or High. Then click the Update Constraint-button
to update the constraint formula in the constraints spreadsheet.

Note: Click a row in the spreadsheet defining a constraint in two factors and
MODDE displays the graphical constraint.

88
 Constraints and inclusions

Candidate set with a constraint

When defining constraints the only designs available are D-Optimal designs. To create
D-Optimal designs a candidate set is created. When there is a constraint present the
resulting candidate set is formed by the extreme vertices of the irregular region,
defined by the linear constraints.
If there in addition are qualitative or quantitative multilevel factors, the final candidate
set is the product of the full factorial in the qualitative or quantitative multilevel factors
times the candidate set resulting from the linear constraints (extreme vertices, center of
edges, etc. of the irregular experimental region).

Constraints in qualitative or quantitative multilevel factors

Qualitative factors and quantitative multilevel do not appear in the constraint
spreadsheet and cannot be used in constraints.
In the case it is needed to constrain a region defined by a qualitative or quantitative
multilevel factor:
1. Select a D-Optimal design and in the Change D-Optimal settings page of
the design wizard, open the candidate set by clicking the Edit button under
Candidate Set.
2. In the candidate set that opens, find the settings that are undesirable and
delete those rows.
3. When finished, click the Generate D-Optimal button and the Design
Wizard D-Optimal page opens up again.
4. Continue creating the design.

Note: To sort the candidate set in order to find undesirable factor

combinations you need to create a D-Optimal design, click Design | D-
Optimal | Candidate Set, and then click Edit | Sort.

89
User Guide to MODDE

Inclusions
In MODDE designs can be augmented either using Complement Design (see the
section Complement Design in chapter File menu) or Inclusions.
Inclusions are extra runs that will be part of the worksheet. You can include a set of
experimental runs (inclusions), either at the end of the worksheet or to be part of a D-
Optimal design.
The Inclusions spreadsheet can be opened by clicking Design ⏐ Inclusions or by
clicking the import or Edit buttons in the Change D-Optimal settings page in the
Design Wizard.

Inclusions vs. complement design

Using Inclusions to augment a design is preferred when:
• The extra experiments to include are found in another investigation or in a
text-file as complement design can only complement the current
investigation.
• The experiments were not saved in a MODDE investigation or a text file. In
Inclusions such experiments can be entered manually or pasted.
• When adding experiments after the design has already been created. That is,
when the inclusions should not be part of the design generation.
Using Complement Design to augment a design is preferred when:
• The desired design should be a classical design. Use Fold over or Estimate
square terms in a screening design. When using inclusions D-optimal
designs is the only available choice.
• The desired design should include star points. Use Estimate square terms
in a screening design and change the Star distance.

Inclusions added to the worksheet

Inclusions can be added to the worksheet after the design and worksheet have been
created.
Inclusions can be specified before or after the worksheet is generated. If the worksheet
already exists when you enter the inclusions, click the Add to Worksheet button to
add the inclusions last in the worksheet. If you enter the inclusions before the
generation of the worksheet, click the Save and Close button, reopen the Inclusions
spreadsheet after creating the worksheet and click the Add to Worksheet button.
If the inclusions are entered before the generation of a D-Optimal design the Include
in design check box on the D-Optimal page of the design wizard has to be cleared to
avoid including the inclusions.

Note: The inclusions are added to the worksheet only when you click the Add
to Worksheet button

90
 Constraints and inclusions

Inclusions as part of the design

With D-Optimal designs Inclusions runs can be a part of the design or added at the
end of the worksheet.
If the inclusions are entered before the generation of a D-Optimal design the Include
in design check box on the D-Optimal page of the design wizard is default selected
and the inclusions are used when creating the D-Optimal design.

Note: When generating D-Optimal designs, and the Include in design check
box is selected, the inclusions are a part of the design and included in the
number of runs.

91
User Guide to MODDE

Generating inclusions
Click Design | Inclusions to open the Inclusions spreadsheet, or click the Edit button
in the Inclusions area in the D-Optimal page in the design wizard.
In the inclusions spreadsheet you can add experiments by typing or pasting, by
importing from file, and by importing the current worksheet. You can do several
imports.

Adding experiments in the spreadsheet

Factor and response values can be entered directly in the inclusions spreadsheet. Right-
click the spreadsheet and click Insert Rows to insert as many rows as you need or
press the down arrow key on the keyboard. The rows needed when pasting are created
automatically.

Importing from file

Inclusions can be imported from a tab separated text file (*.txt), or another MODDE
investigation with the same factors, by clicking the Import button. Select either a text
file, a MODDE file (*.mip) or a MODDE 4.0 worksheet (*. dat).
When importing, all the factors defined in the MODDE investigation have to be
present in the file, including uncontrolled, filler, and constant factors.
See also the Design generation criteria section in the D-Optimal chapter.

Importing worksheet
Click the Import Worksheet button to import the current worksheet to use as
inclusions.

Modifying inclusions
If the inclusions already exist, clicking Design | Inclusions or the Edit button in the D-
Optimal page in the design wizard, opens the spreadsheet with the inclusions for
editing.
To delete rows, mark them, press the DELETE key or right-click the spreadsheet and
click Delete.

92
Objective, model and design

Introduction
The Objective is the purpose for creating the design. MODDE recognizes two
objectives: Screening (first stage of an investigation when little is known) and
Response Surface Modeling (RSM) (optimization with the important factors.). The
Split Objective supports both screening and RSM. Paste Data defaults to the
screening objective with a linear model.
After defining your factors and responses, clicking Design ⏐ Objective opens the
design wizard which guides you through the selection of objective, design, and model
of the investigation.
The following sections describe the definition of the objective and selection of model
and design. See the Design Appendix chapter for details concerning the available
designs.
There are two dialogs associated with the menu item Objective:
• First: the Select Objective dialog to select the purpose.
• Second: the Select Model and Design dialog to select the type of design and
model.

93
User Guide to MODDE

Selecting the objective

Open the Objective dialog by clicking Design | Objective. Select one of four options
Screening, Response Surface Modeling (RSM), Split Objective, or Paste Data.

Screening objective
Select the Screening objective when:
• You are starting an investigation and know little about the effects of the
factors on the response, the behavior of the response in the experimental
region, or the true size of that region.
• The goal is to reduce the number of factors to those with the largest effect on
the response.
This objective is available for all types of factors and factor combinations.

RSM objective
Select the RSM objective when:
• A lot is known about the investigation i.e. important factors, the size of the
region etc.
• The goal is to approximate the response by a mathematical model for the
purpose of prediction, optimization or finding a region of operability.
This objective is not available when all factors are qualitative.

Split Objective
Select the Split Objective when the investigation holds both process and mixture
factors AND you want to specify separate models for each.
If you want to specify one model for both mixture and process factors, select
Screening or RSM as objective.
The split objective is only available when there are both process and mixture factors
available.

94
 Objective, model and design

Paste Data
Select Paste Data when you have the design and want to paste it instead of MODDE
creating one for you.
After selecting Paste Data and clicking Finish, the MODDE worksheet will expand
dynamically to fit the size of the pasted data. Click Analysis | Evaluate to view the
condition number of the current worksheet and model.
See also the Import design from file section in the File chapter.

Selecting model and design

After selecting the objective and clicking Next the Select the model and design page
opens. In this page you can clear or select the Show extended list of designs check
box resulting it displaying:
• only the recommended designs or
• all available designs,
for the current objective and number of factors, with the number of runs and the
associated models.

Note: Sort the list on a selected column by clicking its header.

Designs in MODDE
The design is the protocol for varying the factors in each experiment. Thus the design
is a set of experimental runs spanning the experimental region.
See the Design appendix for more details concerning the designs available in
MODDE.

95
User Guide to MODDE

Recommended designs
According to the selected objective and number of factors, MODDE recommends the
two most likely designs. Continue with the recommended design or select another one
by pointing and clicking or pressing the UP and DOWN arrow keys on the keyboard.
MODDE recommends, whenever possible, classical designs.
The recommendations are marked First and Second in the Recommendation column.

Note: By clearing the Show extended list of designs check box you can
display all supported designs in MODDE available for the defined factors and
selected objective.

Runs in design
In the Runs column the number of runs in the design is displayed. When there is a '+'
and/or a '-' sign after the number that means that the number of runs can be changed for
that particular design.

Model
MODDE supports polynomial models, such as linear, interaction, and quadratic. Third
order terms such as cubic or three factor interactions may be added to the model in
Design ⏐ Edit Model after the design generation.
The model for each design is listed in the Model column.

Screening models
Linear and Interaction models are appropriate for the screening objective. When the
model you select is:
• Linear MODDE generates the linear model. You may edit the model and
enter selected interactions.
• Interaction MODDE generates the full interaction model, i. e. all the two
factor interactions are included.

RSM models
Quadratic models are used for the RSM objective. For classical mixture designs cubic
designs are also available. When the model you select is:
• Quadratic MODDE generates the full quadratic model holding all two-factor
interactions and all the square terms of all the factors.
• Special cubic or cubic MODDE generates models accordingly. Such models
are only supported with mixture factors. Such models include all two-factor
interactions, all square terms, and some or all cubic terms.

Split models
When selecting the Split Objective, the model for the process factors and the mixture
factors can be specified independently of each other by clicking the Settings button.

96
 Objective, model and design

Pseudo resolution for blocked designs

The pseudo resolution applies to designs when they are blocked.
The pseudo resolution of the design is the resolution of the design when all the block
effects (blocking factors and all their interactions) are treated as main effects under the
assumption that there are no interactions between blocks and main effects, or blocks
and main effects interactions.
See also the section Blocks in this chapter and the section Orthogonal blocking in the
Statistical appendix.

Design runs
The Design runs box displays the number of runs for the selected design.

When there exists 2 or more fractional factorial designs of the same resolution, with
different number of runs, the number of runs, in the Runs column, is marked with a
“+”. MODDE defaults to the design with smallest number of runs. Use the Design
runs arrow to select the larger design.
For example, with the screening objective for 7 or 8 factors there exist two-resolution
IV design, one with 16 runs and the other with 32. MODDE selects the one with 16
runs. To select the design with 32 runs, click the Design runs arrow.
With D-Optimal designs the number of runs, in the Runs column, is marked with a ‘+’
and ‘-’ indicating that there exists smaller and larger designs.
When augmenting a design D-Optimally, the number of runs includes the number of
inclusions.

97
User Guide to MODDE

Center points
The Center points box displays the number of center points. MODDE always
recommends 3 center points. To change the number of center points:
• Type the desired number
• Click the Center points arrows and click a number.
• Mark the Center points box and press the up or down arrow keys on the
keyboard.

Replicates
The Replicates box displays the number of times to replicate the whole design
including center points. The default is '0', meaning that the design is not replicated.
Enter '1' here to replicate the design once.
To change the number of replicates:
• Type the desired number
• Click the Replicates arrows and click a number.
• Mark the Replicates box and press the up or down arrow keys on the
keyboard.

Total runs
After Total runs, the total number of runs included in the worksheet is listed and
includes: runs in the design plus center points and replicates.

98
 Objective, model and design

Settings
For some designs the Settings-button is active.
Click the Settings button to:
• Edit the generators and/or model for fractional factorial designs of
resolution III, V, and V.
• Change the star distance for a CCC design.
• Specify the model when you have selected the split objective.

99
User Guide to MODDE

Editing the model and generators for classical screening designs

Before creating a fractional factorial design the model and generators can be changed
to better take into account user knowledge. That is, it is possible to unconfound certain
model terms if desired by changing the generators.
Click the Settings button and click Model to open the Edit Model dialog and add
interactions. Adding interactions makes the confounding pattern clear in Generators.
Click the Settings button and click Generators to change the generators of the design.

Note: The model and generators can be edited outside the design wizard by
clicking Edit | Model and Edit | Generators.
For more details see, the sections Model / reference mixture and Generators in the
Edit chapter.

Star distance of CCC designs

With CCC designs the star distance can be changed from the default by clicking the
Settings button and clicking Star Distance. The default star distance is calculated as
√√(2K) where K is the number of factors (square root of the square root of 2 to the
power of K).
Note that from 5 factors and upward the factorial part of the design is reduced and the
K used in the calculation of the star distance is that of the full factorial part. This
means that the default star distance value is 2 for both 4 and 5 factors.

100
 Objective, model and design

Specify the models with split objective

When there are both process and mixture factors present the only designs available are
the D-Optimal designs.
Select the split objective to specify separate models for the mixture factors and the
process factors. Click the Settings button, click Model and the Select Model dialog is
opened.

Select the desired models and select the Add interaction between linear process and
mixture factors check box to add interactions between the process and mixture
factors.
Click the Edit model button in the D-Optimal page to edit the models further.

Note: It is not possible to have interactions between the mixture factors as

these are part of the quadratic model. Scheffé Models are not supported for
investigations with both process and mixture factors.

Description
Click the Description button, positioned below the Settings button, to display a short
description of the selected design. To hide the text, click the button again.

101
User Guide to MODDE

Blocks
MODDE supports Orthogonal Blocking for the 2 levels Factorial, Fractional factorial,
Plackett Burman, CCC, Box Behnken, and D-Optimal designs.
The maximum number of blocks supported by MODDE is 8, with a minimum block
size of 4.
Select the number of blocks to include in your design from the Blocks box.

Orthogonal blocking
The method of dividing experiments into blocks, so that the block effect is
uncorrelated with the main factor effects is called orthogonal blocking.
Orthogonal blocking is a way to deal with extraneous sources of variability that are not
included in the model. For example if one is making 32 experiments and the batches of
raw material are sufficient for 8 experiments, one would like to run the experiments in
blocks of 8 such as the variation between batches of raw material does not affect the
estimate of the main factor effects.
See also the Orthogonal blocking section in the Statistical appendix.

Block interaction
An interaction between a main effect and a block effect is called a block interaction.
When the design supports the interactions between the block effects and the main
effects, the Block interactions check box, in the Select the model and design page is
active. You can select the check box if you want to add the block interactions to your
model.
For details see the Orthogonal blocking section in the Statistical Appendix.

102
D-Optimal

What are D-Optimal designs?

D-Optimal designs are computer generated designs, tailor made for a specific
problem. They allow great flexibility in the specifications of your problem. They are
particularly useful when you want to constrain the region and no classical design
exists.
“D-Optimal” means that these designs maximize the information in the selected set of
experimental runs with respect to a stated model.
Given a model, the D-Optimal algorithm selects “N” experimental runs from the
candidate set, as to maximize the information in X.
You can change the number of runs N suggested by the system. The candidate set is
the set of all potentially good runs. The extended design matrix X is created from the
“N” experimental runs expanded with extra columns for the constant, the squares and
cross terms according to the model.

When do I use D-Optimal designs?

Whenever possible you should use classical designs and these are the default designs
of MODDE. However when classical designs are impossible to apply, D-Optimal
designs are the preferred choice.
MODDE suggests a D-Optimal design when:
1. There is a linear constraint on the factor settings, reducing the experimental
region to an irregular polyhedron. There are no classical designs that can
well investigate an irregular region. A D-Optimal design is then the
preferred choice as it makes efficient use of the entire experimental space.
2. There are formulation factors, with lower and upper bounds, and possibly
additional constraints, making the region an irregular polyhedron.
3. There are qualitative factors, with more than two levels and there is no
mixed level design available. Or the mixed level design suggests too many
runs to be acceptable.
4. The objective is RSM and there are qualitative factors.
5. The number of experimental runs affordable is smaller than the number of
runs of any available classical design.
6. Both process and mixture factors are present.

103
User Guide to MODDE

D-Optimal pages in the design wizard

There are two D-Optimal pages in the design wizard: the Change D-Optimal settings
page and the D-Optimal results page.
The first page of the design wizard opens, after selecting a D-Optimal design in the
Select model and design page and clicking Next.

This Change D-Optimal settings page consists of three sections relating to:
1. Design Generation Criteria
2. Design Alternatives
3. Candidate set

Design generation criteria section

The Design Generation Criteria concerns the criteria on which the design is built.

Design runs
Design runs is the number of runs the D-Optimal algorithm will generate, not
including the center points. You can change this number as desired. The smallest
number of runs accepted is the number of terms currently included in the model.

Model terms
The number of terms currently in the model is listed after Model terms. This number
is updated after changes in Edit Model.

104
 D-Optimal

Editing the model

Click the Edit Model button to edit the model. The edit model dialog opens and you
can edit the model by adding or deleting terms in the specified model. This modifies
the number of model terms.

Note: When the investigation contains only mixture factors, the Edit Model
button is unavailable. The D-Optimal design is always generated from the full
model specified in the design page.
With investigations containing both mixture and process factors, you can only edit the
process factor terms and the interactions between mixture and process factors.

Potential terms
By default MODDE includes a set of potential terms, i.e. additional terms not included
in your model that might be important. The objective is to select a D-Optimal design
rich enough to guard for the potential terms. If you want your design to be just optimal
for your specified model, clear the Use potential terms box.

Inclusions
To use runs available from file as inclusions, click the Import button.
To edit the available inclusions, or paste/type runs to use as inclusions, click the Edit
button.
If you have specified runs as inclusions in the Design | Inclusion window prior to
entering the design wizard, the Include in design check box found under Inclusions, is
by default selected and the inclusions will automatically be part of the D-Optimal
design. Clear this check box if you do not want the inclusions to be part of the D-
Optimal design (but rather manually added at the end of the worksheet).
To add the inclusions after generating the worksheet, open the Inclusions under the
Design menu, and then click Add to worksheet.

Degrees of freedom
Number of Degrees of freedom of the residuals is calculated as:
Number of design runs – Model terms +1 (when you have center points)
The number of degrees of freedom recommended for D-Optimal designs in MODDE is
at least five.

105
User Guide to MODDE

Design alternatives section

The Design alternatives section controls the number of designs generated by the D-
Optimal algorithm.

Design runs span

The performance of a D-Optimal design, depends on the selected number of runs, N,
and the number of terms in the model, p.
MODDE can generate several D-Optimal designs, varying the specified number of
runs N and then evaluate them (G-efficiency, Condition Number, Determinant) as
functions of N.
In the Design Runs Span box, you can select the number of designs to generate with
varying N.
If, for example, you select N ± 3 and 1 repetition, MODDE generate 7 designs ranging
from N-3 to N+3. The default is to generate 25 designs with N ± 2 and 5 repetitions.

Repetitions
In the Repetitions box, select the number of designs you want to generate with the
same number of runs, N. This will give a set of designs for each value of N.

Balancing the design

When you have a qualitative factor, or when you have selected to block the design, you
may want the design to have the same number of runs at each level of the qualitative
factor. Thus, the design would be Balanced with respect to the qualitative factor.
If you want a balanced design, select the qualitative factor in the Balance on box. With
a blocked design, by default, the qualitative variable '$Blo' is selected.

If you want MODDE to only select balanced designs, select the Use balanced only
check box.
To be able to get a balanced design, the selected number of design runs must be a
multiple of the number of levels of the qualitative factor. The number of design runs
may be updated, if necessary, to be a multiple of the number of levels of the qualitative
factor.

Note: It is not always possible to generate balanced designs. When MODDE

does not succeed in generating a balanced design, it issues a message. In this
case, to generate a design, you must clear the Use balanced only check box.

106
 D-Optimal

Candidate set section

The Candidate set section concerns the set of design runs to select the D-Optimal
design from.

Generating a new candidate set

Generate new is by default selected the first time the D-Optimal page is opened. Click
Generate new when you change the model or the use of potential terms and you want
to generate a new set of candidate runs.

Using the current candidate set

Use the current candidate set is available after importing or creating a candidate set.
Once the candidate set has been generated, the Use the current candidate set option is
by default marked.

Editing the candidate set

Click the Edit button to edit the candidate set. This can be done both with Generate
new and Use the current candidate set selected. A spreadsheet opens with the
candidate set. Make your changes and click the Generate D-Optimal button to return
to the D-Optimal page.

The candidate set can also be opened for editing by clicking Design | D-Optimal |
Candidate set.

Importing a candidate set

You can import a candidate set from many file types.
To import the candidate set:
1. Click the Import button found in the Candidate set section.
2. Find the file holding the candidate set and click Open. Many file types are
supported.
3. The Import Candidate Set window opens allowing you to specify the row
containing the factor names, and optionally the column holding the
experiment names. Here you can exclude and include rows and columns too.
The row defined as Factor Name in the candidate set-file must contain the
factor names and they must be identical to those defined in the MODDE
investigation. Including uncontrolled, filler, and constant factors is optional.

Size of candidate set

The size of the candidate set in MODDE is by default limited to 512 000 rows when
MODDE creates the candidate set for you.
You can change the limit in General Options on the View menu, tab General, under
Program Limits you find Maximum candidate set size.
The maximum size of the candidate set that you can create and generate a design from
is limited by the RAM in your computer.

107
User Guide to MODDE

D-Optimal results
When you click Next on the Change D-Optimal settings page, MODDE generates the
D-Optimal designs and displays them in the D-Optimal results page.

By default, the best design according to G-Efficiency is selected. Use the Auto-select
design by box to instead select the best design according to Determinant or
Condition number. Or select another design manually by marking the design.
Click any column header to sort the list.
To see the D-Optimal results as a plot, select the Display as plot check box.

The columns with the grid pattern represent the currently selected design.

108
 D-Optimal

Right-click the plot and click Properties to open the D-Optimal Design Plot dialog
allowing:
• Selection of which of the criteria to display, G-efficiency, Determinant, or
Condition number under Show.
• Sorting on Type instead of Design (default) under Sort by.
• Selection of which layers to display when D-Optimal onion designs have
been generated in the Show Layer box.

Click Finish to generate the worksheet. Any already existing design and
worksheet will be deleted.
Click Design | D-Optimal | Generate to regenerate the D-Optimal designs as many
times as needed.

Note: The menu Design | D-Optimal | Generate is not available for onion
designs. To generate a new onion design, select Design | Objective.

D-Optimal on the Design menu

After creating a D-Optimal design, the items on Design | D-Optimal are available. The
onion plots are only available when an onion design was generated while Generate is
only available when a regular D-Optimal design has been generated.

Generate
Click Design | D-Optimal | Generate to open the Change D-Optimal Settings page
to re-enter the D-Optimal pages and generate a new set of D-Optimal designs.
See the section D-Optimal pages in the design wizard previously for more.

Candidate set
Click Design | D-Optimal | Candidate Set to open the Candidate set for viewing or
editing.
See the section Candidate set previously for more.

109
User Guide to MODDE

Evaluate
Click Design | D-Optimal | Evaluate to open the D-Optimal Results page to view the
other generated designs and their properties. Here you can also select one of the other
designs as your worksheet by marking and clicking Finish.
See the section D-Optimal Results previously for more.

Onion plot, onion 3D scatter

The onion plots are available after creating a D-Optimal onion design. Click Design |
D-Optimal | Onion Plot or Onion 3D Scatter to display onion plots.
See the section D-Optimal onion design for more.

Design plot
Select Design | D-Optimal | Design Plot to display the same information as Evaluate
in a column plot. MODDE displays G-efficiency, Log of the determinant of X'X, and
the condition number of X, for the D-Optimal designs.
When you generate several D-Optimal designs with different N (number of runs), you
can plot any of the D-Optimal criteria (G-efficiency, Condition No, Log of the
determinant of X'X) as a function of N. This plot can also be created from the Design |
D-Optimal | Evaluate and selecting the Display as plot box.
See the Design appendix for more information.

Note: All of the statistics available in the D-Optimal Design Plot are
computed from the runs selected D-optimally and do not include the possible
center points added to the worksheet. With mixture factors, the condition
number refers to the slack variable model with all mixture components scaled
orthogonal.

110
 D-Optimal

D-Optimal onion design

Onion designs are available for process factors only. You can also import a candidate
set from one of the supported file formats or a SIMCA-P file (.usp) to create onion
designs from.
Onion designs are made in a number of layers (shells), with a separate D-Optimal
design for each layer. Typically the number of layers is two or three.

Candidate set
The D-Optimal onion design in MODDE is created from a candidate set. The candidate
set can be created by MODDE, imported from one of the supported file formats, or
imported from SIMCA-P.

Candidate set created by MODDE

When you have defined only process factors and enter the Select model and design
page, you can select to generate an Onion design.
MODDE will then create the same number of candidate sets as layers specified. The
high and low limits for each factor in the candidate set will be based on the percentile
defined for each layer.
E.g. for a factor with Low= -1 and High=1 with the four layers, 0% - 15%, 15% - 30%,
30% - 75% and 75% - 100%, the candidate sets will be generated with the low/high
settings -0.15/0.15, -0.3/0.3, -0.75/0.75 and -1/1. The number of points generated in
each candidate set depends on the number of factors.

Candidate set imported from a file

If you want to create an onion design using factors found in a file, see the Advanced
designs section in the File chapter.
After importing the candidate set, selecting an Onion design and selecting the intervals
(percentile) for the layers, the candidate set is divided into sub candidate sets for each
layer, based on the experiments distance. The most distant experiment will define
100% and the center will define 0%.
The distance of a specific experiment from the center is calculated as the “geometrical
distance”, i.e. the square root of the sum of squared factor values. The factors are
orthogonally scaled.

Candidate set from SIMCA-P

To create an onion design using scores from SIMCA-P as design variables (factors),
see the Advanced designs section in the File chapter.
When you select to create an onion design, the candidate set is parted in layers.

111
User Guide to MODDE

Generating the design

After selecting an Onion design, and clicking Next, the Layers page is displayed. This
page is organized by layer – from inner (first layer) to outer (last layer).

The following is listed:

1. The number of the Layer (starting from inside).
2. The number of Candidate Runs in the layer for imported candidate sets.
3. The span of the layer defined by its % From (Percentile) and % To distance
to the center of the multivariate space. You can change the span of a layer as
long the number of runs in the candidate set remains one and half times
larger than the number of design runs in that layer. Overlapping span
between layers is not allowed. When you change the span of the layers,
MODDE updates the number of candidate set runs in each layer. If the span
of the layers overlap, or the number of runs in the candidate set is not large
enough, the layer is colored in red and a message indicating the problem is
displayed. You must fix the problem before clicking Finish.
4. The number of Design Runs in each layer. You can change the number of
design runs. The number of desired runs must be at least equal to the number
of terms in the model. The recommended number of runs includes 3 degrees
of freedom for the outer layer and 1 degree of freedom for the rest of the
layers.
5. Select the number of D-Optimal designs, in each layer, you want to generate
with the same number of runs. The default number for Repetition is 1.
6. The Model for each layer. You can change the model in each layer. Click the
model you want to change and select another model or mark the layer and
click Edit Model to customize the model. After editing a model, MODDE
writes Model edited in the Comment column. MODDE updates the design
runs according to the new selected model.

112
 D-Optimal

When you click Finish, MODDE generates several D-Optimal designs in each layer
varying the number of runs by plus and minus 2, and displays the Onion D-Optimal
results.

The table on this page displays, for every layer, the generated designs statistics. By
default, in this table, the designs with the highest G-efficiency are selected.
You can select a different design in a given layer by marking it in the list or using the
Auto-select design by box and selecting a different criterion.

D-Optimal on the Design menu with Onion

Generate
With Onion D-Optimal designs, you cannot generate a new set of D-Optimal design by
using the menu Design | D-Optimal | Generate.
If you want to generate a new set of Onion D-Optimal designs, click Design |
Objective. The worksheet will be deleted and you can follow the wizard to generate a
new design and worksheet.

113
User Guide to MODDE

Candidate set
Click Design | D-Optimal | Candidate set to display the candidate set.
The columns in the spreadsheet are as follows when the candidate set was imported:
1. Design Run number. Corresponds with the experiment number in the
worksheet.
2. The Exp Name (experiment name) when available.
3. The Layer number (the innermost layer = 1).
4. The distance to the center of the multivariate space in Percent.
5. The design variables.

Runs in the candidate set that are not used to generate the D-Optimal design (not
included in the selected percentile ranges), are colored light gray.
When the candidate set is generated by MODDE the additional columns Layer and
Percent are unavailable. The layer belonging is displayed in the onion plots and when
listed (right-click and click Create List) the list is organized according to layer.

Evaluate
Click Design | D-Optimal | Evaluate to display the Onion D-Optimal results page.
You can use the table to select different designs, in selected layers.
See the D-Optimal Results section previously for more.

114
 D-Optimal

Onion plots
There are two onion plots to visualize the candidate set and the selected D-Optimal
design, the Onion Plot and the Onion 3D scatter.
For the onion scatter plots, the property page has two tabs: Select Factors and Plot
Labels. Use Select Factors to select which factors to display on the X, Y, and Z-axes.
Use Plot Labels to select which labels to display in the plot.

Onion plot
To create the 2D onion plot, click D-Optimal on the Design menu, and then click
Onion Plot.
The onion plot is a 2D scatter plot of the candidate set. The candidate set runs are
colored by layer, and the selected design runs are black.

115
User Guide to MODDE

Onion 3D Scatter
To create the 3D Onion plot click D-Optimal on the Design menu, and then click
Onion 3D Scatter.
The Onion 3D scatter plot displays the candidate set colored by layer with the
selected design runs in black.
You can customize the plot using the plot settings. For more, see the Plots and List
chapter.

116
Design Wizard

Introduction
The Design Wizard opens when you click File | New, to create a new
investigation, and guides you from the start of the investigation to the generation of the
worksheet. The design wizard can also be opened by clicking Design | Design Wizard.
Exit the wizard at any time by clicking Finish.
The accelerator for the Design Wizard is CTRL+W.
Following is a description of the pages in the Design wizard.

Defining factors
The first page of the design wizard is the Define Factors page. On this page you can
define (enter new factors), modify, and/or delete factors.

117
User Guide to MODDE

All functionality available in the Factor spreadsheet described in the Factor chapter
is available in this page of the design wizard. Specific for the design wizard factor
page:
• The New and Edit-button open the Factor Definition dialog.
• The Delete-button deletes the factor(s) currently marked.
• Selecting the Place constraints on the experimental region box and
clicking Next opens the Constraints page of the design wizard. The
Constraints spreadsheet, including graphical constraints, is described in the
chapter Constraints and inclusions.

Note: The graphical constraint using the interface to define the constraint is
not available from the design wizard. If you want to use the graphical
constraint, click Design | Constraints
Clicking Next opens the Define responses page.

118
 Design Wizard

Defining responses
In the Define responses page you can define (enter new response), modify, or delete
responses.

All functionality available in the Responses spreadsheet described in the Response

chapter is available in the design wizard. Specific for the design wizard response page:
• The New and Edit-buttons opens the Response Definition dialog.
• The Delete-button deletes the response(s) currently marked.
Clicking Next opens the Select the objective page.

119
User Guide to MODDE

Selecting the objective

In the Select the objective page you select the objective of your
investigation: Screening, RSM, Split Objective, or Paste Data. Objectives are
described in detail in the Objective chapter, section Selecting objective.

Clicking Next opens the Select the model and design page.

120
 Design Wizard

Selecting model and design

The Select the model and design page lists all designs, their resolution, the associated
models and number of runs, compatible with your objective and number of factors. See
the Selecting model and design section in the Objective chapter for details.
The Pseudo resolution applies to designs when they are blocked. See the section
Blocks in the Objective, model and design chapter and the section named
Orthogonal blocking in the Statistical appendix for more on Blocks.
If your design is classical, click Finish to generate the worksheet. If your design is D-
Optimal click Next to open the D-Optimal page of the wizard.

Note: You can sort the Design list on any column by clicking on its header.

121
User Guide to MODDE

D-Optimal pages in the design wizard

The Change D-Optimal settings page, the D-Optimal results page that appears after
clicking Next, and the creation of D-Optimal designs are described in detail in the D-
Optimal chapter.
When you click Next, MODDE generates the D-Optimal designs and displays the
results in the evaluation list consisting of:
1. The design number.
2. The number of runs in the design not including the 3 center points.
3. Statistics on the design.

The selected design is highlighted and marked with the worksheet icon.

Note: Sort the list according to any column by clicking its header.

122
Worksheet

Introduction
After you have selected the model and design, MODDE generates the worksheet. The
worksheet is a spreadsheet used for storing the data (factors and response values) and
is where you enter the experimental results. The worksheet is by default sorted in
standard order.
Whenever you change the design (by editing the generators or selecting another
design) both the design and the worksheet are deleted and new ones are generated.
MODDE issues a message whenever the worksheet is regenerated.
The data in the worksheet are used when selecting to plot or list from the Worksheet
menu.

Worksheet menu
After the worksheet has been created and you have entered results, there are a number
of plots and lists available under the Worksheet menu.
All responses, regular and derived, are available in the plots and lists of the Worksheet
menu.

Opening the worksheet spreadsheet

To open the worksheet spreadsheet, on Worksheet menu click Worksheet or click the

Worksheet button .

123
User Guide to MODDE

Setting run order

Randomizing the run order is done to avoid that the effect of external variability, such
as room temperature or who performs the experiment, coincides with the effect of a
factor. By default the worksheet is Fully randomized.
With screening designs you can randomize To detect curvature. To do that, before
performing any experiments click Worksheet | Set Run Order and in the dialog
displayed, click To detect curvature. To display this dialog every time when you
create a screening worksheet, select the Always display this dialog after generating a
new design check box.

To re-randomize the run order after the worksheet has been created but before entering
results, on the Worksheet menu, click Set Run Order.
The run order can only be randomized for experiments with no results in the
worksheet.

Fully randomized
With RSM designs and Screening designs at more than 2 levels, Fully randomized is
the order in which you should perform the experiments and this is also the only
available order for these cases.

Run order to detect curvature

With 2 level screening designs, it is desirable to guard against strong curvature in the
response caused by too wide ranges in the factors. Strong curvature in the response
masks the effect of the factors. In this case you should select To detect curvature.
To detect curvature, one should first perform the following experiments:
1. A center point
2. A point with as many factors at high (+) as possible
3. A point with as many factors at low (–) as possible
After selecting To detect curvature and creating the worksheet you will find the three
points above at run order 1-3 and the rest of the runs randomized.

124
 Worksheet

Curvature diagnostic plot

Once the first three experiments are performed and the results are entered in the
worksheet, on the Worksheet menu, click Curvature Diagnostic plot to evaluate the
result.

Strong curvature
If the Curvature Diagnostic Plot exhibits strong curvature as is shown above, you
should first re-measure the center point and re-do the plot. If the plot still exhibits
strong curvature, reduce the ranges of the factors by 2 / 3 and restart the project.

No curvature
If the Curvature Diagnostic Plot does not exhibit curvature, as the one below,
continue performing the rest of the experiments.

125
User Guide to MODDE

2D and 3D scatter plots

For 2D plots, select the variable to be plotted on the X-axis by marking it and clicking
the arrow ‘=>’. Mark the other variable(s) and click the arrow to Series.
For 3D plots, select the variables to be plotted on X, Y, and Series axes.

Click the Delete button in the dialog to remove factors or responses from the Y-
axis or from Series. To change what to display on the X-axis, mark and click the arrow
to add the new variable.
Click the Color by Variable tab to color by a factor or a response. With the scatter
plot created from the Worksheet menu you can also color by run order and experiment
number.

You can customize the 3D plot using the property page and plot settings. See the Plots
and List chapter.

126
 Worksheet

Histogram
On the Worksheet menu click Histogram to display the histogram of the currently
selected response.
Select the desired response or add more responses by right-clicking the plot and
clicking Properties, or by making the selection in the Response box.

Transform in Histogram
You can transform a response by right-clicking the Histogram plot and clicking
Transform.

127
User Guide to MODDE

Descriptive statistics
Descriptive statistics can be displayed both as plot and in a list for all available
responses.

Descriptive statistics plot

On the Worksheet menu, click Descriptive Statistics, then click Plot to open a Box
Whisker plot for the selected response.
The Box Whisker plot illustrates how the response values are distributed around the
response mean. The plot uses a box defined by the 25th and 75th percentiles and
whiskers ending at the maximum and minimum values.
Select the desired response or add more responses by:
• Right-clicking and then clicking Properties.
• Selecting in the Response box.

Descriptive statistics list

The descriptive statistics list summarizes the descriptive statistics for all responses.
On the Worksheet menu, click Descriptive Statistics, and then click List.

128
 Worksheet

Correlation
The linear correlation coefficients R between all the terms in the model and all the
responses are displayed in the Correlation Matrix and Correlation Plot.
Process factors are transformed, scaled, and centered as specified in the
factor definition for MLR (default = orthogonal scaling). Responses are transformed as
specified in the response definition.
Formulation factors are always scaled orthogonally.
The value of the correlation coefficient R represents the extent of the linear association
between two terms. The value of R ranges from -1 to 1. When R is near zero there is no
linear relationship between the terms.

Correlation matrix
On the Worksheet menu, click Correlation, and then click Matrix.
Correlation coefficients above the threshold, between a term in the model and the
responses are colored green and those between terms of the model are colored red.

To change the threshold, colors, or number format, right-click and click Properties.

Correlation plot
On the Worksheet menu, click Correlation, and then click Plot.
The default plot displays the 10 largest correlation coefficients.
To change number of correlations to display or limit the number of correlations
according to a threshold:
1. Right-click the plot and click Properties.
2. Make the change, for instance click Show absolute correlations above
threshold and enter a value. With '0' all correlations are displayed

129
User Guide to MODDE

Replicate plot
In the replicate plot the values of the response are plotted vs. experimental runs
displaying the variation in the response for replicated experiments.
On the Worksheet menu click Replicate Plot to display the plot.
Select the desired response or add more responses by right-clicking and clicking
Properties, or by making the selection in the Response box.

Note: When the response has been transformed the Replicate plot displays the
back transformed values. To display the plot in the transformed metric, select
the Show transformed values check box in the Options tab in Properties.

Replicated experiments
MODDE checks the rows of all the factors (both included and excluded) in the
worksheet for replicates. Rows in the worksheet with the same factor values plus or
minus a tolerance are considered replicates.
The default Replicate tolerance is 0.1 (10%). You can change the Replicate
tolerance used in General Options on the View menu, tab General.
The replicates are used for the computation of the pure error and displayed on the same
Replicate Index in the Replicate Plot.

130
 Worksheet

Worksheet spreadsheet
Description of the worksheet
Experiment number: Exp No start with number one and are assigned sequentially.
They cannot be edited.
Experiment name: MODDE assigns a default experiment name, Exp Name, on the
form Nxx, where xx is the experiment number. You may edit the name and enter your
own identification. The Plot Label named Experiment Name displays the text entered
under Exp Name when plotted.
Run order: The Run Order is the order in which the experiments should be
performed. MODDE suggests a randomized run order. Sort the worksheet according to
run order before performing the experiments.
Include or exclude: The fourth column labeled Incl/Excl indicates if the experiment is
included or excluded from the analysis. When the worksheet is generated all
experiments are marked Incl and are included in the analysis. To exclude an
experiment from the analysis select Excl in the worksheet.

Note: Excluded rows are excluded from the analysis for all responses. To
exclude the response value for only one response, right-click the cell and click
Exclude value(s).
Factors: In the Factor columns the factors are listed in original units.
Blocking: When you have selected Blocks in the Select the model and design page,
the column $BlockV displays which block each experiment has been assigned to.
For details on blocking, see the Orthogonal blocking section in the Statistical
appendix.
Responses: In the columns to the far right all responses are found. The response values
are listed in original units.

Missing values in the worksheet

When responses have missing values, in the analysis, MODDE creates individual
models for all responses excluding only the row with the missing value for the relevant
response.
Missing values in controlled factors are not allowed.

Deleting the worksheet

You cannot delete the worksheet; MODDE will automatically delete the worksheet
when you make modifications to the factors.

Displaying the worksheet

On the Worksheet menu click Worksheet to display the spreadsheet or click the
worksheet button.

131
User Guide to MODDE

Adding experiments in the worksheet

To add extra runs to the worksheet:
• Open the worksheet window, then click Edit | Add Experiments.
• Open the worksheet window, right-click and click Add Experiment.
• On the Design menu, click Inclusions. Type values or import the
experimental runs you want added to the worksheet. Then click the Add to
Worksheet button. The inclusions will be added at the end of the worksheet.
The first four columns of the worksheet are automatically filled in when adding
experiments.

Sorting the worksheet

To sort a column in the worksheet:
• Right-click the desired column and then click Sort.
• Mark the worksheet, then click Edit | Sort.

Colors in the worksheet

Suspicious values in the worksheet are colored in red. Non-transformable values have a
red background. Mark a colored cell to display a message about why it is colored in the
status bar.

132
Analysis

Introduction
After entering the response values in the worksheet, analyze the resulting data in the
menu Analysis.
Use the Analysis Wizard to guide you through from raw data analysis to interpretation
and diagnostics.
You can also manually fit the model to the data by using either MLR (Multiple
Linear Regression) or PLS (Projection to Latent Structure) and clicking Fit. To review
the fit, display as lists or plots, the summary of the fit, the coefficients, the effects, and
the analysis of variance (ANOVA). Residual plots and the Box-Cox plot (only for
MLR) are available for diagnostic purposes.

Organization of the Analysis menu

The Analysis menu is organized as follows:

133
User Guide to MODDE

Evaluate
Click Evaluate on the Analysis menu to display an evaluation of the current worksheet
and model. The table includes condition number, (number of) worksheet runs, (number
of) model terms, DF (degrees of freedom) residual, DF lack of fit, and DF pure error
individually for each response. These values differ between the responses when they
have different models or excluded values.

Condition number
The Condition Number is the ratio of the largest and the smallest singular values of X
(eigenvalues of X'X) where X is the extended design matrix. This condition number
represents a measure of the sphericity of the design (orthogonality). All factorial
designs, without center points, have a condition number of 1 and the design points are
situated on the surface of a sphere. For more see the Statistical appendix.
With factors orthogonally scaled all classical screening designs have a condition
number =1 without center points and <3 with center points. The condition number of
classical RSM designs varies according to the number of factors but remains <10.

Note: For a constrained region, a higher condition number is acceptable

For a definition of the condition number, see the Statistical appendix.

Condition number with mixture factors

The condition number with mixture data depends on the method of fit and the type of
model. For details see the Statistical appendix.

Runs, terms and degrees of freedom

In addition to the condition number the evaluation table also displays:
• Worksheet runs: the number of runs included in the Worksheet spreadsheet.
• Model terms: the number of terms included in the current model.
• DF residuals: The degrees of freedom of the residuals.
• DF lack of fit: the degrees of freedom of the Lack of Fit
• DF pure error (repl. runs): degrees of freedom of the pure error calculated
using the replicated runs (experiments). If there are no replicated runs the
pure error cannot be calculated.
For details on degrees of freedom see the Statistical appendix.

134
 Analysis

Analysis Wizard
The Analysis Wizard guides you through the main steps from review of the raw data
and the fit, to the diagnostics and refining of the model.
When opening the Analysis Wizard, the model is automatically fitted using the default
fit method.
In the Analysis Wizard each response is handled separately in a step wise manner
where you start looking at plots, pruning the model etc. for one response, and when
done you step over to the next response.
The following features are available as buttons in the Analysis Wizard:
• Display or hide Min, Target, and Max limits when available in the response
definition.

• Transform the response in the Histogram Plot

• Exclude model terms or severe outliers for the current response.

• Undo after exclude.

• Edit model in the Coefficient Plot for the current response.

• Display regression line in the Residual Normal Probability Plot and

Observed vs. Predicted Plot.

Note: All changes done in the Analysis Wizard take effect immediately.
Clicking Close closes the Analysis Wizard but all changes remain.

Open the Analysis Wizard

To open the Analysis Wizard, click Analysis | Analysis Wizard and select a starting

response, or click the button in the Standard toolbar. Clicking the Analysis
Wizard button opens the Analysis Wizard for the first response.

135
User Guide to MODDE

Analysis Wizard content

The Analysis Wizard includes the following plots with a descriptive text: Replicate
Plot, Histogram Plot, Summary Plot, Coefficient Plot, Residual Normal
Probability Plot, and Observed vs. Predicted Plot.

Customize the Analysis Wizard text

You can customize the text displayed in the Analysis Wizard by opening the
'AnalysisWizard.zip' file in the program folder and editing the .mht-files.

Fitting the model to the data

When fitting the model to the data MODDE uses the default fit method unless you
select a different fit method.
To select fit method, click Select Fit Method on the Analysis menu and click your
choice. Only change the fit method when you have a reason for it. Normally you can
leave the MODDE default Auto as fit method.
To fit the data click Fit on the Analysis menu.

136
 Analysis

Selecting fit method

The following fit methods are available: Auto, MLR, PLS, Scheffé MLR, MLR with
Pseudo Components, PLS with Pseudo Components, and Scheffé MLR with
Pseudo Components.

Auto, MLR, PLS

Select Auto to use the default. MODDE defaults to using Multiple Linear
Regression (MLR) as long as the condition number permits. When the condition
number becomes too large, MODDE defaults to using PLS. You may override the
default by selecting PLS.

Note: If your X matrix has a condition number > 3000, MODDE will only fit
the model with PLS and the condition number selecting MLR is displayed as
infinite.

Scheffé MLR
Select Scheffé MLR to fit the mixture data with a Scheffé type model. When you select
this fit method, the model is restored to its default specification. When your
investigation contains both mixture and process factors Scheffé MLR is unavailable as
such models are only available in MODDE for experiments with mixture factors only.

Pseudo components (MLR, PLS, Scheffé)

Select MLR, PLS or Scheffé with pseudo components to analyze the mixture data
transformed to pseudo components.
When you select a fit method with pseudo components, MODDE displays all mixture
designs (the design matrix not the worksheet) with the mixture factors transformed to
pseudo components. When the mixture region is a simplex, transforming to pseudo
components gives all mixture factors the range 0 to 1. When the mixture region is not a
simplex, pseudo components stretch the experimental region.

Fitting the model

To fit the data click Fit on the Analysis menu.

Fitting with MLR

When fitting with MLR, MODDE will separately but automatically fit all of the
responses. Use the Response box to select the desired response, or right-click, click
Properties, and tab Select Responses.
If some response values are missing, MODDE excludes the row(s) with missing data
for that specific response and keeps it for all others in the calculations.

137
User Guide to MODDE

Fitting with PLS

With PLS all responses are fitted simultaneously.
PLS handles missing values in the responses, without excluding the runs from the
analysis when the same model is used for all responses. When the models are not
identical, the fit is done separately for each response and missing is handled as for
MLR.
When fitting the model with PLS, MODDE computes as many PLS components as
significant by cross validation. See statistical appendices for significance rules. To add
more PLS components click Next Component on the Analysis menu.
Once the model is fitted the command menus to display results and perform
diagnostics are available. Specific menus pertaining only to PLS are unavailable when
fitting the model with MLR.
To exclude response(s) from the analysis, set their unit variance modifier to zero, in the
response dialog box. This will give the response(s) zero variance, and hence exclude
them from the analysis.
Note that with PLS the X matrix is always scaled and centered to unit variance. The
centered responses are scaled as you selected in the response definition menu. The
default is unit variance.
For more details on PLS see the Statistical appendix.

Note: The default method of fit with the Cox reference mixture model is PLS.
When the model obeys mixture hierarchy you can if you want fit the model
with MLR. When fitting the model with PLS, the condition number refers to
the X matrix, with unit variance coding.

MODDE Analysis Advisor automatically opened

The advisor opens when you fit the model and guides through the analysis. To turn on
or off the advisor:

• Click the question mark button on the Standard toolbar.

• On the View menu, click Dockable Windows, and then click Analysis
Advisor.

Next component (only PLS)

If you want to extract more components than significant according to the cross-
validation rules, click Next Component on the Analysis menu. All open plots and lists
are automatically updated.

138
 Analysis

Displaying the summary of fit

After fitting the model, review the fit in plots and lists. If the model was fitted with
MLR the PLS Summary plots are unavailable.

Summary of fit plot

To display the summary of fit plot, on the Analysis menu click Summary, then click
Plot.
For every response MODDE displays 4 columns: R2, Q2, Model Validity, and
Reproducibility.

Note: R2 and Q2 provide the best summary of the fit of the model. R2 is an
overestimated and Q2 an underestimated measure of the goodness of fit of the
model

Saturated models
R2 and R2 Adjusted are not available for saturated models, i.e. models with DF
(degrees of freedom) equal to zero (see statistical appendices). However, with PLS Q2
can still be computed for saturated models and is hence displayed in plots and lists.

Statistics
In the plot footer MODDE displays:
N = Number of experimental runs.
DF = N-p (the degrees of freedom of the residuals).
Cond. no. = Condition number of the extended design matrix coded as selected in the
factor definition box: MLR scaling, or for PLS, unit variance.
2
R
The first column in the summary plot is R2 and is the fraction of the variation of the
response explained by the model:
R 2 = SS REG /SS
SSREG = the sum of squares of Y corrected for the mean, explained by the
model.
SS = the total sum of squares of Y corrected for the mean.
R2 overestimates the goodness of fit.
The R2 value is always between 0 and 1. Values close to 1 for both R2 and Q2
indicate very good model with excellent predictive power.
For details see the Statistical appendix.
You may select to plot R2 Adjusted instead of R2 by clicking it in the
Properties page or set it to be default displayed by clicking Investigation
Options on the View menu, tab R2.
R2 Adjusted: The fraction of variation of the response explained by the model
adjusted for degrees of freedom.

139
User Guide to MODDE

Q2
The second column in the summary plot is Q2 and is the fraction of the variation of the
response predicted by the model according to cross validation and expressed in the
same units as R2.
Q 2 = 1 - PRESS/SS
PRESS = the prediction residual sum of squares.
SS = the total sum of squares of Y corrected for the mean.
Q2 underestimates the goodness of fit.
The Q2 is usually between 0 and 1. Q2 can be negative for very poor models. With PLS
negative Q2 are truncated to zero for computational purposes. Values close to 1 for
both R2 and Q2 indicate a very good model with excellent predictive power.
For details see the Statistical appendix.

Model validity
The third column in the summary plot is the Model Validity and is a measure of the
validity of the model.
When the model validity column is larger than 0.25, there is no lack of fit of the model.
This means that the model error is in the same range as the pure error.
When the model validity is less than 0.25 you have a significant lack of fit and the
model error is significantly larger than the pure error (reproducibility).
A model validity value of 1 represents a perfect model.
Validity = 1 + 0.57647*log(plof)
where plof = p for lack of fit.

Reproducibility
The forth column in the summary plot is the Reproducibility which is the variation of
the response under the same conditions (pure error), often at the center points,
compared to the total variation of the response.
Reproducibility = 1 - (MS(Pure error)/MS(total SS corrected)).
MS = Mean squares, or Variance.
A reproducibility value of 1 represents perfect reproducibility.

140
 Analysis

Summary of fit list

To open the Summary List, on the Analysis menu, click Summary, and then click
List.
The list displays for each response: R2, R2 Adjusted, Q2, SDY=Standard Deviation of
the Y (response), RSD=the Residual Standard Deviation, N=number of experiments,
model validity, and reproducibility. For more details on SDY and RSD, see the
Statistical appendix.

PLS summary plot (only PLS)

To display the PLS Total Summary plot, on the Analysis menu, click PLS
Summary, and then click Summary Plot.

For every fitted response the plot displays R2 and Q2. The definition for R2 and Q2 is
the same as in the Summary of Fit Plot.
You may select to plot R2 Adjusted instead of R2 by selecting it in the Properties
page or setting it as default in View | Investigation Options, tab R2.
The condition number is calculated for the extended design matrix with the factors
scaled to unit variance.

141
User Guide to MODDE

PLS response plot (only PLS)

To display the PLS Summary for 'response' plot, on the Analysis menu click PLS
Summary, then click Response Plot.

This plot displays the R2 and Q2 per PLS component for the selected response. You can
change the selected response using the Response box. You may select to display R2
adjusted instead of R2 in the Property page and in the Investigation Options menu.

PLS summary list

To display the PLS Summary List, on the Analysis menu, click PLS Summary, and
then click List.
The PLS summary list displays R2, R2 adjusted and Q2 per PLS component for all the
responses (Total) and for each response.

Saturated models
R2 and R2 Adjusted are not available for saturated models, i.e. models with DF
(degrees of freedom) equal to zero (see statistical appendices). However, with PLS Q2
can still be computed for saturated models and is hence displayed in plots and lists.

142
 Analysis

Investigating diagnostics
Use the diagnostic plots and lists to find outliers, needed transformations etc.

Normal probability plot of residuals

To display the normal probability plot of residuals, on the Analysis menu, click
Normal Prob. Plot Residuals.
The residuals are plotted on a cumulative normal probability scale.
This plot makes it easy to detect:
• Normality of the residuals. If the residuals are normally distributed, the
points on the probability plot follow close to a straight line
• Outliers. These are points deviating from the normal probability line, and
having large absolute values of studentized residuals i.e. larger than 4
standard deviation indicated by red lines on the plot.

143
User Guide to MODDE

Residuals
Under Analysis | Residuals three residual plots and one list are available.

Residuals vs. predicted response

To display the Residuals vs. Predicted Y plot, on the Analysis menu, click Residuals,
and then click vs. Predicted Response.
The plot shows the residuals vs. the fitted values. This plot is particularly useful to
detect non-constant variance of the residuals. If the spread of the residuals increases
with the fitted values, you may need to transform your response by taking its logarithm
or its square root.

Residuals vs. Run Order

To display the Residuals vs. Run Order plot, on the Analysis menu, click Residuals,
and then click vs. Run Order.
This plot shows the residuals vs. run order (the order in which you performed the
experiments) and helps you detect any dependency of the residuals on time.

144
 Analysis

Residuals vs. Variables

To display the Residuals vs. Variable plot, on the Analysis menu, click Residuals,
and then click vs. Variable.
You may plot residuals vs. any factor or response in the model. Patterns in this plot
may help detect systematic effects left out of the model.

Right-click the plot and click Properties to select which variable to display on the x-
axis.

Residual list
To display the Residuals List, on the Analysis menu, click Residuals, and then click
List.
The number under the response name, is the experiment number.
Observed: The value of the response as listed in the worksheet.
Predicted: The predicted value for that observation.
Observed - Predicted: The residual for that observation.
Confidence Interval: The 95% confidence interval on the predicted value. You can
change the confidence level in the Property page and in Investigation Options.

145
User Guide to MODDE

Residual types available in MODDE

Each plot type can display different types of residuals: Raw, Standardized, or Deleted
Studentized.
To change the default type of residual to display, on the View menu, click
Investigation Options, and in tab Residuals click to make your change.
Raw residuals
The raw residual is the difference between the observed and the fitted (predicted)
value.
Standardized residuals
The standardized residual is the raw residual divided by the residual standard deviation
(RSD). With PLS and models with less than 2 degrees of freedom, MODDE uses as
default the standardized residuals.
Deleted studentized residuals
The deleted studentized residual is the raw residual eIi divided by its standard deviation
(si) where the standard deviation (si) is computed with observation (i) left out of the
analysis, and corrected for leverage. Deleted studentized residuals, requires at least two
degrees of freedom.
For MLR models with 2 or more degrees of freedom, deleted studentized residuals are
the default when plotting residuals.
With PLS, deleted studentized residuals are not available.

Distance to the model in the Y space – DModY (only PLS)

To open the distance to model in y space plot, on the Analysis menu, click Distance to
Model (Y).
The RSD of an object in the Y space is proportional to the object distance to the hyper
plane of the PLS model in the Y space. MODDE computes the object distance to the
PLS model (DModY) in the Y space and displays them as columns in a plot.
A large DModY value indicates that the experiment may be an outlier.

146
 Analysis

Box Cox Plot (MLR only)

To open the Box Cox plot, on the Analysis menu click Box Cox Plot.

The Box Cox plot displays the maximum likelihood as a function of the power of the
transformation by plotting values of lambda, λ, vs. the maximum likelihood.
If the response values vary more than a magnitude of ten in the experimental domain, a
transformation is often recommended.
The maximum point on the Box Cox plot gives the value of (lambda, λ) for the
response transformation Yλ that gives the best fit of the model. This is the maximum
likelihood estimator for λ. For more, see the Statistical appendix.

Box Cox recommending to transform

MODDE displays λmax and its 95% confidence interval as λlower and λupper in the footer
and on the plot as 3 vertical lines.
If λ=1 is included in that interval, then no transformation is recommended.
If λ=1 is not included in the interval then Yλmax is the recommended transformation.
You do not have to use the precise value of λmax but a near convenient value.
Common transformations are:
• λmax = -1, use the Power transformation and C3 = -1.
• λmax = 0, use the Logarithmic (10Log) transformation.
• λmax = 0.5, use the Power transformation and C3 = 0.5.

147
User Guide to MODDE

Observed vs. predicted

To display the observed vs. predicted plot, on the Analysis menu, click Observed vs.
Predicted.

The observed vs. predicted plot displays the plot of the observed values vs. the fitted or
predicted values. Plots with the points close to straight line indicate good models.
A regression line can be fitted by clicking the regression button on the Plot toolbar.

148
 Analysis

Lack of fit plot

To display the lack of fit plot, on the Analysis menu, click Lack of Fit Plot.

The lack of fit plot compares the Lack of Fit (LoF) component to the pure
error component and displays a graph with 3 bars.
• SD-LoF: Shows the variation of the response due to the lack of fit of the
model (i.e. the model error) adjusted for degrees of freedom and in the same
units as Y. This is the square root of MS (mean square) lack of fit.
• SD-pe (Pure error): Shows the variation due to the replicated experiments
(observations) adjusted for degrees of freedom and in the same units as Y.
This is the square root of MS (mean square) pure error.
• SD-pe*sqrt(F(crit)): Shows SD pure error (second bar) multiplied by the
square root of the critical F.
The critical F is the value of the F-distribution over which SD LoF is statistically
significant at the 95% confidence level.
Hence, when the third bar is smaller than the first, the lack of fit is significant at
the 5% level (see statistical appendices).

149
User Guide to MODDE

Analysis of Variance (ANOVA)

The analysis of variance (ANOVA) partitions the total variation of the response (Sum
of Squares, SS, corrected for the mean) into a component due to the regression model
and a component due to the residuals.

ANOVA plot
To display the ANOVA plot, on the Analysis menu, click ANOVA, and then click
Anova Plot.

In the ANOVA plot the regression component is compared with the residual
component and 3 bars are displayed.
• SD Regression: Shows the variation of the response explained by the model,
adjusted for degrees of freedom and in the same units as Y. This is the square
root of MS (mean square) regression.
• RSD: Shows the variation of the response not explained by the model,
adjusted for degrees of freedom and in the same units as Y. This is the
residuals standard deviation.
• RSD*sqrt(F(crit)): Shows RSD (second bar) multiplied by the square root
of the critical F.
The critical F is the value of the F-distribution over which SD regression is statistically
significant at the 95% confidence level.
Hence, when the third bar is smaller than the first, the model is significant at the
5% level. For more see the Statistical appendix.

150
 Analysis

ANOVA table
To open the ANOVA table, on the Analysis menu, click ANOVA, and then click
Anova Table.

The analysis of variance (ANOVA) table is displayed for the selected response.
If there are replicated observations, the residual sum of squares is further partitioned
into PURE ERROR and LACK OF FIT. A goodness of fit test is performed by
comparing the MS (mean square) lack of fit to the MS (mean square) pure error. See
the Statistical appendix for more information.

Replicated observations
MODDE checks the rows of the factors in the worksheet for replicates. Rows in the
worksheet with the same factor values plus or minus a 10% tolerance interval are
considered replicates and used for the computation of the pure error. The replicate
tolerance can be changed in General Options.

Note: The red coloring of the p-values always refer to the 95% resp. 5%
levels.

Footer of the ANOVA plots and tables

At the bottom of plots and tables the following is displayed:
N = Number of Runs.
DF = N-p degrees of freedom of the residuals.
R2, R2 adjusted, Q2 and RSD (residual standard deviation).

151
User Guide to MODDE

Reviewing and interpreting the fit

When you are satisfied with the diagnostic part of the evaluation you can start the next
phase: reviewing and interpreting the model. To review and interpret the model, use
the coefficient, effect, and variable importance plots and lists.

Coefficient plots and lists

There are two coefficient plots and two coefficient lists available in MODDE.
When confoundings are present, the coefficient plots and lists display a bracket # after
the term. Point to the column to view the confounded terms.

Coefficient plot
To create the coefficient plot, on the Analysis menu click Coefficients, and then click
Plot.

• The coefficient plot displays the coefficients, when changing from 0 to high,
for the selected response with the confidence interval as error bars. By
default, the coefficients refer to the data scaled and centered.
• You can select which type of coefficient to display from Properties. Select
Scaled and centered (default), Normalized, Unscaled, or PLS orthogonal
(only available for PLS).
• When you have confounded terms in your investigation these terms are
marked with a bracket #. Hoover over the column in the plot and you will get
information about which term(s) it is confounded with. This information is
available also in the coefficient overview plot.

152
 Analysis

Coefficient overview plot

To create the coefficient overview plot, on the Analysis menu click Coefficients, and
then click Overview Plot.
The overview plot displays the coefficient values for every response as bar graphs side
by side.
To make the coefficients comparable when responses (Y's) have different ranges,
MODDE displays the coefficients in Normalized form that is the coefficients are
divided by the standard deviation of their respective response. The Normalized mode
is the default for the overview plot. You can change it to regular scale and centered
coefficients by right-clicking and then clicking Properties.

153
User Guide to MODDE

Coefficient list
To create the coefficient list, on the Analysis menu click Coefficients, and then click
List.

P-values signaling non significant coefficients at the selected confidence interval are
colored in red.
For the selected response(s), this list includes:

Terms: Under the response name the name of the terms included in the model are
listed. To display the list for another response, or more than one response, use the
Response bar or Properties.
Coefficients: Value of the coefficient.
Standard error: Standard error of the coefficient
P Value: Probability to get the displayed value for the coefficient if its true value was
zero.
Confidence interval: The 95% confidence interval on the coefficient value. To select a
different level for the confidence interval open Properties or Investigation Options.

Coefficients overview list

To create the coefficient overview list, on the Analysis menu click Coefficients, and
then click Overview List.
The coefficient overview list displays the scaled and centered coefficients for all the
responses. Non significant coefficients at the selected confidence interval are colored
in red.

154
 Analysis

Effects plots and list

In MODDE you can create four effects plots:
1. Effect plot: Displays the effect calculated as twice the MLR coefficient and
sorted descending in absolute value.
2. Effect normal probability plot: Displays the effects on a normal probability
scale.
3. Main effect plot: Displays predicted values of the selected response, when
the factor varies from its low to its high level.
4. Interaction plot: Displays predicted values of the response, when a factor
varies from its low to its high level, plotted for all the combinations of levels
of the other factor(s).
The Effects List displays the effects and their confidence intervals.

Note: When an expanded list of the qualitative levels is desirable, use the
coefficients plots and lists to display or list the coefficients for every level of a
qualitative variable instead of the effects plots and lists. Note that the effects
for linear and interaction models are twice the corresponding coefficients.

Sorted effects plot

To open the effects plot, on the Analysis menu, click Effects, and then click Plot.
For process factors the values of the effects (computed as twice the MLR coefficients)
are plotted sorted (in absolute value) in descending order. The ± 95% confidence
interval is shown as error bars.

For mixture factors this plot displays the adjusted Cox effects (unavailable for Scheffé
models). This effect represents the change in the response values when component k
varies over its range, all other mixture factors kept in the same proportion as in the
reference mixture.
For details on how the mixture effects are calculated, see Statistical appendix, section
Mixture data in MODDE.

155
User Guide to MODDE

Normal probability plot of effects

To open the effects normal probability plot, on the Analysis menu, click Effects, and
then click Normal Probability Plot.
The plot displays the effects plotted on a cumulative normal probability scale.
You should only use this plot when you have a saturated model (model with as many
terms as experimental runs). For saturated models MODDE cannot compute standard
errors, p values and confidence intervals. Use the N-Plot to help you determine the
important effects.

This plot, proposed by Daniel's in 1954, is based on the fact that if all estimated effects
were noise, they would have a normal distribution and when plotted on a normal
cumulative plot, would fall on a straight line. Hence effects significantly different from
zero (noise) will fall outside the normal line.
Note that this plot assumes independent effects, and that all estimable effects are
plotted. Hence, it is only relevant for screening designs with saturated models DF = 0.
Also for this plot to be meaningful, one needs models with at least 10 effects. If these
conditions are not met MODDE will warn you that this plot may not be statistically
correct.

Note: The normal probability of effects plot is not available with mixture
factors

156
 Analysis

Main effect plot

To open the main effects plot, on the Analysis menu, click Effects, and then click
Main Effect.
To switch factors, right-click the plot, click Properties, click the Select Factor tab,
and then click the factor.
For process factors the plot displays the predicted values of the selected response,
when the factor varies from its low to its high level, all other factors in the design held
constant at their averages.
If the design has replicated points for the displayed factor where the other factors are
also at their averages, the observed values of these points are displayed with red
symbol.

Main effect plot for mixture factors

When you selected to display a mixture factor Xk, this plot displays the predicted
change in the response when Xk varies from its low to its high level, the relative
amounts of all other mixture factors are kept in the same proportion as in the standard
reference mixture.
For details, see the Statistical appendix, section Mixture data in MODDE.
With formulation factors you can adjust according to reference or to range using
Properties.

157
User Guide to MODDE

Interaction plot
To open the interaction plot, on the Analysis menu, click Effects, and then click
Interaction Plot.
To switch to another interaction and/or switch the factor displayed on the x-axis:
1. Right-click the plot and click Properties.
2. In tab Interaction Effects select the term in the Interaction term box and/or
select the factor in the Factor on X-axis box.

Note: This plot is only available for process factor. No interaction plots are
available for mixture factors.
When you select a 2 factor interaction, the predicted values of the response, when one
factor varies from its low to its high level, are plotted for both levels of the other factor,
all remaining factors in the design being set on their average.
If you have mixture factors in the model, these are all set at the standard reference
mixture.

158
 Analysis

3 factor interaction plot

When you select a 3-factor interaction, the predicted values of the response, when a
factor varies from its low to its high level, are plotted for all the combinations of levels
of the other two factors.

159
User Guide to MODDE

Effects list
To open the effects list, on the Analysis menu, click Effects, and then click List.
The values of the effects (twice the coefficients) are listed with their 95% confidence
interval sorted (in absolute value) in descending order.

160
 Analysis

Variable importance in the projection – VIP (only PLS)

The VIP values reflect the importance of terms in the model both with respect to Y, i.e.
its correlation to all the responses, and with respect to X (the projection). With
designed data, i.e. close to orthogonal X the VIP values mainly reflect the correlation
of the terms to all the responses.

VIP plot (only PLS)

To open the VIP plot, on the Analysis menu, click Variable Importance (VIP), and
then click Plot.

The VIP plot displays the VIP values as a column plot sorted in descending order.

VIP list (only PLS)

To open the VIP list, on the Analysis menu, click Variable Importance (VIP), and
then click List.

The VIP list displays the sorted VIP values and the PLS coefficients for all responses
in the investigation.

161
User Guide to MODDE

PLS score and loading plots

The score and loading plots complement each other. The position of an observation in
a given direction in a score plot is influenced by variables lying in the same direction
in the loading plot.
There are four types of PLS plots available:
• Score Scatter Plot – displays the score vectors t and/or u in a scatter plot.
Use the score plots to reveal groups, trends, outliers, and similarities. The
plot marks represent your experiments.
• Score Column Plot – displays the score vectors t or u in a column plot.
• Loading Scatter Plot – displays the loading vectors p, c, w and/or wc in a
scatter plot. Use the loading plots to investigate the correlation between
terms in your model. The plot marks represent the terms currently in the
model and/or the response-variables. The response variables are displayed
when plotting the c-vectors.
• Loading Column Plot – displays the loading vectors p, c, w or wc in a
column plot.

Score plots (only PLS)

To open a score plot, on the Analysis menu, click PLS Plots, and then click Score
Scatter Plot or Score Column Plot.

The score plots reveal groups, trends, outliers, and similarities.

You can create three different score scatter plots:
1. T scores (for ex.: t1 vs. t2): t scores are windows in the X space displaying
the objects as situated on the projection plane or hyper plane.
2. U scores (for ex.: u1 vs. u2): u scores are windows in the Y space, displaying
the objects as situated on the projection plane or hyper plane.
3. T vs. U scores (for ex.: t1 vs. u1): Displays the objects in the projected X (T)
and Y (U) space, and how well the Y space coordinate (u) correlates to the X
space coordinate (t).
Score column plots can only be created for one vector at a time.

162
 Analysis

Score plot examples (only PLS)

T scores: t1 vs. t2, t1
These plots are projections from the X space displaying the objects as situated on the
projection plane or hyper plane.

U scores: u1 vs. u2, u1

These plots are projections from the Y space, displaying the objects as situated on the
projection plane or hyper plane.

T vs. U scores: t1 vs. u1

These plots display the objects in the projected X (T) and Y (U) space, and how well
the Y space coordinate (u) correlates to the X space coordinate (t).
You can add a regression line to the plot by using the Plot toolbar.

Loading plots (only PLS)

To open a loading plot, on the Analysis menu, click PLS Plots, and then click
Loading Scatter Plot or Loading Column Plot.

The loading plots display the correlation between the X variables T(X) and the Y
variables U(Y).

163
User Guide to MODDE

You can create four different loading plots:

1. p loadings (for ex.: p1 vs. p2): These plots show the importance of the X
variables in the approximation of the X matrix.
2. w loadings (for ex.: w1 vs. w2): The w's are the weights that combine the X
variables (first dimension) or the residuals of the X variables (subsequent
dimensions) to form the scores t. These weights are selected so as to
maximize the correlation between T and U, thereby indirectly Y. X variables
with large w's (positive or negative) are highly correlated with U (Y).
Variables with large w's are situated far away from the origin (on the positive
or negative side) on the plot.
3. c loadings (for ex.: c1 vs. c2): These plots display the correlation between the
Y variables and the X scores T (X). The c's are the weights that combine the
Y variables with the scores u; so as to maximize their correlation with X. Y
variables with large c's are highly correlated with T (X).
4. wc loadings (for ex.: wc1 vs. wc2): These plots show both the X-weights (w)
and Y-weights (c), and thereby the correlation structure between X and Y.
One sees how the X and Y variables combine in the projections, and how the
X variables relate to Y.
Loading column plots can only be created for one vector at a time.
For details see the Statistical appendix.

Loading plot example (only PLS)

The default loading scatter plot is the wc1 vs. wc2 plot. The w's are the weights that
combine the X variables to the scores t, so as to maximize their correlation with Y. X
variables with large w's are highly correlated with U(Y). Variables having large w's are
positioned far away from the zero point in the plot.

164
Prediction

Introduction
To make prediction using the model means:
• Using contour plots for interpretation.
• Making predictions in the prediction plots and list.
• Optimizing for selection of “best conditions”.
• Investigating robustness to disturbances using the Design Space.
The prediction menu includes:
• Contour Plot Wizard
• Prediction Plot Wizard
• Response Prediction Plot
• Prediction List
• Scatter Plot
• Sweet Spot Plot
• Optimizer
• Design Space Validation - only briefly described here but more thoroughly
in the Design Space chapter and Appendix D: Design Space.

Note: The Prediction menu applies to all responses, regular and derived.

165
User Guide to MODDE

Contour plot wizard

The contour plot wizard guides you through the selection and specification of 2D and
4D contour plots for mixture and process factors and 2D Surface plots for process
factors.
To open the contour plot wizard, on the Prediction menu, click Contour Plot Wizard.

Inner plot type

Under Inner plot type, the default plot type for the inner axes is selected. If you have
both process and formulation factors in the investigation, click the type of factor to
display on the inner axes: Process or Mixture.
On the outer axes you can vary process factors only.

Selecting responses
You can select to display all responses for the 2D contour plots but with more than 9
the plots become very small. The contours are not overlaid, but displayed next to each
other.
Select which response(s) to display by marking in Available responses and clicking
the => and/or marking in Selected responses and clicking <=.

Using constraints
Select the Use constraints box if you want the available constraints to be displayed in
the plot.

166
 Prediction

Plot options
To select the resolution of the plot, that is, the grid calculated to create the contour plot,
click Plot Options. Note that you can type a resolution value here or click one of the
predefined resolutions.
You can also select to scale the subplots equally, to lock the contour levels, to produce
the plot with/without color and with/without contour level labels.
For more, see the Customizing contour plots sections in the Plots and lists chapter.

2D contour
The 2D contour plot displays the predicted response values, spanned by two factors, in
a response surface contour plot. For mixture the plot is spanned by three factors.
On the first page of the contour wizard, under Plot type, click Contour.
Under Inner plot type, if you have both process and mixture factors in the model,
click Process or Mixture to indicate which factors you want to display on the inner
axes.
Select which responses to display and click Next.

Factors on the axes

In the Axes and Constants dialog, select the factors to be plotted on the x and the y
axes. Change the default ranges as desired. When your factors are mixture, select the
three mixture factors to be plotted.

167
User Guide to MODDE

Factors kept constant

By default, all constant factors are set at their mid-range values; change these values as
desired. After the plot has been created the constant factors are found to the right in the
plot. When you change the value of the constant factors the contour plots are updated.

To hide the constants, right-click the window, and clear View Constants.

Zooming subplot
To zoom in on a subplot, click Subplot in the Zoom plot menu from the Plot toolbar.

168
 Prediction

4D contour
The 4D Contour plot displays the predicted response values, spanned by two factors,
in 9 response surface contour plots in a 3x3 grid spanned by another two factors. For
mixture the plots are spanned by three factors.
On the first page of the contour wizard, under Plot type, click 4D Contour.

Note: The 4D plot is available for investigations with only process

factors, and with both mixture and process factors, but not with mixture
factors only.

Under Inner plot type, if you have both process and mixture factors in the model,
click Process or Mixture to indicate which factors you want to display on the inner
axes.
Select which response to display and click Next.

169
User Guide to MODDE

4D contour plot axes

When the model includes both process and mixture factors, the mixture factors can
only be selected as inner factors.

Inner axes factors

Select two process factors for the axes under Factors at the plot axes, or three mixture
factors
Outer axes factors
Select two process factors for the outer axes. The response contours are plotted for the
low, middle, and high levels of these factors.
You can also select qualitative factors for the outer axes and select for which settings
to display the contour plots.
When there are more than 4 factors in the model, the remaining factors are held
constant

170
 Prediction

By default all plots are equally scaled, that is, the color coding is the same for all plots.

171
User Guide to MODDE

Response Surface
The Response Surface plot displays the predicted response values, spanned by two
factors, in a response surface plot. This plot is only available for models with two or
more process factors and can only display one response.
On the first page of the contour wizard, under Plot type, click Surface.
Select the responses to display and click Next.

Factors on the axes

In the Axes and Constants dialog, select the factors to be plotted on the x and the y
axes. Change the default ranges as desired.

Factors kept constant

By default, all constant factors are held constant at their mid-range values; change
these values as desired. After the plot has been created the constant factors are found to
the right in the plot. When you change the value of the constant factors the contour
plots are updated.

To hide the constants, right-click the plot and clear View Constants.

172
 Prediction

Prediction plot wizard

The prediction plot wizard guides you through the selection and specification of
prediction plots. In the prediction plots the predictions of the selected responses are
displayed for their low, center, and high levels. The predictions of each subplot are
adjusted for all the other factors.
To open the prediction plot wizard, on the Prediction menu, click Prediction Plot
Wizard.

Prediction plot wizard first page selections

You can create two types of plots in the prediction plot wizard: the Prediction plot and
the Overlay prediction plot. The prediction plot displays the predicted value for the
low, center, and high values of up to 3 factors and up to 3 responses with confidence
intervals when the Show confidence intervals check box is selected. The overlay
prediction plot displays the predicted value for the low, center, and high values of up to
3 factors and up to 9 responses. No confidence intervals can be displayed for the
overlay plot.
On the first page of the prediction plot wizard you need to select: plot type, factor type,
responses, and whether to display confidence intervals.

Plot type
To select to create a prediction plot, under Plot type click Prediction or Overlay
prediction on the first page of the prediction plot wizard.

Factor type
Under Factors at the X-axes, click the type of factor to vary: Process or Mixture.
You cannot vary simultaneously both process and mixture factors.

Selecting responses
You can select to display up to 3 responses for the prediction plot and 9 for the overlay
prediction plot. Select which response(s) to display by marking in Available responses
and clicking the => and/or marking in Selected responses and clicking <=.

173
User Guide to MODDE

Showing confidence intervals

Select the Show confidence intervals check box to display the 95% (default)
confidence intervals. Change the confidence level in Investigation Options under the
View menu or right-click the plot and click Properties.

Axes and constants

After clicking Next on the first page of the Prediction Plot Wizard, the Axes and
Constants dialog box is displayed.

Factors on the axes

Select the factors to be plotted under Factors at the X-axes. Change the default ranges
as desired.

Factors kept constant

Select values for the factors when they are kept constant under Constant factors.
When a mixture factor varies, the relative amounts of all other mixture factors are kept
in the same proportion as in the standard reference mixture and no mixture factors are
displayed in the Constant factors box. If no standard reference mixture is specified,
the centroid of the constrained region is used as the default.

Range or reference
You can select to keep the relative amount of the other mixture factors in the same
proportion as their ranges, rather than the reference mixture (default) by clicking
Adjusted to range.

Overlay prediction plot

In the Overlay Prediction Plot, the predictions for all the selected responses (max. 9)
are displayed in the same plot for up to 3 factors.

174
 Prediction

Response prediction plot

The response prediction plot displays the predicted response values for one factor (the
default factor in Investigation Options) and for all levels present for that factor in the
worksheet.
This plot displays a spline representing the variation of the fitted response when the
selected factor varies over the range defined in the design, adjusted for all remaining
factors. The 95% confidence intervals are displayed.
Right-click the plot and click Properties to:
• Select the response(s) on the Select Responses page. You can also use the
Response box.
• Select which factor to display on the Select Factor page. For mixture factors
you can also select to Adjust proportional to reference mixture or Adjust
proportional to ranges
• Select confidence level on the Confidence Level page.

Factor type
The response prediction plot can be displayed for process and mixture factors although
only one at a time.

Process factor
When the selected factor is a process factor, all other factors are kept constant on their
averages.

Mixture Factor
When the selected factor is a mixture factor, the relative amounts of all other mixture
factors are kept in the same proportion as in the standard reference mixture. If no
standard reference mixture is specified, the centroid of the constrained region is used
as default.
Response prediction plot example

175
User Guide to MODDE

Prediction list
In the prediction list you can type or paste factor settings to make predictions. The
lower and upper level 95% confidence intervals for these predictions are also
calculated.
To open the prediction list, on the Prediction menu, click Prediction List.
To insert rows, right-click the list and click Insert Rows or press the DOWN arrow
key when on the last row.
If the model has been fitted the predictions are calculated automatically after entering
settings for all factors. If you do not want the predictions to be automatically updated,
right-click the list and clear Auto Update. To make predictions with auto update
cleared, right-click the list and click Update Predictions or press the F5 key.
To change the confidence level of the confidence intervals, right-click the list and click
Properties.

Note: With PLS and an X matrix with large condition number, the standard
error of predictions is computed and displayed instead of the confidence
interval.

Scatter plot
In the prediction scatter plot you can view your factors and predicted responses as 2D
and 3D scatter plots.

Note: The points displayed in the scatter plots are the points in the current
prediction list. The scatter plot is updated with new points when you enter
them in the prediction list.
To create a prediction scatter plot, on the Prediction menu, click Scatter Plot.
For 2D plots, select the variable to be plotted on the X-axis by marking it and clicking
the arrow ‘=>’. Mark the other variable(s) and click the arrow to Series.
For 3D plots, select the variables to be plotted on the X, Y, and Series axes.

Click the Delete button in the dialog to remove factors or responses from the Y-
axis or from Series. To change what to display on the X-axis, use the arrow to add the
new variable.
Click the Color by Variable tab to color by a factor or a response.
You can customize the 3D plot using the property page and plot settings. See the Plot
settings for 3D scatter and Onion 3D plots section in the Plots and Lists chapter.

176
 Prediction

Sweet spot plot

The Sweet Spot plot highlights the areas were the responses are within the user
specified ranges. The sweet spot plot can be displayed as 2D or 4D for process or
mixture factors.

Creating a sweet spot plot

To open the sweet spot plot, on the Prediction menu, click Sweet Spot Plot.

Inner plot type

If the investigation contains both mixture and process factors, select the type of factor
you want on the axes for the 2D and for the inner axes for the 4D.

Plot type
To select to create the 2D sweet spot plot click Sweet Spot and to select the 4D with
up to four factors (5 with mixture) click 4D Sweet Spot. Click Next.

Response Selection
In the Response Selection page, enter the settings for the relevant responses.

Note: If you have entered Min and/or Max values in the response definition,
this page is automatically filled with those values. To update with updated
values from the response definition, click the Get Limits button.
For each response you have to select:
• To Include or Exclude each response under Incl/Excl.
• Which type of values, Value or Percent, you are entering under Min and
Max.
• Type the values that are of interest under Min and Max. MODDE has
entered the smallest and the largest values found in the worksheet. Change
them according to your desired sweet spot. You can also select or clear the
Use Constraints check box and change the resolution in the Resolution box.

177
User Guide to MODDE

Plot axes
Click Next to open the Axes and Constants page, or for 4D sweet spot, the 4D Axes
page.
Mixture factors can only be selected as inner factors in a 4D plot.

Select two process factors for the axes under Factors at the plot axes, or three mixture
factors
For the 4D, select two process factors for the outer axes. The sweet spot contours are
plotted for the low, middle, and high levels of these factors.

178
 Prediction

Colors in the sweet spot plot

The sweet spot plot uses the color scale from green to blue with:
• Green for the ‘sweet spot’, that is the areas where all responses are within the
selected range.
• Blue for areas where one of the responses is within its selected range.
• White for areas where none of the responses are within their selected ranges.
• Other colors for areas with more than one response within its range but not
all.
The above are the default settings and you can define specific colors in the plot settings
dialog.

Sweet spot plot example

The constants are displayed to the right in the sweet spot plot window. Make a change
in the constants and the plot is updated automatically. The constants can be hidden by
right-clicking the plot and clearing View Constants.

179
User Guide to MODDE

Optimizer
You can use the optimizer to find an experimental area limited both by factor settings
and response criteria.
To open the optimizer, on the Prediction menu click Optimizer. MODDE opens a
dialog box with 3 spreadsheets.

The optimizer can be set up for different objectives:

1. Limit optimization – where the objective is to reach a solution where all
responses are within the specification limits. This is default in MODDE.
2. Target optimization – where the objective is to reach a solution where all
responses are as close to target as possible. For the target optimization it is
necessary that all responses can be optimized close to or to reach the target.
Otherwise you may end up with an unacceptable solution.
3. Focus optimization – where you want to favor one or several responses over
the others using individual weights.
For more information about the optimizer objectives see Appendix C: Optimizer and
the Optimizer section in the Statistical appendix.

180
 Prediction

Factor spreadsheet in the Optimizer

In the factor spreadsheet all factors are available with their current roles and their
ranges according to the worksheet.

Role of the factor

The Role is set to define whether the factor can vary or not during the optimization. If
the factor can vary within an interval, you should set the role 'Free', if the factor
should not vary you should set the role 'Constant'. By default, all factors included in
the model are 'Free'.
When a factor is 'Free' it is varied during the optimization within its specified range as
defined by Low Limit and High Limit. Default these low and high limits are taken
from the smallest and largest values found for that specific factor in the worksheet.
You can change the range to widen or narrow the search region.
When a factor is 'Constant', it will be held at the selected constant value during the
optimization. The default constant value is the center point. Change this value by
typing another under Value.
The Sensitivity Range is the disturbance added to the factor settings proposed by the
optimizer in the run list. 5% is the default and signifies a disturbance of + 5% of the
factor range for the Monte Carlo simulations. The result is shown in the run list as
DPMO (Defects Per Million Opportunities) outside the accepted response area.

Response spreadsheet
In the response spreadsheet all the responses used in your model are available. Before
starting the optimization you must select the Criteria for your response(s), weights and
limits.
If you have specified Min, Target, and/or Max in the response definition, these
specifications are copied to the Optimizer response section. If no Min, Target, or
Max settings are defined in the response definition, the response will be by default
Predicted.

Note: You can fetch updated limits from the response definition by right-
clicking and clicking Update limits from response definition.

181
User Guide to MODDE

Criteria and limits

You can choose:
• Minimize the response. Type the highest value you can accept under Max
and your target value under Target.
• Maximize the response. Type the smallest value you can accept under Min
and your target value under Target.
• Target the response. Type the smallest, largest, resp. desired value under
Min, Max, resp. Target.
• Predicted response. The response will not participate in the optimization but
the prediction will be displayed.
• Excluded response. The response will not be a part of the optimization nor
displayed in the run list.
When you have not entered Min, Target, or Max values and you choose to Minimize
or Maximize, MODDE makes an educated guess of your limits. It is imperative that
the limits are well chosen and reflect the data at hand.
When the difference between the minimum/maximum and target values is too small
the optimizer will not run. When this happens you should increase the range.

Weight
In the column Weight you can enter a number between 0.1 and 1 reflecting the
importance of the response. Default is 1 indicating that all responses are of equal
importance.
The weight will change the optimization objective described in the first section of this
chapter as follows:
• Weight = 1 for all responses results in a limit optimization (default).
• Weight = 0.2 for all responses results in a strict target optimization.
• Individual weights for the responses results in an optimization where the
responses with higher weights are favored in the quest for all responses to
reach inside the limits.
For more information see Appendix C - Optimizer.

182
 Prediction

Run list
The run list includes the factors, responses, iterations, Log(D), and DPMO. The D in
Log(D) is a normalized distance to the target. See Appendix C: Optimizer for more
information.

Interpret the run list

After running the optimizer the best proposal, lowest Log(D) is selected. Note that if
alternative solutions with Log(D) close to the best are found, another run than the
marked one may be optimal when looking at practical aspects.
Minimum for Log(D) = -10 (on target). A Log(D) < =0 means that all results are
within specification limits or very close.
DPMO gives additional information about how robust the proposed run will be to
disturbances in the factor settings.

In the run list above, row 6 has a DPMO = 0 meaning that with disturbances + 5% on
the factor settings will give a solution inside the specifications. Row 1 has
approximately the same Log(D) but a DPMO = 5600 indicating that a small
disturbance in the factor settings from this point will result in some hits outside the
specifications. Therefore row 6 is preferable.

Scrolling through the optimizer log

After running the optimizer, you can scroll back and forth through the iterations using
the Iteration slider near the Iteration number.

Absolute response limits

You can specify that the minimum and maximum limits for the responses are absolute.
No suggestion from the optimizer will then be shown that have predicted values for a
response outside the specified limits. Note that this may result in that no suggestion is
displayed.

To use absolute limits, select the Absolute response limits check box above the run
list, or right-click the window and click Properties to open the Optimizer Properties,
in tab Options, select the Use absolute response limits check box.

183
User Guide to MODDE

Sensitivity analysis
The Analyze sensitivity check box is by default selected to display complementary
information about the proposed optimal factor settings. The sensitivity is expressed as
DPMO (Defects Per Million Opportunities) outside specifications, based on Monte
Carlo simulations and including prediction error. Note that DPMO is an estimate of the
result after the number of simulation performed; 10 000 simulations will give a fair
estimate.

Optimizer context menu

Most commands available in the optimizer can be reached by right-clicking the
Optimizer window. The two plots Simplex Evaluation and Response Simplex
Evaluation and the Optimizer Properties can only be opened by right-clicking the
Optimizer window and are described here.

Simplex Evaluation plot

The Simplex Evaluation plot displays the Log(D) plotted vs. iterations.
Open the plot by right-clicking the Optimizer window and clicking Plot | Simplex
Evaluation.

Response Simplex Evaluation plot

The Response Simplex Evaluation plot displays the predicted response value vs.
iterations. The target and specified limit(s) are displayed for each response.
Open the plot by clicking Plot | Response Simplex Evaluation on the context menu.
Select which responses to display in the dialog box that opens.

Optimizer Properties
In the Options tab optimizer settings are specified.
Feature Description Default

Use absolute When selected, only the runs where all responses are predicted Not
response limits inside the specified limits are displayed in the run list. selected.

When selected, the DPMO is calculated for runs where all responses
are predicted inside the specified limits. The Sensitivity Range for
Calculate DPMO the factors specifies the range used in the DPMO calculations. Selected.
This is a sensitivity analysis that indicates if a solution is sensitive or
insensitive to small changes.

Include Model When selected, the sensitivity analysis (DPMO) includes the model
Selected.
Error error in addition to the sensitivity range.

The number of simulations in the calculation of the DPMO. The result

Simulations 10 000
is scaled up to the unit 'dots per million operations'.

Include weight in
When selected, the weight specified in the response spreadsheet is Not
calculation of
included when calculating Log(D). selected.
Log(D)

184
 Prediction

Optimizer buttons
There are seven optimizer buttons: Generate start runs, run optimizer, generate start
points from selected, contour plot wizard, copy to predictions, sweet spot plot wizard,
and analyze design space.
The Design Space, opened by clicking the Analyze Design Space - button is described
in the Design Space chapter.

Generating the start runs

If the run list is empty, MODDE automatically generates starting runs when the
optimization starts.
If you want to display and/or modify the starting runs of the simplexes, click the

Generate start points button .

MODDE generates start runs from the corners and center of the experimental
region, plus the three best runs.
For details on how the start runs are selected see the Statistical appendix, section
Optimizer.

185
User Guide to MODDE

Running the optimizer

Start the optimizer by clicking the Run Optimizer (play) button or right-click
the list and click Run Optimizer.
The optimizer runs to completion and displays the results as:
• Final factor settings.
• Predicted responses values.
• Number of iterations.
• Log(D), i.e., the logarithm of the overall distance to Target. The smaller the
Log(D) the better is the result. At Log(D) = -10 all predicted responses are
on target.
• DPMO, estimated number of hits outside specification on one million
simulations. A smaller DPMO means that the solution is less sensitive to
disturbances.
Restarting the optimizer
After convergence, you can always click the Run Optimizer (play) button to restart
the optimizer. It restarts from the displayed resulting runs of the previous search. If you
do not want to continue with the resulting runs click the Generate new starting points
or Generate starting points around selected button to specify other start runs.

Generating new starting runs from a selected run

When one of the simplexes is closest to Target, you may want to restart the optimizer
with new starting runs selected from the corners and center of a fractional
factorial around this “best run”.

Mark the run, and click the Generate start points from selected button or right-
click the list and click New Runs from Selected.

In the dialog box displayed the run you marked is the default run to optimize around.
To switch to another run, enter another run in the Center around optimizer run box.
Enter the percent of the factor range in the Factor range box. The percentage entered
here is used to calculate the new high and low limits for the start runs.

186
 Prediction

Creating contour plots from the optimizer

After convergence of the optimizer you can create contour plots using the results.

Mark the best run and click the Contour Plot Wizard button to open the
Contour Wizard Setup dialog box. You can also open the wizard by right-clicking
the list, clicking Plot and selecting Contour Plot Wizard.

Select factor settings

In the Contour Wizard Setup dialog:
• Center around the optimum found by the optimizer is by default marked,
and the run to use in the center is the one you marked. If you want to select
another run enter the new run number.
• Selecting Factor definitions results in displaying same factor settings as
when you enter the contour plot wizard from the Prediction menu.
• Selecting Optimizer factor setup results in displaying the current factor
settings in the Optimizer.
Center around the optimum found by the optimizer
With Center around the optimum... selected, clicking OK opens the contour plot
wizard dialog box.
If you create a 2D contour plot the first two factors (for process factors; first three
factors for mixture factors) are varied around their optimum settings (20% range) and
the other factors are set constant to their optimal values.
If you create a 4D contour plot the first two factors (for process factors; first three
factors for mixture factors) are varied around their optimum settings (20% range), the
3rd and 4th are set at their low, high, and center values using the 20% optimum range,
and other factors are set constant to their optimal values.
The resulting plot displays the area outside the factor range shaded.

187
User Guide to MODDE

Contour plot displayed from optimizer

In the created contour plot the predicted parts that are outside the original factor
settings are displayed shaded when the plot is extrapolated.
The selected run is displayed in the plot as lines from the axes with arrows pointing
toward the position of the selected run.

Copying to prediction list from the optimizer

To get predicted response values with confidence intervals for the resulting factor

settings, click the Copy to Predictions button or right-click and click Copy to
Predictions.

188
 Prediction

Creating sweet spot plot from the optimizer

When you choose to create the sweet spot plot from the optimizer, MODDE uses the
range of the responses as specified in the response spreadsheet fields Min, Target, and
Max.

To create the sweet spot plot click the Sweet Spot Plot Wizard button . You can
also open the sweet spot plot by right-clicking, clicking Plot and then clicking Sweet
Spot Plot. In the dialog that opens you can select to create the 2D sweet spot plot by
clicking Sweet Spot or 4D by clicking 4D Sweet Spot.
The selected run is displayed in the plot as lines from the axes with arrows pointing
toward the position of the selected run.

189
User Guide to MODDE

Design Space Estimation around the selected setpoint

Limitations with a sweet spot plot presentation are the number of dimensions and the
lack of probability estimate in the predicted surface. With Design Space (DS)
estimation we can show how the factor settings can be varied around a selected
setpoint (optimum) and still fulfill the response criteria.
The estimation of a safe DS region is performed using Monte Carlo simulations on the
factor settings. MODDE performs a search to identify the largest possible range for
each factor that can be used and still meet all response requirements. The default limit
is less than 10 000 (1%) hits outside the limits for each response. The results are
displayed in the Predictive Design Space Estimate window.
The Predictive Design Space Estimate window is opened by clicking the Analyze

Design Space button in the Optimizer .

Design Space Validation

Design Space Validation is a way to test if the system investigated is robust against
disturbances in the investigated region. The test is done with Monte Carlo simulations,
meaning that a number of random disturbances on the factors will give a distribution of
predictions. The function is described in Appendix D: Design Space.
To open the Design Space Validation window, click Prediction | Design Space
Validation. The window has two parts, a factor spreadsheet and a response
spreadsheet.
For more see the Design Space chapter next.

190
Design Space

Introduction
The calculation of the design space is a search function that expands the possible factor
ranges from a setpoint (optimum) to the largest possible range where all response
predictions are still within the specifications.
Predictions in the design space are done with Monte Carlo simulations. The resulting
distribution of predictions simulates a real situation with a random combination of
factor setting disturbances within a given range.
There are two Design Space features in MODDE:
• Predictive Design Space Estimation for optimization.
• Design Space Validation for robustness testing.
DS is used as an abbreviation for Design Space in this user guide.

Design Space Estimation around the selected setpoint

Limitations with a sweet spot plot presentation are the number of dimensions and the
lack of probability estimate in the predicted surface. With Design Space (DS)
estimation we can show how the factor settings can be varied around a selected
setpoint (optimum) and still fulfill the response criteria.
The estimation of a safe DS region is performed using Monte Carlo simulations on the
factor settings. MODDE performs a search to identify the largest possible range for
each factor that can be used and still meet all response requirements. The default limit
is less than 10 000 (1%) hits outside the limits for each response. The results are
displayed in the Predictive Design Space Estimate window.
The Predictive Design Space Estimate window is opened by clicking the Analyze

Design Space button in the Optimizer .

191
User Guide to MODDE

Design Space Validation for robustness testing

Design Space validation is a way to test if the investigated system is robust against
disturbances in the investigated region.
The aim of robustness testing is to evaluate if a process, or a system, performs
satisfactory even when some influential factors are allowed to vary. In other words, we
want to investigate the system’s sensitivity (or preferably lack of sensitivity) to
changes in certain critical factors. The advantages of a robust process or system
include simpler process control, a known range of applicability and an ensured quality
of the product or process.
A robustness test is usually carried out before the release of an almost finished product,
or analytical system, as a test to ensure quality. Umetrics recommends the use of DoE
for robustness testing and such a design is usually centered on the factor combination,
which is currently used for running the analytical system, or the process. We call this
the setpoint. The setpoint may have been found through a screening design, an
optimization design, or some other identification principle, such as written quality
documentation. The aim of robustness testing is, therefore, to explore robustness close
to the chosen setpoint.
In this case we use Monte Carlo simulations on the regression model and simulate
random disturbances within the investigated range of operation for all factors. The
regression model originates from a low resolution design supporting linear models
since we assume that small disturbances have mainly linear effects. Fractional factorial
resolution III and Placket Burman designs are recommended.

Design Space window

The Design Space window is parted in two. The upper part displays the factor section
and the lower part the response section. The window displayed below was created from
the Optimizer.

192
 Design Space

Factor spreadsheet
In the factor spreadsheet the following functionality is available for each factor:
Item Description Setting

For DS Validation: by default the low,

center, and high values from the factor
definition.
Low,
Optimum, The acceptable factor range For Predictive DS Estimate: by default
High. the Optimum is the value for the selected
run in the run list. The Low and High
values are the 95%* confidence with
normal distribution.

St.Dev The standard deviation of the factor Calculated.

‘Free’ means that the largest possible

range of variation for the specific factor
is used, with respect to the settings for For DS Validation: by default 'Locked'.
Role other factors and response For Predictive DS Estimate: by default
specifications. 'Free'.
‘Locked’ means that the range settings
of the factor are locked.

The Distribution of each factor range.

‘Uniform’, ‘Normal’, ‘Triangular’ or
‘Target’.
‘Uniform’ means that all factor settings
within the specified range have the same
probability to appear. For quantitative factors, by default
‘Normal’ means that the simulations are 'Normal'.
Distribution
normally distributed within the factor For formulation factors, by default
range. 'Triangular'.
‘Triangular’ means that the distribution
has the shape of a triangle; a good way
to get a skewed distribution for a factor.
‘Target’ means that the factor will be set
to a fixed value, the "Optimum" value.

The left side of the T bar in the

Estimated acceptable range is the
Estimated Min estimated minimum factor value for Calculated.
which the predictions still fall inside the
specifications.

The right side of the T bar in the

Estimated acceptable range is the
Estimated Max estimated maximum factor value for Calculated.
which the predictions still fall inside the
specifications.

The yellow lines are the factor settings of the selected optimal run in the optimizer.
The red lines are the Low and High factor settings of the experimental region.
Estimated The black T bar represents the region of acceptable variability valid for that factor
acceptable when all other factors are locked at the optimum. Valid means that all predictions of
range the responses are within the specifications. No model error is considered in this
search.
The blue region represents the 95%* part of random factor variability with normal
distribution where all predictions are within the specifications.

*95% is the default. In the Design Space Properties you can change to 99%.

193
User Guide to MODDE

Response spreadsheet
In the response spreadsheet the following functionality is available for each response:
Item Description Default

Min, Target, Min, Target, and Max as

The optimization range
Max specified in the Optimizer.

'Minimize’, ‘Maximize’,
‘Target’, and ‘Predicted’ as
specified in the optimizer.
Criterion What the algorithm is aiming for. When the search does not
reach inside the limits for a
response, the Criterion is set
to 'Not Met'

A Process Capability Index, Cpk, which originates from

the SixSigma statistics and is estimated in this Estimated by MODDE when
Cpk
simulation. Cpk =1 means that approximately 0.13%* selected.
of the predictions will fall outside the specifications.

Defects Per Million Opportunities is an estimate of how

many predictions will be outside the specification per
DPMO Estimated by MODDE.
one million predictions in the selected DS with the
selected distribution.

The yellow line represents Target value for the responses as specified in the
Predicted Optimizer.
response The red lines are the specification limits for each response as specified in Optimizer.
profile The faded green region represents the probability of a prediction for a random
distribution of factor settings in the given ranges (low-optimum-high), the DS.

* See table in the DPMO and Cpk section in Appendix A: Statistical notes.

Design Space buttons

There are four design space buttons: Run the Monte Carlo simulations, present the
frequency histogram over the responses, show the individual response DS estimation,
and properties.

From left to right clicking:

• Resample reruns the Design Space calculations.
• Create Histogram opens the response histogram plot.
• Individual response analysis displays a detailed DS estimate for the
individual responses. This window displays an overview of the acceptable
factor ranges which makes it easier to understand which the limiting
responses are. In the window below the response Soot has the smallest
acceptable interval and will therefore be the most limiting response, affecting
the complete region of operability for each

factor.
• Properties opens the Design Space Properties dialog. For more see the
Design Space Properties sub section.

194
 Design Space

Design Space Properties

Parameters section
In the Parameters section the settings used in the design space estimation are
displayed and can be adjusted.
Option Description Default

Acceptable range Number of simulations done in each step of the search for the
20 000
simulations acceptable range for the factors.

Response profile Number of simulations for the final predictions of the response
100 000
simulations profile.

Defects Per Million Opportunities outside the specification target.

DPMO target The first response that exceeds this target will stop the expansion 1 000
of the accepted factor range.

Stop criterion will be the total number of predictions outside the

Not
Use total DPMO target for all responses. When this check box is not selected the
selected.
DPMO target is for each response.

Includes model error in the predictions of the response

Include model error Selected.
distribution.

Any change in the settings results in a recalculation of the Design

Space.
Automatic update As this calculation includes many computational operations you Selected.
may want to inactivate it and do the calculations when all settings
have been adjusted instead of after each adjustment.

Defines the Low and High values in such a way that 95%, in the
Limits at 95 or 99 %
default case, of the Monte Carlo simulations are inside the limits.
confidence for 95%
Selecting 99% widens the included area by lowering the Low limit
normal distribution
and increasing the High limit in the factor spreadsheet.

195
User Guide to MODDE

Show section
In the Show section what to display and how can be adjusted.
Option Description Default

Columns shown in the factor spreadsheet of the DS. The

available fields are: By default all the columns but
Factor
fields Factors (factor names), Low, Optimum, High, St.Dev, Possible Min and Possible
Role, Distribution, Possible Min, Possible Max and Max are displayed.
Estimated acceptable range.

Columns shown in the response part of the DS. The By default Responses, Min,
Response available fields are: Responses (response names), Min, Target, Max, Criterion,
fields Target, Max, Criterion, Cpk, DPMO, Average, St.Dev, DPMO, and Predicted
%Outside, Median, 1st Quartile, 3rd Quartile, and response profile are
Predicted response profile. displayed.

Color Blue for factors, green for

Displays the range of colors of the distribution bars.
range responses.

Factor histogram
When double-clicking the estimated acceptable range for the factors, the Factor
Histogram opens. This histogram displays the distribution of the factor settings used
for the simulation.

196
 Design Space

Response histogram
The result of the Monte Carlo simulations can be presented as frequency histograms
by:
• Double-clicking Predicted response profile.

• Clicking the Create Histogram button .

• Right-clicking the Design Space window and clicking Response
Histogram.

Design Space Statistics list

All statistics can be shown in a specific list, opened by right-clicking the Design Space
window and clicking Design Space Statistics.

197
User Guide to MODDE

Final factor adjustments

After displaying the Design Space final adjustments can be made to find a safe region
of variability for all factors where all results are within specifications (DS). In some
publications the selected region inside DS where we have selected to operate the
process is called “Control Space”.
Reasons for final adjustments can be practical and/or economical. A limitation in one
factor will result in a wider range for another factor. Different type of distributions can
also be selected for different factors.

198
Show

Introduction
On the Show menu the following items are available: Objective list, Design Matrix,
Design Region plot, Confoundings list, D-Optimal Summary table, Model list, and
Reference Mixture list.

Objective
To open the Objective list, on the Show menu click Objective. The Objective list
displays the selections made in the Objective pages of the design wizard

The following information is listed:

Maximum Runs: the maximum number of runs that MODDE can include in a design
created by MODDE.
Objective: the selected objective.
Process Model: the type of model created for the process factors.
Mixture Model: the type of model created for the mixture factors.
Design: the selected design.
Runs in Design: the selected number of runs in the design created by MODDE. If you
have added runs after creating the design they will not be included here.
Center points: the number of center points selected.
Replicates: the number of times the entire design has been replicated.
N = Actual Runs: the number of runs created by MODDE.

199
User Guide to MODDE

Design matrix
To display the Design Matrix, on the Show menu, click Design Matrix.
The Design Matrix displays the experimental plan in coded unit for quantitative
factors, as in the worksheet for qualitative factors and in pseudo components for
formulation factors.
If you have qualitative factors at more than two levels, you can select to display the
design with the qualitative factors extended.
To display the design matrix with the qualitative factors extended:
1. Right-click the matrix and click Properties.
2. Click Extended – shows all settings and click OK.
3. Optionally switch back by clicking Regular – shows all orthogonal
settings.
By default the Design Matrix is derived from the worksheet, and reflects any changes
(excluded runs, changed values, additional runs etc.,) done to the factor part of the
worksheet after it’s generation.
To display the original design matrix generated by MODDE:
1. Right-click the matrix and click Properties.
2. Click The design as generated by MODDE and click OK.
3. Optionally switch back by clicking The current Worksheet scaled and
centered.

200
 Show

Design region
Open the Design Region plot to get an overview of your experimental plan.
To open the Design Region plot, on the Show menu, click Design Region.
Use the Response box or right-click the plot and click Properties to switch to another
response.

Design region properties

The Design Region plot:
• Is displayed as one or more cubes.
• Can be displayed for classical designs with up to 5 process factors.
• Displays the response values at the star points on the face of the cubes for
CCC designs.
• Displays the points in the design region plot color coded according to the
response values entered in the worksheet. The response range is parted
equally resulting in three groups named High, Medium, and Low.
• Displays points where the factor settings are not at the original value, at the
closes intersection for low, center, and high factor settings. In this plot, the
replicate tolerance is therefore NOT used to identify replicates.
• Displays a black point, Conflicting colors when the response values to be
displayed have been assigned to different color groups (High, Medium, and
Low).

Hint: When you want to view 3 factors in 3D, use the Scatter Plot found under
the Worksheet and Prediction menus.

201
User Guide to MODDE

Design region for mixture designs

The Design Region plot is not available for mixture designs. Enter any values and use
the Prediction | Contour Plot Wizard, with the Use constraints check box selected
when applicable, to investigate the design region. Or use the Worksheet | Scatter
Plot.

Confoundings
Open the Confoundings list to see which terms that are mathematically identical in the
current design. For instance, in the example below the term M*TH is included in the
model, but the effect of this term is confounded with the effect of H*S. This means that
using this design there is no way of telling whether the coefficient displayed for M*TH
reflects M*TH, H*S, or a mixture of both.
To list the confoundings click Confoundings on the Show menu.
For factorial designs resolution III or IV, the Confoundings list displays the
confounding pattern for the complete interaction model.
In the Term column, the background of the terms included in the model is colored.
In the coefficient plots and lists, confounded terms are marked with a bracket #-sign.

202
 Show

Summary D-Optimal
To displays a list summarizing the generation of a D-Optimal design click D-Optimal
Summary on the Show menu.

Under Candidate set the properties of the used candidate set are listed in the form of
Extreme Vertices, Edge points, Centroid of high dim. Surfaces, and Total Runs.
Under D-Optimal the properties of the selected design are listed in the form of
Objective, Model Type, Potential Terms, Number of Inclusions, Constraints,
Design Runs, Selected Design Number, G-Efficiency, log(Det. of X' X), Norm.
log(Det. of X' X), and Condition number.

203
User Guide to MODDE

Model
On the Show menu click Model to display the selected model.
If you have qualitative factors at more than two levels and want to display the model
with the qualitative factors extended:
1. Right-click the Model list.
2. Click Properties.
3. Click Extended – Show all settings.

Reference mixture
To display the reference mixture used in the analysis of the design click Reference
Mixture on the Show menu.
To change the reference mixture, click Model / Reference Mixture on the Edit menu
and click the Reference Mixture tab.

204
Plots and lists

Introduction
You can customize the plots in MODDE using the Plot Settings page. You can change
the properties of plots and lists from the property page accessed by right-clicking the
plot or list and clicking Properties.
Most plots can be transformed into lists by right-clicking the plot and selecting Create
List.

Properties page
Opening property page by right-clicking
To open the property page of a plot or list, right-click the plot or list and click
Properties.

Making a change in the property page

With Properties open, click the desired option from the context menu and the plot or
list is updated when you click OK or Apply. The default of most properties available
from the Properties page can be changed in Investigation Options available from the
View menu.

Automatic update of plots and lists

If you, after fitting the model, make changes to the responses (add, delete or
transform), the worksheet (include, exclude runs or values), the model (add or remove
terms), or change fit method, MODDE refits the model and all open plots or lists are
updated.

Saving plots and lists

Save plots and lists by:
• With the plot or list active, on the File menu, click Save Plot/List As.
• Right-click the plot or list and click Save Plot/List As.
For details, see the section Save plot/list as in the File chapter.

205
User Guide to MODDE

Generating multiple plots or lists

When there are many responses in your investigation you can select to display a
multiple plot with all or selected responses. Click the desired responses or All
Responses in the Response box.

Note: When displaying multiple plots, opening the Properties page displays
the properties for the first displayed response.

Plot settings
Use Plot Settings to customize the most common attributes of the axes, of the plot area
and of the header and footer.
There are two different types of plot settings dialogs in MODDE:
• Plot settings for 3D scatter plot and contour, response surface, and sweet spot
plot where all options are in the same dialog.
• Plot settings for other plots are divided in Axis, Header and Footer, and
Plot Area pages.
Open Plot Settings by double-clicking the plot or right-click and click Plot Settings,
then when applicable click Axis, Header and Footer, or Plot Area.
After customization, most features can be saved as default plot settings in two ways:
• Click the Save Settings button in the Plot Settings dialog.
• Right-click the plot and click Save as Default Plot Settings.

206
 Plots and lists

Axis
To change the settings of the plot axes, right-click the plot, click Plot Settings, and
then click Axis. This dialog is also opened if you double-click one of the axes.
All of the properties apply to the selected axis: X, Y, or Y2 (the second Y-axis).
In this dialog you can change general settings, such as scale, gridlines, titles, and fonts
by clicking the appropriate tab.

Scale
To change the scale, enter the Minimum and Maximum data values and the value to
Increment by. You can specify the spacing of the minor tick marks and the number of
Decimal places to display on the tick label.
Click the Recalculate Scale button to restore the Minimum and Maximum values.

Tick mark label

You can change the tick label from the Normal (default) number to Scientific notation
or Time. The value in Rotation controls the orientation of the label in degrees.

Miscellaneous
By default the axes are in normal scale. You can change them to Logarithmic scale or
Values in reverse order by selecting the corresponding check box. The axes are
default displayed. To hide an axis, clear the Show axis check box.
The Always recalculate scales check box is by default selected. If you do not want
MODDE to recalculate the scale you should clear the check box.

207
User Guide to MODDE

Gridlines
In the Gridlines tab, select the Show gridlines check box to display the grid lines of
the selected axis. The grid lines are placed on the tick marks. Select the Pattern,
Color, and Width of the gridline.

Title
In the Title tab, select to show or hide the axis title, change the text and its orientation.

208
 Plots and lists

Font
In the Font tab, select the font for both the axis titles and the tick mark labels.

For how to customize the axes of the 3D scatter plots, see the section later in this
chapter.

Header and Footer

You can customize or remove/add the headers and footers of the plot.
To access the header and footer titles and fonts, right-click the plot, click Plot Settings,
and then click Header and Footer to open the Format Header/Footer page, click the
Title or Font tab as desired.
In this page you can also select to not display the time stamp by clicking Time stamp
under Titles, and then clearing the Is visible check box. Make this the default by
clicking the Save Settings button if desired.

For how to customize the header and footer of the 3D scatter plots, see the section later
in this chapter.

209
User Guide to MODDE

Plot Area
To change the settings of the interior of the plot, right-click the plot, click Plot
Settings, and then click Plot Area. This dialog is also opened if you double-click the
plot area.
In this dialog you can change symbol style, line style, data labels, and font by clicking
the appropriate tab.

Symbol style
Select the shape, color and size of all the symbols in a series.

Line style
Click the Line Style tab to change the properties of lines in line plots.

Data labels
Click the Data Labels tab to change the attributes of all the labels on data points inside
the plot area. Color, alignment, or orientation (Rotation) applies to all the labels in a
given series.

Font
Click the Font tab to select the font for all the data labels.

210
 Plots and lists

Background
Click Background, found under Series to the left in the dialog, to change the borders
of the window, plot, and chart areas.

Legend
Click Legend, found under Background to the left in the dialog, and select or clear the
Show Legend check box to show or hide the legend. Here you can also change text
placement, color, background and border styles of the legend.

211
User Guide to MODDE

Column style
When you have a column plot you can change the pattern, color, column width, and
overlap for each or all series in the Format Plot Area dialog.

For how to customize the plot area of the 3D scatter plots, see the section later in this
chapter.

Saving plot settings

After customizing the plots you can save the settings of some attributes, such as fonts,
gridlines symbol type etc.:
• Click the Save Settings button in the Plot Settings dialog.
• Right-click the plot and click Save as default Plot Settings.
You can always restore Umetrics default Plot settings in View | General Options |
Restore.

212
 Plots and lists

Customizing contour plots using the property page

Right-click the contour plot and click Properties to open the property page.
In tab Contour Plot Options you can select the Resolution, select to Scale subplots
equally, select to Lock contour levels, select to Use color in the plot, and select to
Show contour level labels.

Resolution
Resolution is the precision used when creating the contour plot. Selecting a higher
resolution requires more calculations and is therefore more time consuming.
To select the resolution of the plot, click one of the predefined resolutions or type a
resolution value here.

Scale subplots equally

In tab Contour Plot Options in the property page of the Contour Plot you can select
the Scale subplots equally (subplots share contour levels) check box.
When the Scale subplots equally box is selected the colors of all contour subplots
represent the same values.
The plot has subplots when you display the 4D contour or you have selected to display
more than one response in the 2D contour plot.

Lock contour levels

You can select the Lock contour levels check box to keep the current contour level
colors and limits.

Use color
By clearing the Use color check box you can choose to display the contour and surface
plots without colors.

213
User Guide to MODDE

Show contour level labels

Clear the Show contour levels labels check box to display the contour plots without
the level labels.

Plot settings for contour plots

To change the fonts on the labels, headers and footers, or the attributes of the axes,
double-click the plot or right-click the plot and then click Plot Settings.

Axis
Click Axis to change settings of the axes. For more, see the Plot settings for 3D
scatter and Onion 3D plots section later in this chapter.

Header
Click Header or Footer to customize the positioning and coloring. For more, see the
Plot settings for 3D scatter and Onion 3D plots section later in this chapter.

Regions
Use the Region style page to customize how the area outside the factor setup is
visualized. By default, this area is shaded white.

Labels
Click Labels to:
• Clear the Show label check box to hide the plot labels.
• Select the position of the plot labels in the Anchor box.
• Select the Connect with attach point check box when the label is separated
from the line (using Offset) and you want a line between the label and the
point.
• Customize the Text and Background color and Transparency of the plot
label.
• Select the Is visible check box under Border to display a border around each
label. Enter custom values in the Margin and Width fields.
• Click the Font tab to customize the font.

Contour
In Contour Level Colors in the Plot Settings page you can customize levels and
colors according to the below.
The default plot displays a number of contour levels. To display fewer or more contour
levels, type a new value in the Number of Levels box. In Individual level colors the
new number of levels will be displayed.

Note: To for instance display the contour levels for 10, 20, 30 …100 you need
to type Min=0 and Max=110 in Color level range, and in the Number of
Levels box type 10.

214
 Plots and lists

After Color range on the contour levels the color buttons, defining the color scale
used in the plot, are positioned.
To change from the default colors, click the respective buttons, and click the color to
use.
To change the color of one of the available levels under Individual level colors, mark
the level and click the Color button, and then click the new color.
To remove one of the available levels, mark it and click the Remove button.
You can also add levels by typing a value in the field under the Add button, and then
clicking the Add button.
Click the Contour Line Style tab to customize the contour line color, width, and
pattern.

Plot settings for sweet spot plots

To change the fonts on the labels, headers and footers, or the attributes of the axes,
double-click the labels or the axes, or right-click and click Plot Settings.
The Plot Settings dialog for the Sweet Spot Plot is very similar to the one for the
contour plots and 3D plots.

Axis
Click Axis to change settings of the axes. For more, see the Plot settings for 3D
scatter and Onion 3D plots section later in this chapter.

Header
Click Header or Footer to customize the positioning and coloring. For more, see the
Plot settings for 3D scatter and Onion 3D plots section later in this chapter.

Contour
In Contour Level Colors in the Plot Settings page you can customize the colors
according to the below.

215
User Guide to MODDE

The default plot displays up to 5 colors in the legend. These levels are by default
colored from blue to green where green represents the sweet spot.
To change the color of one of the available levels:
1. Under Individual level colors, mark the level and click the color button.
2. Then click the new color.
To change the range used, click the respective color buttons and click the new color.

Plot settings for 3D scatter plots

The plot settings described here are available for all 3D scatter plots created by
MODDE, both regular and Onion. In the plot settings dialog you can customize: the
cube the plot is displayed in, the axes, the header, footer, legend, plot symbols and plot
labels. Open plot settings by right-clicking the plot and selecting Plot Settings.

Cube
Click Cube to:
• Clear the Color cube sides check box to make the cube sides transparent.
When the Color cube sides check box is selected the sides are colored in the
color specified in Side color.
• Customize the Side color.
• Select/clear the Show gridlines and Gridlines on minor ticks check boxes
to show/hide the gridlines.
• Change the Line width, Pattern, and Line color to specify the properties of
the gridlines.

216
 Plots and lists

Axis
Click Axis to change settings of the axes. For each axis you can select:
• To display the annotation of the axis.
• The minimum and maximum values of the axis and the step size.
• To autoscale the axis.
• The axis title.
In the Axis General tab you can:
• Customize the axes color and size.
• Customize the annotations color and distance from the axis.
• Select/clear the Show axis arrows check box to display arrows/regular axes.
• Select the axis arrow color.
• Select the level of Transparency for the axes and annotation respectively.
• Adjust autoscaling properties.
In the Ticks tab you can:
• Customize the tick's direction and size for normal and minor ticks.
• Clear the Show ticks and Show minor ticks check boxes to hide the ticks.
In the Font tab you can select the font and size of the annotation and titles of the axes.

217
User Guide to MODDE

Header
Click Header to:
• Select/clear the Is visible check box under Header to show/hide the header.
• Select the position of the header in the Anchor box.
• Customize the Border and text color of the header.
• Customize the Background color of the header.
• Select/clear the Is visible check box under Border to show/hide the border.
• Customize the Margin and Width of the border.
In the Font tab you can select the font and size of the header.

Legend
Click Legend to:
• Select/clear the Show legend check box to show/hide the legend.
• Select the position of the legend in the Anchor box.
• Select the orientation of the legend in the Orientation box.
• Select the text adjustment of the legend in the Text adjust box.
• Customize Border and Text color and Background color of the legend.
• Select/clear the Is visible check box under Border to show/hide the border.
• Customize the Margin and Width of the border.

Footer
Click Footer to:
• Select/clear the Is visible check box under Footer to show/hide the footer.
• Select the position of the footer in the Anchor box.
• Customize the Border and text color of the footer.
• Customize the Background color of the footer.
• Select/clear the Is visible check box under Border to show/hide the border.
• Customize the Margin and Width of the border.
In the Font tab you can select the font and size of the footer.

218
 Plots and lists

Symbols
Click Symbols and the individual series to change the properties of the symbols. When
you mark the individual series you change the properties of that series only. When you
mark Symbols you change the properties of all series. In these pages you can
• Select the Shape of the symbol.
• Customize the Color of the symbol.
• Select the Size of the symbols.
• Select the Draw style of the symbol, where the choices are Fill, Wireframe,
and Point. Fill is the default.
• Select the Line style when the Draw style is Wireframe.

Labels
Click Labels to:
• Select/clear the Show label check box to show/hide the plot labels.
• Select the position of the plot labels in the Anchor box.
• Select the Connect with point check box when the labels are separated from
their position (using Offset) and you want a line between the label and the
point.
• Customize the Offset in X, Y, and Z space of the plot labels.
• Customize the Text color of the plot label.

Colors
Click Colors to:
• Change the Highlight Style displayed when hovering over a point. For more
about the content on this page, see the Symbols topic above.
• Change Marking Color for the marked points.

219
User Guide to MODDE

Zoom and rotate

Turn the 3D scatter plot or response surface plot by holding down the left mouse-
button and moving the mouse in the direction you want to turn the plot.
Zoom in or out in the plot by using the mouse wheel. To zoom in a regular plot, see the
Plot toolbar section in the View chapter.

220
Report generator

Introduction
MODDE has an automatic report generator. You start the report by clicking File |
Generate HTML Report. A dialog opens where you can select the MODDE default
template, or any other report as a template.
In the report generator, basic formatting functionality is available for writing text.
Plots, lists, and model results of MODDE can be added to the report at any time. These
items are added to the report as placeholders.
A placeholder stands in the place of contents which MODDE will provide, let it be a
plot, list or any text or number.
The placeholders enable you to use the same report, as a template, in different
investigations. You can then edit the text, and just click the Update Report button to
update all MODDE results from the current investigation.

Starting the report generator

To open the report generator, click File | Generate HTML Report or press CTRL+R.
The following window opens and you can select any template or report you want to
open.

If you have saved a report with the same name as the investigation, MODDE default
suggests opening that report.
When your investigation has not been fitted MODDE will ask to fit the investigation so
it can automatically fill all the placeholders. You can prevent this question if you select
under View | General Options, to automatically fit investigations when opened.

221
User Guide to MODDE

Report generator window

The Generate Report window contains:
• A command menu bar.
• A standard toolbar, named Generate Report, with commonly used
commands.
• A format report toolbar with commonly used formatting commands.
• A main window showing the report template.
• A placeholder window with a list of built-in placeholders.
• A Report Generator FAQ window with a short introduction how to use the
report generator.
• A Properties window where plot size and placeholder properties can be
edited.

Command menu bar

The command menu consists of the File, Edit, View, Insert, Format, Tools, and Help
menus.

File menu
On the File menu you find the general Windows commands New, Open, Save As,
Print Preview, Print and Exit. Additionally you find Continue Edit Report With,
Templates, and View in Browser.

222
 Report generator

General Windows commands

Click New to create a new report from the selected template or report.
Click Open to open a report saved in HTML format.
Click Save As to save the report in HTML format. The report is saved with
placeholders and can be used as templates.
Click Print to print the report. Click Print Preview to preview the report.
Click Exit to close the report.

Continue edit report with

You can continue to work with your report in the editor of your choice by clicking
Continue Edit Report With on the File menu, and then selecting the editor. The
applications listed here are the applications that have registered that they can edit
HTML text with Windows.
Continue Edit Report With is also available as a button on the Generate Report
toolbar.

Templates
You can save templates, restore templates and add or remove custom templates by
clicking Templates on the File menu.
Click:
• Save as Default Template when you have changed/created a template
according to your wishes and want to use it as the default template next time
you generate a report.
• Restore Default Templates if you have made changes to the default
templates and want to remove those changes.
• Save as Custom Template when you have changed/created a template
according to your wishes and want to save it to be able to use it again.
Custom templates will be listed in the “Select template or open existing”
dialog and when you click Insert | Template.
• Add / Remove Custom Templates when you want to add an already created
template or remove one of your custom templates.

View in browser
To view the current report in your default internet browser, on the File menu click
View in Browser. This works with Internet Explorer and Mozilla Firefox.

223
User Guide to MODDE

Edit menu
On the Edit menu you find the standard commands Undo (CTRL+Z), Redo, Copy
(CTRL+C), Paste (CTRL+V), Paste Unformatted (CTRL+SHIFT+V), Clear (press
the Delete key), Select All (CTRL+A), and Find (CTRL+F).

View menu
On the View menu you can select to hide or show the following:
• Generate Report toolbar opened/closed by clicking View | Toolbar |
Generate Report. For more, see the Generate report toolbar section later
in this chapter.
• Format toolbar opened/closed by clicking View | Toolbar | Format. For
more, see the Format toolbar section later in this chapter.
• Status bar which displays an explanation when you point to a button. To
show/hide it, click View | Status Bar.
• Placeholders window which displays the placeholders that can be added to
the report. For more see the Placeholders window section.
• Properties window. The properties of plots and images can be customized in
the Properties window. To display the window click Properties. For more
see the Properties window section.
• Click Customize to customize toolbars and menus as in Office 2003 and
later. Find a short introduction in the Customize section in the View chapter.
Insert menu
Use the Insert menu to insert a Hyperlink, Image, File, or Template in the current
report. Here you also can toggle the Grab Plot or List mode explained below.

Hyperlink
To insert a hyperlink, select text in the report and then click View | Hyperlink, also
available by right-clicking the report and clicking Insert Hyperlink. In the dialog that
opens, enter the address of your hyperlink the URL field.

Image
Click View | Image to insert a picture in the report. Also available by right-clicking the
report and clicking Insert Image.
Click the Browse button to find your file.

File
Select View | File to insert a Web page file (*.htm, *.html), a Text file (*.txt), or a
picture file (*.jpg, *.png, *.gif, *.bmp.)

Template
Clicking View | Template opens a dialog where you can select a custom template to
insert in the report. Templates must first have been added using File | Templates |
Save as Custom Template.

224
 Report generator

Grab Plot or List

Click Insert | Grab Plot or List to toggle the Grab Plot or list mode. When selected,
you can insert a plot or list from the MODDE window into your report. When you
display a plot or list, a hand appears in the MODDE window. Click it and the plot or
list is inserted at the insertion point into your report.
When done click the menu again to deactivate the Grab mode.

Format menu
On the Format menu you can customize Font and Styles and Formatting.

Tools menu
On the Tools menu, find the commands Update Report, Update Placeholder, Show
All Placeholders, Show Placeholder, Remove All Placeholders, and Remove
Placeholder.

Update Report
Click Update Report to update all placeholders with the plots and lists of the current
investigation.

Update Placeholder
Click Update Placeholder to update the marked placeholder.

Show all Placeholders

Click Show All Placeholders to show the underlying placeholders.

Show Placeholder
Click Show Placeholder to show the underlying placeholder of marked plot, list, or
item.

Remove all Placeholders

Click Remove All Placeholders when you do not want any items, plots, or lists to be
updated.

Remove Placeholder
Click Remove Placeholder when you do not want a certain item, plot, or list to be
updated. Remove Placeholder is also available as a button on the Generate Report
toolbar.

225
User Guide to MODDE

Help menu
To access the FAQ of the report generator, click Welcome Page and FAQ on the
Help menu.

Generate report toolbar

The Generate Report toolbar by default includes the standard command buttons New,
Open, Save, Cut, Copy, Paste, and Undo, and additionally the specific command
buttons Update Placeholders, Remove all Placeholders, Grab Plot or List, and
Continue Edit With. The standard command buttons work according to Windows
standard except for the New command.

New
Click the arrow next to the New button and the following commands are displayed.

• Click New on the menu displays the generate report dialog from which you
can select which report/template to use or to open an existing
report/template.
• Click New Blank Report to start a new report with no text.
• Click New From Default Template if you have created a template that you
have saved as default template. Save a report as a default template by
clicking Templates on the File menu and then clicking Save as Default
Template. Umetrics’ default template is used if no other template has been
specified.

Generate report specific buttons

The Generate Report toolbar additionally includes Update Placeholders, Remove all
Placeholders, Grab Plot or List, and Continue Edit With.

For more on the Placeholder buttons see the Tools menu section.
For more on the Grab Plot or List button see the Insert menu section.
For more on the Continue Edit With button see the File menu section.

Format toolbar
The Format toolbar is the standard toolbar for formatting text with three additional

buttons: Insert Hyperlink and Insert Image , and View in Browser .

For more, see the Insert menu and File menu sections in this chapter.

226
 Report generator

Placeholder window
Open the Placeholder dockable window by clicking View | Placeholders.

The combo box lists different categories of placeholders.

To insert a placeholder in the report, mark the placeholder and click Insert. To update
the inserted placeholder, click the placeholder then on the Tools menu click Update
Placeholder. You can also click the Update Report button on the Generate report
toolbar to update all placeholders in the report.
Click Show Placeholders to show the underlying placeholders.

227
User Guide to MODDE

Properties window
Open the Properties dockable window by clicking View | Properties.

In the Properties window you can change the default plot size and to save a plot as
.png, .bmp, or .jpg.
Properties for placeholders are displayed when you click the placeholder. You can
change the properties of the placeholder in the Data field in the properties window.
Click the Data field to view a description on how you can change the properties of the
current placeholder.

Adding plots and lists to the report

To add a plot or list to the report, click the desired position in the report, and then
right-click the plot or list in MODDE and click Add to Report.

228
Help

Introduction
MODDE’s help is based on this user guide. The user guide documents are transferred
in to a compiled HTML file. To read the Help file Internet Explorer version 4.0 or
higher must be installed but does not need to be your default browser.

HTML help
The HTML help file is installed to include interactive help and stand alone where the
program is installed.
Open the help by:
• Clicking Contents and Index from the Help menu.

• Clicking the Help-button in one of the dialogs or wizards.

• Clicking MODDE Help from the Program menu.
• Pressing F1 opens the context sensitive help.
Use the Contents, Index, or Search tabs to find what you are looking for.
Additionally, the Analysis Advisor is available to guide you through the analysis. For
more on the Analysis Advisor see that section in the View chapter.

Registration and activation

To register and activate, follow the instructions delivered with the delivery letter.
If you choose to register later, click Register on the Help menu and follow the
instructions.

Manage Licenses
If your company has a license server that handles you licenses, follow the instructions
delivered with the delivery letter.
If you choose to activate later, click Manage Licenses on the Help menu and then
follow the instructions delivered with the delivery letter.

229
User Guide to MODDE

Umetrics on the Web

If you have an Internet connection, you can visit the web page of MKS Umetrics
(www.umetrics.com) to get the latest news and other information by clicking Umetrics
on the Web from the Help menu.

About MODDE
To find the version number of MODDE, on the Help menu, click About MODDE.

230
Appendix A: Statistical notes

Fit methods
MODDE supports Multiple Linear Regression (MLR) and PLS (Projection to Latent
Structures) for fitting the model to the data.

Multiple Linear Regression (MLR)

Multiple linear regression is extensively described in the literature, and this chapter
will only identify the numerical algorithms used to compute the regression results, the
measures of goodness of fit and diagnostics used by MODDE. For additional
information on MLR, see Draper and Smith “Applied Regression Analysis”, Second
Edition, Wiley, New York.
MODDE uses the singular value decomposition (SVD) to solve the system of
equations:
Y = XB+E
where
Y is an n*m matrix of responses.
X (the extended design matrix) is an n*p matrix, with p the number of terms in the
model including the constant.
B is the matrix of regression coefficients.
E is the matrix of residuals.
See Golub and Van Loan (1983) for a description of the SVD and its use to obtain the
regression results.
In case of missing data in a row, this row is excluded for the relevant response only
before the MLR fitting.

231
User Guide to MODDE

Partial Least Squares (PLS)

When several responses have been measured, it is useful to fit a model simultaneously
representing the variation of all the responses to the variation of the factors. PLS deals
with many responses simultaneously, taking their covariance's into account. This
provides an overview of the relationship between the responses and of how all the
factors affect all the responses. This multivariate method of estimating the models for
all the responses simultaneously is called PLS.
PLS contains the multiple regression solution as a special case, i.e. with one
response and a certain number of PLS dimensions, the PLS regression coefficients are
identical to those obtained by multiple regression.

Note: When the models for the responses are different, PLS fits each response
separately.
PLS has been extensively described in the literature and only a brief description is
given here.
PLS finds the relationship between a matrix Y (response variables) and a matrix X
(predictor or factor variables) expressed as:
Y = XB+E
The matrix Y refers to the characteristics of interest (responses). The matrix X refers to
the predictor variables and to their square or/and cross terms if these have been added
to the model.
PLS creates new variables (ta) called X-scores as weighted combinations of the original
X-variables: ta = Xwa, where wa is the combinations weights. These X-scores are few,
often just two or three, and orthogonal (independent). The X-scores are then used to
model the responses.
With several responses, the Y-variables are similarly combined to a few Y-scores (ua)
using weights ca, ua = Yca. The PLS estimations are done in such a way that it
maximizes the correlation, in each model dimension, between ta and ua, One PLS
component (number a) consists of one vector of X-scores (ta), and one of Y-scores (ua),
together with the X and Y-weights (wa and ca).
Hence the PLS model consists of a simultaneous projection of both the X and Y spaces
on a low dimensional hyper plane with new coordinates T (summarizing X) and U
(summarizing Y), and then relating U to T. This analysis has the following two
objectives:
• To well approximate the X and Y spaces by the hyper-planes
• To maximize the correlation between X and Y (u and t).
Mathematically the PLS model can be expressed as:
X = TP' + E
Y = TC' + E

232
 Appendix A: Statistical notes

Geometrically, we can see the matrices X and Y as n points in two spaces, (see figure),
the X-space with p axes, and the Y-space with m axes, p and m being the number of
columns in X (terms in the model) and in Y (responses).

X3 Y3
t1
u2
t2
u1
X2 Y
2

X1 Y1

t1

u
1

The model dimensionally, (number of significant PLS components), is determined by

cross validation (CV), where PRESS (see below) is computed for each model
dimension. One selects the number of PLS dimensions that give the smallest PRESS.

Model predictive power

The predictive power of an MLR or a PLS model is given by Q2, which is based on the
Prediction Residual Sum of Squares, PRESS. This is a measure of how well the model
will predict the responses for new experimental conditions. The computations are
repeated several times with, each time, different observations kept out of the
calculation of the model. PRESS is then computed as the squared difference between
observed Y and predicted Y when the observations (rows in the tables X and Y) were
kept out from the model estimation. Q2 is computed as:
Q2 = (SS - PRESS)/SS
Here SS = sum of squares of Y corrected for the mean. A Q2 larger than zero indicates
that the component is significant (predictive). An overall Q2 is computed for all PLS
components, for all the responses and for each individual response, and represent the
percent variation of Y that is predictive. Large Q2, 0.7 or larger, indicates that the
model has good predictive ability and will have small prediction errors. Q2 is the
predictive measure corresponding to the measure of fit, R2, (the percent variation of the
response explained by the model).
R2 = (SS - SS resid )/ SS
Q2 gives a lower estimate to how well the model predicts the outcome of new
experiments, while R2 gives an upper estimate.

233
User Guide to MODDE

Automatic cross-validation significance rules

A PLS component is cross-validated if:
Rule 1: PRESS for all Y's together < 1.2
or
Rule 2: PRESS for at least M1/2 Y's < 1.2
and
Rule 3: SS explained for all Y' s together > 1%
or
Rule 4: SS explained for all separate Y's > 2%
MODDE computes a minimum of two PLS components (if they exist), even if not
significant.

MLR solution derived from PLS

Because PLS contains multiple regression as a special case, you can with PLS derive
the same solution as when you fit the Cox model with Multiple Regression. When you
extract as many PLS components as available you get the same solution as MLR.
With MODDE you do the following:
• First fit the model. MODDE extracts only the significant PLS components.
This is the PLS solution.
• Then click Next Component menu and continue extracting PLS components
until no correlation between X and Y remains. This is the MLR solution.

Model
You may edit the model and add or delete terms for individual responses. You may add
up to third order terms (cubic terms, or 3 factors interaction).
If your design is singular with respect to your model, MODDE will fit the model with
PLS, and MLR will not be available.

Hierarchy
MODDE enforces hierarchy of the model terms. You cannot delete the constant term.
You can only delete a linear term if no higher order term containing the factor is still in
the model.

234
 Appendix A: Statistical notes

Scaling
Scaling X
When fitting the model with multiple linear regression, the design matrix X is scaled
and centered as specified in the factor definition box: MLR scaling. If the choice is not
orthogonal, the condition number will differ from the one displayed when clicking
Analysis | Evaluate.
When fitting the model with PLS the X matrix is always scaled to unit variance.
If warranted, the scaled X matrix is extended with squares and / or cross terms
according to the selected model.
The choices of scaling are:
(x denotes the original factor value and z the scaled one)
Orthogonal scaling:
zi = (xi - M)/R
Where M = Mid-range, R = Range/2.
Mid-range scaling:
zi = (xi - M)
Unit variance scaling:
zi = (xi - M)/s
Where m = average, s = standard deviation computed from the worksheet.
Note that Orthogonal and Mid-range scaling are only available with MLR.
MODDE default scaling for MLR is the orthogonal scaling.

Scaling Y
The matrix of responses Y, when fitting the model with PLS, is by default scaled to
unit variance. You can modify the unit variance scaling weight by using the PLS
scaling box in the factor definition. With MLR the Y's are not scaled.

235
User Guide to MODDE

Condition number
The condition number of the orthogonally scaled and centered extended design matrix
using the SVD (Singular value decomposition) is computed when clicking Evaluate on
the Analysis menu. The X matrix is taken from the worksheet. The calculation depends
on fit method (MLR, PLS) and which factors are involved.

Condition number definition

The condition number is the ratio of the largest and the smallest singular values of X
(eigenvalues of X'X). This condition number represents a measure of the sphericity of
the design (orthogonality). All factorial designs, without center points have a condition
number of 1 and the design points are situated on the surface of a sphere.
The condition number is calculated for the extended design matrix (X). The extended
design matrix is created as follows:
1. The factor values, taken from the worksheet, are centered and scaled
according to the factor definition box, MLR scaling. With PLS the condition
number is calculated with factors scaled to unit variance.
2. The design matrix is then extended according to the selected model and the
condition number is computed.
If you select Mid-range scaling, and your factors have different ranges, the
condition number of the worksheet becomes very large. This is only a numerical
artifact, but due to the fact that MODDE uses the SVD with MLR, the model
should be fitted with PLS.

Note: If you selected a different scaling than orthogonal, the condition

number will be different than the one computed in Analysis | Evaluate. In
particular if you select Mid-range scaling and your factors have different
ranges, the condition number of the worksheet becomes very large. When
fitting the model with PLS, the condition number refers to the X matrix, with
unit variance coding.

Condition number with mixture factors

The condition number with mixture data depends on the method of fit and the type of
model.

PLS and Cox reference mixture model

When the method of fit is PLS (Cox model) the data are scaled and centered. The
condition number is computed from the worksheet, with the slack variable model
(mixture factor with the largest variance removed) and all mixture factors scaled
orthogonal.

MLR (regression) and the Cox model

The condition number displayed is the condition number of the Cox model (with the
Cox constraints), derived from the worksheet, with all mixture factors unscaled and
uncentered.

236
 Appendix A: Statistical notes

MLR (regression) and Scheffé model

The condition number of the Scheffé model, derived from the worksheet, with all
mixture factors unscaled and uncentered.

Note: With formulation factors and fitting with PLS, the condition number is
computed by excluding the factor with the largest range, and scaling the
remaining ones orthogonal. When fitting with MLR the condition number is
computed without centering and scaling the factors.

Missing data
Missing data in X
Missing data in X are not allowed, and will disable the fit. This does not apply to
uncontrolled X-variables. For MLR experiments with missing in an uncontrolled factor
results in excluding that row in the calculations while PLS can handle this.

Missing data in Y with Multiple Linear Regression

When fitting with MLR, each row with missing data in Y is excluded for that specific
response. Hence N, displayed on plots and lists is the number of observations
(experiments) without missing data.

Missing data in Y with PLS

With PLS, missing data are handled differently when the model for all responses is the
same. When all Y values are missing in a row, that row is excluded from the analysis.
When there are some “present” Y-data in a row, the row is NOT excluded, but
included in the projection estimation in PLS. This leads, however, to minor differences
in the displayed N and DF at the bottom of plots and lists.
When the responses have different models, missing is handled as for MLR, see above.

N-value
The N-value used in ANOVA, and for the computation of R2 adjusted, is the actual
number of non-missing observations (experiments) for each response-column. This N-
value and DF = N-p are displayed at the bottom of the ANOVA plots and lists, and on
all residual plots, including observed vs. predicted Y.

Residual Standard Deviation (RSD)

For PLS with the same model for all responses, the residual standard deviation RSD,
displayed in the summary table and at the bottom of all plots and lists including
ANOVA, is computed using the total number of observations (experiments) without
excluding the missing values.
For MLR and PLS with different models, RSD is calculated using the actual number of
non-missing experiments for each response.
This is the RSD used in the computation of confidence interval, for coefficients and
predictions.

237
User Guide to MODDE

ANOVA
The analysis of variance (ANOVA) partitions the total variation of a selected response
SS (Sum of Squares corrected for the mean) into a part due to the regression model and
a part due to the residuals.
SS = SSregr + SSresid
If there are replicated observations (experiments), the residual sum of squares is further
partitioned into pure error SSpe and Lack of fit SSlof.
SSresid = SSpe + SSlof
DFresid = (n - p)
SSpe = ∑ ( eki - ek )2
DFpe = ∑ ( nk - 1 )2
DFlof = n - p - ∑ ( nk - 1 )2
1. where the ∑ loops over ki resp k.
2. n = number of experimental runs (excluding missing values)
3. nk = number of replicates in the kth set
4. p = number of terms in the model, including the constant
5. ek = average of the nk residuals in the kth set of replicates
6. j = jth residual in the kth set of replicates
A goodness of fit test is performed by comparing the MS (mean square) of lack of fit to
the MS of pure error:
Two ANOVA plots are displayed:
1. The regression goodness of fit test
2. The LoF goodness of fit test

Checking for replicates

MODDE checks the rows of the worksheet for replicates. Rows in the worksheet are
considered replicates if they match all factor values plus or minus a tolerance which is
by default 10% but can be altered in View | General Options.

238
 Appendix A: Statistical notes

Measures of goodness of fit

MODDE computes and displays the following:

Q2
Q2 = (SS - PRESS)/SS
with

(Yi − Y$i )2
PRESS = ∑ 2
i (1 − hi )
where hi is the ith diagonal element of the hat matrix:
X(X'X)-1X'

R2
R2 = (SS - SSresid)/SS
R2 adj = (MS - MSresid)/MS
MS = SS / (n - 1)
MSresid = SSresid / (n - p)
RSD = Residual Standard Deviation = √MSEresid

Degrees of freedom
MODDE always computes the real degrees of freedom RDF of the residuals:
RDF = n - p - ∑( ni - 1 )
where the ∑ loops over i
n = number of experimental runs
ni = number of replicates in the ith set
p = number of terms in the model, including the constant

Saturated models
When RDF = 0 the model is saturated, and MODDE does not compute or display R2,
R2 Adjusted or Q2 when fitting the model with MLR. With PLS, only Q2 is computed
and displayed.

Singular models
Singular models (condition number > 3000) are only fitted with PLS.
If p > n - ∑( n i - 1 ) , the degrees of freedom of the residuals are computed as:

DFresid = 0, with no replicates in the design

DFresid =∑ (n i - 1), with replicates in the design

239
User Guide to MODDE

Coefficients
Scaled and centered coefficients
The regression coefficients computed and displayed by MODDE refer to the centered
and scaled data. You may also select to display the “unscaled and uncentered”
coefficients.

Normalized coefficients
In the overview plot, to make the coefficients comparable between responses, the
“centered and scaled” coefficients are normalized with respect to the variation of Y.
That is, they are divided by the standard deviation of their respective Y's.

PLS orthogonal coefficients

The “centered and scaled” coefficients of PLS refer to factor values scaled to unit
variance.
The PLS orthogonal coefficients re-express the coefficients to correspond to factors
centered and orthogonally scaled, i.e. using the Mid-range and Low and High values
from the factor definition.
For matrices with condition number < 3000, MLR and PLS compute confidence
intervals on coefficients as:
-1
√((X’X) ) * RSD * t(α/2, DFresid)
For matrices with condition number > 3000, PLS does not compute confidence
intervals on the coefficients.

Confidence intervals
Confidence intervals of coefficients and predictions are computed using the total
number of observations, regardless of missing values for PLS models with identical
models for all responses. For MLR and PLS with different model for the responses, the
total number of observations is the number of non-missing values per response. This
total number of observations is displayed as N at the bottom of all other plots and lists.
The approximation for PLS with identical models is possible because the confidence
intervals computed with the regression formulas are somewhat too large because the
PLS solution is a shrunk estimator with smaller prediction errors than those of
regression. Hence a small number of missing elements in Y does not make the PLS
confidence intervals larger than those computed with the regression formulas and the
total number of observations.

240
 Appendix A: Statistical notes

Coding qualitative factors at more than 2 levels

If a term in the model comprises a qualitative factor, C, at k levels, there will be k-1
expanded terms associated with that term. For example, if the levels of the qualitative
factor C are (a, b, c, d) the three expanded terms C(j) are as follows:
C C(2) C(3) C(4)

a -1 -1 -1

b 1 0 0

c 0 1 0

d 0 0 1

The coefficients of these expanded terms are given as the coefficients for level 2 (b), 3
(c), and 4 (d) of C, while the coefficient for level 1 (a) is computed as the negative sum
of the three others. MODDE displays all the four coefficients in the coefficient table
but notes that they are associated with only three degrees of freedom.

Residuals
Raw residuals
The raw residual is the difference between the observed and the fitted (predicted) value
ei = Y i – Ŷ i
The raw residuals are displayed in the residual lists.

Standardized residuals
The standardized residual is the raw residual divided by the residual standard deviation
ei / s (s = RSD)
These are MODDE default for PLS Residual plots.

Deleted studentized residuals

With MLR, for models with 2 (required) or more degrees of freedom, deleted
studentized residuals are MODDE default when plotting residuals.
Deleted studentized residuals are not available with PLS.
The deleted studentized residual is the raw residual ei divided by its “deleted” standard
deviation (si) which is the residual standard deviation (si) computed with observation
(i) left out of the analysis, and corrected for leverage, i.e.:
ei = ei /(si √(1 - hi))
where
si = is an estimate of the residual standard deviation with observation i left out of the
model
hi is the ith diagonal element of the hat matrix: X(X'X)-1X'
For more information see Belsley, Kuh, and Welsch (1980).

241
User Guide to MODDE

Predictions
For X matrices with condition number < 3000, both MLR and PLS computes a
confidence interval for the average predicted y:
Yi + √hi * RSD * t(α / 2, DFresid)
hi is the ith diagonal element of the hat matrix: X(X'X)-1X'
For X matrices with condition number > 3000 and for all Cox mixture models, PLS
computes only the standard error of the average predicted Y:
SE(Y) = √[(1 / N) + t'0 * (T'T)-1* t'0] * RSD

PLS plots
Both scores and loading plots are available:

Plot loadings
WC plots (PLS)
Plots of the X- and Y-weights (w and c) of one PLS dimension against another, say,
no.'s 1 and 2, show how the X-variables influence the Y-variables, and the
correlation structure between X's and Y's. In particular one better understands how the
responses vary their relation to each other and which ones provide similar information.

Plot scores
TT, UU, and TU plots (PLS)
The tt and uu plots, of the X- and Y-scores of, say, dimensions 1 and 2 (i.e. t1 vs. t2, and
u1 vs. u2), can be interpreted as windows into the X- and Y-spaces, respectively,
showing how the design points (experimental conditions, X) and responses profile (Y)
are situated with respect to each other. These plots show the possible presence of
outliers, groups, and other patterns in the data.
The tu plots (t1 vs. u1, t2 vs. u2, etc.) show the relation between X and Y, and display the
degree of fit (good fit corresponds to small scatter around the straight line), indications
of curvature, and outliers.

PLS coefficients
PLS computes regression coefficients (Bm) for each response Ym expressed as a
function of the X's according to the assumed model (i.e. linear, linear plus interactions
or quadratic,). These coefficients are (columns of B) computed as:
B = W(P'W)-1 C'
W and C are (p*A) and (m*A) matrices whose columns are the vectors wa and ca.
p = number of terms in the model
m = number of responses
A = Number of PLS components

242
 Appendix A: Statistical notes

Box-Cox plot (only MLR)

A useful family of transformation on the necessarily positive Y's is given by the power
transformation:
For not equal to zero Z = Yλ
For equal to zero Z = lnY
MODDE computes Lmax, for values of between -2 and 2, and plots it against the values
of λ with a 95% confidence interval.
Lmax (λ) = ½ ln(SSresid / n) + (λ - 1)* ∑ lnY
SSresid is the Residual Sum of Squares after fitting the model Z = X * β + e for the
selected value of λ.
The value of λ that maximizes Lmax(λ) is the maximum likelihood estimator of λ.
The Box-Cox plot displays the values of lambda, λ, vs. the maximum likelihood.
The system uses your data to compute the best mathematical transformation of the
response to achieve:
• A simple and parsimonious model
• An approximately constant model error variance
• An approximately normal model error distribution.
If the response values vary more than a magnitude of ten in the experimental domain, a
transformation is often recommended.
The maximum point on the Box-Cox plot gives the value of (lambda, λ) for the
response transformation Y that gives the best fit of the model. This is the maximum
likelihood estimator for λ.
For more information see Draper and Smith “Applied Regression Analysis, Second
Edition” Wiley, New York or Box and Draper Response Surface Modeling.
The Box-Cox plot is not available for PLS.

Mixture data in MODDE

Mixture factors only
Model forms
When the investigation includes mixture factors only there are three model types
available: Slack variable model, Cox reference model, and Scheffé model.
Slack variable model
When you define a mixture factor as filler, MODDE generates the slack variable model
by omitting the filler factor from the model. The model is generated according to the
selected objective and is treated as a non-mixture model. You may select MLR or
PLS to fit the model as with ordinary process factors. With MLR the factors will be
orthogonally scaled.

243
User Guide to MODDE

Cox reference model

When all mixture factors are formulation factors, MODDE generates, by default, the
Cox reference model, and i.e. the complete polynomial model linear or quadratic.
MODDE supports also a special cubic and a full cubic model (see section Objective,
model and design).
Scheffé model
You may select to fit a Scheffé model, by selecting Scheffé MLR as fit method on the
Analysis | Select Fit Method menu. MODDE expresses the mixture model in the
Scheffé form. The full cubic model is not supported as a Scheffé model.

Analysis and fit method

In MODDE, the default fit method with mixture factors is PLS, and the model form is
the Cox reference mixture model. All factors, including mixture factors are scaled to
unit variance, by default, prior to fitting. This is also done with mixture factors that
have been transformed to pseudo components.
Cox reference model
The Cox reference model can be fitted by MLR (when obeying mixture hierarchy) and
in all cases by PLS.
The coefficients in the Cox model are meaningful and easy to interpret. They represent
the change in the response when going from a standard reference mixture (with
coordinates sk) to the vertex k of the simplex. In other words when component xk
changes by Δk, the change in the response is proportional to bk. Terms of second or
higher degree are interpreted as with regular process variable models. The presence of
square terms, though they are not independent, facilitates the interpretation of quadratic
behavior, or departure from non-linear blending. The constant term is the value of the
response at the standard reference mixture.
• Changing the Standard Reference Mixture.
Click Model / Reference Mixture on the Edit menu to change the
coordinates sk of the standard reference mixture. By default MODDE selects
as reference mixture the centroid of the constrained region.
• Mixture Hierarchy with the Cox reference model.
By default all Cox reference models, linear and quadratic, obey “mixture
hierarchy”. That is the group of terms constrained by:
Σbksk = 0
Σckjbkjsk = 0 for k = 1,,,,q (1) and for j = 1,,,,q
(ckj = 1 when j ≠ k and ckj = 2 when k = j.)
are treated as a unit, and terms cannot be removed individually.
If you want to remove terms individually, as with regular process models, clear the
Enforce the mixture model hierarchy check box in the Edit | Model / Reference
Mixture dialog. When the mixture hierarchy is not enforced (this includes cubic
models), the Cox reference model can only be fitted by PLS. The coefficients are the
regular PLS coefficients computed from the projection and not re-expressed relative to
a stated standard reference mixture. Note that in all cases model hierarchy is enforced a
term cannot be removed, if a higher order term containing that factor is still in the
model.

244
 Appendix A: Statistical notes

ANOVA with the Cox model

In the ANOVA table, the degrees of freedom for regression are the real degrees of
freedom, taking into account the mixture constraint. These are the same as for the
equivalent slack variable model.
Screening plots
When the objective is to find the component effects on the response, the coefficients of
the Cox reference linear model are directly proportional to the Cox effects. The Cox
effect is the change in the response when component k varies from 0 to 1 along the
Cox axis. That is the axis joining the reference point to the kth vertex.
Effect plot
The effect plot displays the adjusted Cox effects. The adjusted effect of component k
is:

k = rk*tk
rk = Uk - Lk
tk = bk/(T-sk)
where:
rk is the range of factor k
tk is the total Cox effect
T is the mixture total. In most cases T=1.
bk is the unscaled uncentered coefficient
sk is the value of the factor at the reference mixture
The Effect Plot is only available for screening designs using the Cox model.
Main effect plot
For a selected mixture factor Xk, this plot displays the predicted change in the response
when Xk varies from its low to its high level, adjusted for all other mixture factors, that
is, by default, the relative amounts of all other mixture factors are kept in the same
proportion as in the standard reference mixture (MODDE does not check if the other
mixture factors are kept within their ranges).
For example, if the Main effect of the mixture factor X1 is being displayed, when X1
takes the value x1, the other mixture factors are assigned the values: xj = (T - x1)* (sj /
T - s1).
Sk are the coordinates of the standard reference mixture. The standard reference
mixture is the one used in the model.
You can change this default and select to have all other mixture factors kept in the
same proportion as their ranges (this ensures no extrapolation).
Interaction Plot
Interaction plot is not available when you only have mixture factors.

MLR and the Cox reference model

In MODDE you can fit Cox reference mixture models (linear or quadratic) with MLR,
only when they obey mixture hierarchy. When fitting the model with MLR the mixture
factors are not scaled and are only transformed to pseudo components when the region
is regular. The model is fitted by imposing the following constraints on the
coefficients:

245
User Guide to MODDE

Linear models
Σbksk = 0 (1)
Quadratic models
Σbksk = 0 (1)
Σckjbkjsk = 0 for k = 1,,,,q (1) and for j = 1,,,,q (2)
Here ckj = 1 when j ≠ k and ckj = 2 when k = j.
and sk are the coordinates of the standard reference mixture.

PLS and the Cox reference mixture

With PLS the standard reference mixture is not stated a priori as with multiple linear
regression, and no constraints on the coefficients are explicitly imposed. PLS fits the
mixture models, and deals with all collinearities by projecting on a lower dimensional
subspace. The PLS coefficients can be interpreted as in the Cox model, relative to a
reference mixture resulting from the projection, but not explicitly stated.
Expressing PLS coefficients relative to an explicit standard reference
mixture
With linear and quadratic models obeying hierarchy, it is easy to re-express the PLS
coefficients relative to a stated reference mixture with coordinates sk. (sk expressed in
pseudo component, if pseudo component transformation was used)
On the fitted PLS model one imposes the following constraints, on the uncentered,
unscaled coefficients (See Cox).
Linear models
Σbksk = 0 (1)
Quadratic models
Σbksk = 0 (1)
Σckjbkjsk = 0 for k = 1,,,,q (1) and for j = 1,,,,q (2)
Here ckj = 1 when j ≠ k and ckj = 2 when k = j.
The scaled and centered coefficients are recomputed afterwards.

Note: In MODDE, with linear and quadratic models obeying the mixture
hierarchy, (i.e. terms constrained by (1) or (2) can only be removed as a
group, and not individually), by default the PLS coefficients are always
expressed relative to a stated standard reference mixture.
With models containing terms of the third order (cubic), or disobeying mixture
hierarchy, no constraints are imposed on the PLS coefficients. The coefficients are in
this case, the regular PLS coefficients and the reference mixture is implicit and results
from the projection.

Scheffé models derived from the Cox model

With the linear or quadratic Cox reference model, one can re-express the unscaled
coefficients as those of a Scheffé model. The following relationship holds:
Linear
Scheffé‚ bk = Cox (PLS) b0 + bk

246
 Appendix A: Statistical notes

Quadratic
Scheffé‚ bk = Cox (PLS) b0 + bk + bkk
Scheffé‚ bkj = Cox (PLS) bkj - bkk - bjj

Scheffé models
The Scheffé models are only fitted with MLR and only the main effect plot is
available.
Scheffé models are only available for investigation with all mixture factors.
ANOVA
As described by Snee in “Test Statistics for Mixture Models” (Technometrics, Nov.
1974), the degrees of freedom in the ANOVA table are computed in the same way as
with the slack variable model.

Using the model

Prediction plot
This plot is available for all objectives and all model forms. As with process
factors, this plot displays a spline representing the variation of the fitted function, when
the selected mixture factor varies over its range, adjusted for the other factors. As with
the main effect plot, this means that the relative amounts of all other mixture factors
are kept in the same proportion as in the standard reference mixture. If no standard
reference mixture is specified, the centroid of the constrained region is used as default.
Mixture contour plot
Trilinear contour plots are available with mixture factors but no response surface plots.

Process and mixture factors

When you have both process and mixture factors, you can select to treat them as one
model, or to specify separate models for the mixture factors, and the process factors.
With both mixture and process factors, the only model form available is the Cox
reference mixture model.
When the model obeys mixture hierarchy, the PLS coefficients are expressed relative
to a stated standard reference mixture. The following constraints are imposed on the
coefficients:

For linear models

Σbksk = 0

For quadratic models

Σbksk = 0 (1)
Σckjbkjsk = 0 for k = 1,,,,q (1) and for j = 1,,,,q (2)
Here ckj = 1 when j ≠ k and ckj = 2 when k = j.
If γ (gamma) are the coefficients of the interactions between the process and mixture
factors:
Σγksk = 0

247
User Guide to MODDE

Note: When the model contains terms of order 3, or contains qualitative and
formulation factors, the PLS coefficients are not adjusted relative to a stated
standard mixture.

MODDE plots
All MODDE plots are available when you have both mixture and process factors. For
both the Main Effect and prediction plots, when you select to vary a process factor, all
of the mixture factors are set to the values of the standard reference mixture. When you
select to vary a mixture factor, process factors are set on their average and the other
mixture factors are kept in the same proportion as in the standard reference mixture or
their ranges.

Optimizer
The Optimizer uses a Nelder Mead simplex method with the fitted response functions,
to optimize an overall desirability function combining the individual desirability of
each response.
For details on how to use the Optimizer, see the Appendix C: Optimizer chapter.

Desirability
For every response y, the desirability function is computed as follows:
f(g(y)) = 100*(e^(λ*g(y)) - 1)
where g(y) = 100*((y -P)/(T - P))
T, L and P are defined as follows:
T = User desired Target
L = User defined worst acceptable response value(s)
P = Worst response value computed from the starting simplex. P is never closer to the
Target than the L(s).
When the response is to be maximized, L is the smallest acceptable value, when the
response is to be minimized L is the largest acceptable value. When the response is to
be on Target, the user gives the smallest and largest acceptable values.
When the response is to be minimized, we must have T < L and when the response is
to be maximized we must have T > L.
For responses to be on target the user must supply lower and upper limits such as
L(lower) < T < L(upper)
L is generated internally when not supplied by the user.
λ is a scaling parameter computed as follows:
⎡ 100 ⎤
ln ⎢
(100 − Limit ) ⎥⎦
λ=− ⎣ ( L − P)
100
(T − P)

248
 Appendix A: Statistical notes

Where Limit = 90 + 80*Log10(w), and w = the weight (importance) assigned to each

response by the user. The weight w is a number between 0.1 and 1 (default value). W
effects the shape of the desirability function f(g(y)). For more information about the
effects see Appendix C: Optimizer.
This definition of λ makes f(g(y)) = - (Limit) when y = L and gives the exponential
function f(g(y)) the theoretical range: 0 to -100 (this latter limit can only be reached
asymptotically when y gets close to Target).
When the user wants the response to be on target, L(upper) is used in the calculation of
λ when
y > T and L(lower) is used in the calculation when y < T.

Overall desirability
The overall desirability f(ds) is a weighted average of the individual desirability
function. The weights, denoted w, are the user entered weights between 0.1 and 1,
reflecting the relative importance of the responses.

Overall Distance to Target

The “Overall distance to Target”, D, is computed as follows:

⎡ ⎛ yi − T ⎞ ⎤
2

⎢ ∑ wi ⎜ ⎟ ⎥
⎢ ⎝ T − L⎠ ⎥
D = log 10
⎢ M ⎥
⎢ ⎥
⎣ ⎦
M = number of responses.
D = -10 when all responses have reached T.
D is not used in the optimization but is displayed as Log(D) in the run list.

Starting simplexes
The optimizer starts 8 simplexes from 8 starting runs selected as follows:
• The first four are from the corners of a 23-1 design in the factors with the
largest coefficients for the first response.
• The fifth is the overall center point.
• The last three are the 3 “best” runs from the worksheet considering only the
first response and the predicted values.
Duplicated start points will not be shown.
The user can modify these runs or add own.
Each simplex is generated from the starting run by adding an additional run for each
factor with an offset of 20% of the distance from the center to the maximum value, the
other factors being kept at the same values. A check is made that all runs are within the
defined experimental region.

249
User Guide to MODDE

Sensitivity Analysis
Sensitivity Analysis is an estimate of how sensitive the proposed factor settings are to
small disturbances. The sensitivity analysis is done with Monte Carlo simulations
(MC) and displayed as DPMO (Defects Per Million Opportunities outside
specifications). Normally distributed random disturbances of + 5% of the range of each
factor are applied and result in an estimate of the total number of DPMO for all active
responses. The user can modify the sensitivity range and the number of MC’s.
DPMO=0 means that the proposed factor settings represent a robust point of operations
for factor disturbances of + 5%.

Orthogonal blocking
When you cannot perform all of the experiments in a homogeneous way, randomizing
the run order of the experiments may not be sufficient to deal with the extraneous
sources of high variability. You may want to run the experiments in homogeneous
groups, i.e., blocks, in such a way that the external source of variability does not
influence the effects of the factors.
For example, suppose you are running a full factorial with 5 factors and 32 runs, and
the batch size of raw material allow you to perform only 8 runs per batch. You may
want to run your experiment in 4 blocks, each composed of 8 runs using homogeneous
material.
The method of dividing 32 runs in 4 blocks of 8 runs, each such as the difference
between the blocks (the raw material) does not affect the estimate of the factors, is
called Orthogonal Blocking.
MODDE supports orthogonal blocking for the 2 level factorial, fractional factorials,
Plackett Burman, CCC, and Box Behnken designs.
MODDE can also block D-Optimal designs. These designs are more flexible with
respect to the number of blocks and the block size, but the blocks in D-Optimal design
are not usually orthogonal to the main factors. The only restriction with D-Optimal
designs is that the number of runs must be a multiple of the block size.

Note: Blocking introduces extra factors in the design, hence reduces the
degree of freedom of the residuals, and the resolution of the design. You
should only block when the extraneous source of variability is high and
cannot be dealt with by randomizing the run order.

Block interaction
An interaction between a main effect and a block effect is called a block interaction.
When the design supports the interactions between the block effects and the main
effects, the Block interactions check box, in the Select model and design dialog in
the design wizard is active. You can select the check box if you want to add the block
interactions to your model.

250
 Appendix A: Statistical notes

Recoding the blocking factors

When blocking factors are generated, the blocks are assigned according to the
combination of signs of the blocking factors.
For example to generate 4 blocks, the following scheme of signs of the blocking
factors is used:
$B1 $B2

– – Block 1

+ – Block 2

– + Block 3

+ + Block 4

When you select Show | Design Matrix, the design matrix is displayed in coded units
including the blocking factors.
When the worksheet is generated, the blocking factors are recoded and the model is
reparameterized. Rather than keeping the d blocking factors, such as 2d = k (the
number of blocks), MODDE generates one qualitative variable called $BlockV, with k
levels called B1, B2 ...Bk.

Inclusions and blocks

Adding inclusions to a blocked design is not supported, unless the inclusions belong to
one of the blocks present.

Blocking screening designs

Full and fractional factorial designs
The block size and the number of blocks of the 2 level factorial designs are always
powers of 2.
The maximum number of blocks supported by MODDE is 8, with a minimum block
size of 4.
The designs are blocked by introducing blocking factors called $B. There is one
blocking factor for 2 blocks, two for 4 blocks and three for 8 blocks. The block effects
consist of the effects of the blocking factors and all their interactions.
Hence with 8 blocks, there are 7 block effects using 7 degrees of freedom. (It is
equivalent to having added 7 extra factors to your design).
MODDE selects the generators of these blocking factors to achieve the highest
possible pseudo-resolution of the design.
The pseudo-resolution of the design is the resolution of the design when all the block
effects (blocking factors and all their interactions) are treated as main effects under the
assumption that there are no interactions between blocks and main effects, or blocks
and main effects interactions.

Blocking Plackett Burman designs

These designs can only be split into two blocks by introducing one block variable, and
using its signs to split the design.

251
User Guide to MODDE

Blocking RSM designs

RSM designs are orthogonally blocked when they fulfill the following two conditions:
1. Each block must be a first order orthogonal block.
2. The fraction of the total sum of squares of each variable contributed by every
block must equal the fraction of the total observations (experiments) allotted
to the block.

Central Composite Circumscribed designs

The Central Composite Circumscribed designs can be split into two blocks, the cube
portion and the star portion, and satisfying the two above conditions when α (the
distance of the star points to the center) is equal to
α = [k (1+ps ) / (1 + pc) ]1/2
k = number of factors
ps = nso/ns proportion of center points in the star portion
pc = nco/nc proportion of center points in the cube portion
ns = number of star points runs
nc = number of runs from the cube portion
This is the value of α implemented in MODDE when you select blocking a CCC
design.
Smaller blocks
The cube portion of the Central Composite Circumscribed design (CCC) can be split
into further blocks if (a) the factorial or the fractional factorial part of the design can be
split into orthogonal blocks of pseudo resolution 5 and (b) each one of these blocks
have the same number of center points.

Box Behnken designs

These designs can be orthogonally blocked, as specified by Box and Behnken (1960)
and Box and Draper (1987).

Central Composite Face designs

These designs can not be blocked.

Blocking D-Optimal designs

MODDE can block D-Optimal designs, but usually the blocks are not orthogonal to the
main factors.
The following restrictions apply to blocking D-optimal designs:
1. The blocks must be of equal size.
2. You cannot have interactions between the block factor and the other factors
in the model.
3. The selected number of runs of the design must be a multiple of the number
of blocks.
MODDE blocks the D-Optimal design by generating a qualitative factor, $BlockV,
with as many levels as the selected number of blocks. By default, it then selects only
balanced designs with respect to the blocking factor.

252
 Appendix A: Statistical notes

It is not always possible to generate a balanced D-Optimal design with respect to the
blocking factor. In this case you may want to change the model, the number of blocks,
or generate an unbalanced design.

Random versus fixed block factor

You can select to have the block factor treated as fixed or random effect and the
predictions computed accordingly.
Select the block factor as Fixed when the external variability can be set at will (it is
controlled) and the primary objective for blocking is to eliminate that source of
variability.
A fixed block can be modeled as a controlled qualitative factor with a limited number
of levels. All predictions of the responses and contour plots will be made for a selected
block level.
The block is a fixed effect, for example, if you are making 32 experiments, and each 8
runs are done on one of four different machines. There is no other machine than the
four available, not now, nor in the future.
You may want to have 4 blocks to eliminate the variability introduced by the machines,
but all predictions of the response(s) are made for one of the specific machines.
Select the block factor as Random effect when the external variability cannot be
controlled and set at will, and the primary objective is to make predictions without
specifying the block level, and taking into account the external variability.
Since the block level of future experiments is unknown, all predictions of the responses
for random block effects are made without specifying the block level. The confidence
intervals for the responses are increased to account for the uncontrolled external block
variability.
For example, the block is a random effect if you are making 32 experiments, and each
block of 8 runs are made with a different batch of raw material.
Your primary objective is to make predictions for the next unknown batch of raw
material.

Analysis with random effects

When you treat the block factor as Random effect it is often desirable to investigate
the consistency of the factor effects by including in the model all the interactions of the
block factor with the main factors, if possible.
In MODDE the model is always fitted as a fixed effect model, that is with the block
factor treated as a controlled qualitative variable, even when the blocks are specified as
random.
If the random block interaction effects with the main factors are large and significant,
the effect of the main factors varies from block to block, and the confidence intervals
on the prediction will be large due to this uncontrolled variability.
If the random block interaction effects are small and insignificant, the effects of the
main factors are consistent from block to block and the uncertainty of the predictions is
greatly reduced.
To have a realistic size of the confidence intervals, trim the model and remove all
insignificant block interactions effects.
If the block factor is specified as fixed effect, the interactions of the main factors with
the block factor are of less interest.

253
User Guide to MODDE

Predictions with random effect

The prediction of the responses, when the block effect is specified as random, are
computed without specifying the block level.
MODDE uses the average block level to predict the response but the confidence
interval is increased to take into account the variability of the response due to the
different blocks, plus the variability of the response due to uncertainty on the
coefficients of the model including all the terms with the block factor.

Design Space statistics

The calculation of the design space is a search function that expands the possible factor
ranges from a setpoint (optimum) to the largest possible range where all response
predictions are still within the specifications.
Predictions in the design space are done with Monte Carlo simulations. The resulting
distribution of predictions simulates a real situation with a random combination of
factor setting disturbances within a given range.
For more, see also the Appendix D: Design Space and Design Space chapters.

Monte Carlo simulations

The random factor settings used for predictions can have three different distributions,
'Uniform', 'Normal', and 'Triangular'. The default is that the randomization follows a
normal distribution. In the Distribution box 'Target' is also available.
Uniform

Normal

Triangular

254
 Appendix A: Statistical notes

The low and high factor settings are the distribution boundaries. For a normal
distribution 95% of the distribution is found within the boundaries, by default. The
automatic search procedure expands the distribution for each factor until one or more
response limits are exceeded according to the specified DPMO target. The automated
search procedure is symmetrical around the setpoint but random for the factors.

DPMO and Cpk

DPMO is short for Defects Per Million Opportunities outside specifications and is used
as stop criteria in the design space estimation.
In the Design Space Properties dialog you can select to estimate using individual
DPMO as targets or total DPMO as target. The total DPMO is not necessarily the sum
of the individual DPMOs as the same point may be found outside the limits for more
than one response. So while each point outside is only counted once in the total DPMO
it may be counted several times if summarizing the individual DPMO.
DPMO = Ho * (1 000 000 / Ns)
where Ho = Hits outside specifications, Ns = Number of simulations.
Cpk, Capability index, originates from the SixSigma statistics and is another way of
expressing model robustness.

Note: MODDE assumes that the data is normally distributed.

where
USL = Upper Specification Limit.
LSL = Lower Specification Limit.
μ = predicted average.
σ = estimated standard deviation for predictions.

255
User Guide to MODDE

Based on an infinite number of predictions:

Cpk DPMO %Outside
0.4 115070 11.51

0.6 35930 3.59

0.8 8198 0.82

1 1350 0.13

1.1 483 0.05

1.2 159 0.02

1.3 48 0.0048

1.4 13 0.0013

1.5 3.40 0.0003

1.6 0.79 7.93328E-05

1.7 0.17 1.69827E-05

1.8 0.03 3.33204E-06

1.9 0.0060 5.99037E-07

2 0.0010 9.86588E-08

For more information about Cpk (Process Capability Index) search in Wikipedia.

Predictions including model error

Predictions from the Monte Carlo simulations by default include the model error. You
can select to not include the model error in the property page.
MLR models: Y = f(x) + e; DF = degrees of freedom.
1. Compute all Y predictions and confidence intervals for the random
simulations in X.
2. Generate a random t distribution on the confidence intervals in 1. based on
DF and e.
3. Add 1 and 2.
The above is true for PLS models too but PLS models with condition number > 3000
and non hierarchical mixture models display the standard error of prediction instead of
confidence intervals.

256
Appendix B: Designs

Designs for process factors

Screening designs
Screening designs are used in the early stages of an investigation to find which factors
are important and if it is necessary to modify their ranges.
All screening designs support linear models and some support interaction models.
The designs you can select with interaction models, i.e. all interactions, are the full
factorial, the fractional factorial, Rechtschaffner, and D-Optimal designs of resolution
V. Fractional factorials of resolution V are supported for up to 12 factors.
MODDE supports the following screening designs:

Full factorial designs

Full factorial designs can be created at 2 or more levels.
These designs comprise all the possible combinations of the factor levels. For p factors
at 2 levels you need N =2p runs. Full factorial designs are orthogonal (balanced)
designs. Hence, the estimated effect of a factor is independent of the effects of all other
factors.
Full factorials with factors with different number of levels are called Full Factorial
Mixed.

Fractional factorial designs

Fractional factorial designs are 2 level designs with resolution III, IV, V or more.
These designs are balanced subsets (fractions) of the full factorials. The resolution of
the design depends on the size of the subset, i.e. the number of runs selected. The
possible resolutions are:
• Resolution III designs where main effects are confounded with 2 factor
interactions.
• Resolution IV designs where two factor interactions are confounded with
each other.
• Resolution V designs where main effects and all two-factor interactions are
clear of each other (unconfounded). MODDE supports resolution V designs.
With both resolution III and IV designs, you can only select the linear model. You may
edit the model and enter selected interactions. In that case, you may have to edit the
generators of the design.
With resolution V designs, MODDE generates the interaction model.

257
User Guide to MODDE

The default generators used by MODDE for fractional factorial designs are those
recommended by Box, Hunter and Hunter (page 410). You may edit and change the
generators in the Generator dialog available on the Edit menu. When you update the
confounding, MODDE will warn you if some of the effects in your model are
confounded with each other, i.e. if your model is singular.

Plackett Burman designs

Plackett Burman designs are fractional factorial designs of resolution III, generated
with 4, 8, 12, 16, 20, 24, and 28 and more runs. Plackett Burman designs support only
linear models; i.e. you cannot estimate any two-factor interactions.

Plackett Burman Super-Saturated designs

Plackett Burman Super-Saturated designs, PBSS, are fractional factorial designs of
resolution II, generated with 4, 6, 8, 10, 12, 14, 16, and 18 runs. A super-saturated
design is a Resolution II design with fewer runs than factors. Main effects are
confounded with main effects. It is assumed that only very few of the factors
investigated are active.

Three levels fractional factorial designs

Three levels fractional factorial designs are fractional factorial designs from the
Graeco-Latin square family. The available designs are:
• L9: design with up to 4 factors at three levels.
• L27: design with up to 13 factors at three levels.
• L36: design with up to 13 factors at three levels.
• L18 is called mixed as it has one factor at 2 levels and up to 7 factors at three
levels.
With these 3 levels designs MODDE (objective = screening) lets you select only the
linear model, because these designs do not support interactions. In Edit | Model you
may edit the model and include square terms.

D-Optimal designs
D-Optimal designs are computer generated designs that maximize the determinant of
the X'X matrix, X being the extended design matrix.
D-Optimal designs are available for all objectives.
For more see the D-Optimal designs section later in this chapter and see also the D-
Optimal chapter.

Onion designs
Like regular D-Optimal designs, D-Optimal Onion designs can be used both in
screening and in RSM with quadratic models. The Onion designs comprise layers of
designs, usually D-Optimal, where the outermost layer determines which type of model
(screening or RSM) that the Onion design supports. For more see the D-Optimal
onion designs section later.

258
 Appendix B: Designs

Rechtschaffner designs
Rechtschaffner designs are orthogonal, saturated fractions of resolution V of the 2n and
3n factorial designs. They allow the estimation of all main effects and all first order
interactions without confounding. They are saturated designs, with no degrees of
freedom remaining for the estimation of residuals and diagnostics.
The 2n Rechtschaffner designs are well suited when the objective is screening, with 6
or more factors, and little knowledge about the importance of each individual first
order interaction. In this case it is of interest to estimate all first order interactions,
unconfounded, and then eliminate the insignificant (small) ones, hence recovering
some degrees of freedom for diagnostics and residual analysis.
The required number of runs N for the 2n Rechtschaffner designs with k factors is:
N =1 + k + k(k - 1)/2
It is recommended to add 3 to 4 center points to these designs.

RED-MUP designs
The RED-MUP designs are custom designs developed for the use with 96 well plates
(see figure) and larger (384, 1536, etc.). These are widely used platforms for
experimentation in biochemistry, microbiology, pharmaceutical development, etc.,
with some special properties (buildable and extendable to other factor intervals). The
RED-MUP designs consist of two sub-designs corresponding to the vertical and
horizontal directions of the plates, i.e., 8 and 12, respectively, for 96-well plates. The
total design is made by multiplying the two sub-designs together. Hence, this total
design supports a model with all interactions between the factors in the sub-designs,
plus from each sub-design, the main effects, and when these sub-design so support,
interactions, and quadratic effects.
Below, we use n1 and n2 for the number of rows and columns in the plate, i.e., 8 and
12 in a 96 hole plate. A 96-well plate can handle from 5 full “RSM factors” up to 18
factors for a stretched screening situation.
The layout of a 96 well plate has 8 rows and 12 columns. Hence, the vertical direction
has n1=8, and the horizontal direction has n2=12.

If both sub-designs support only main effects, using for example Plackett Burman sub-
designs, up to n1+n2-2 factors can be investigated, i.e., up to 18 factors in a 96 well
plate. Such a sparse design without center points is not recommended. More reliable
designs with center points in the larger sub-design would allow n1-3 + n2-5 = n1+n2-8
factors, i.e., 12 factors for a 96 well plate.

259
User Guide to MODDE

When specifying the RED-MUP design, it is important to distribute the factors over the
two sub-designs (vertical and horizontal) so that (a) the actual experimental protocol
remains simple and doable, (b) the sub-designs and final design make
chemical/biological/engineering sense, and (c) a-priori interesting interactions and
higher order terms can be estimated. Note that all the interactions between each of the
factors in the vertical design and each of the factors in the horizontal designs can
always be estimated. Hence, factor pairs for which interactions are expected should be
split into the two sub-designs. Then their interaction can always be estimated,
regardless of choice of sub-design.
Special designs
When selecting to create a RED-MUP design, there are special designs for the 96 well
plates (8 x 12) which aim to make better use of the plate.

RSM designs
RSM designs are used in later stages of an investigation to develop more elaborate
models (quadratic) in the few important factors, usually not more than 5 or 6.
MODDE supports the following RSM designs:

Full factorial design at three levels

Full factorial design at three levels is the full factorial design, with every factor varied
at three levels

Central composite designs CCC and CCF

The two central composite designs available in MODDE are the Central Composite
design Circumscribed (CCC) and Face Centered (CCF).
MODDE supports CCC and CCF designs for up to 12 factors.
These designs are composed of:
• A full or fractional factorial design.
• Star points.
• Replicated center points.
MODDE also supports a reduced CCC and CCF for four factors, with the fractional
part of the design reduced from 16 to 12 runs.
Note that with the CCC designs you may edit the model and include cubic terms, if you
wish.

Box Behnken designs

Box Behnken designs are three level designs. All the design points are located at the
center of the edges of the cube or hypercube, and are all situated on the surface of a
sphere.

D-Optimal designs
D-Optimal designs are computer generated designs that maximize the determinant of
the X'X matrix, X being the extended design matrix.
D-Optimal designs are available for all objectives.
For more see the D-Optimal designs section later in this chapter and see also the D-
Optimal chapter.

260
 Appendix B: Designs

Onion designs
Like regular D-Optimal designs, D-Optimal Onion designs can be used both in
screening and in RSM with quadratic models. The Onion designs comprise layers of
designs, usually D-Optimal, where the outermost layer determines which type of model
(screening or RSM) that the Onion design supports. For more see the D-Optimal
onion designs section later.

Rechtschaffner designs
Rechtschaffner designs are orthogonal, saturated fractions of resolution V of the 2n and
3n factorial designs. They allow the estimation of all main effects and all first order
interactions without confounding. They are saturated designs, with no degrees of
freedom remaining for the estimation of residuals and diagnostics.
The 3n Rechtschaffner designs are well suited for the RSM objective with 6 or more
factors as they require fewer runs than the classical CCC or CCF non saturated designs.
The intent with these designs is to estimate quadratic terms but performing fewer runs
than with CCC or CCF. Eliminating insignificant terms, after performing the
experiments, results in recovering some degrees of freedom.
The required number of runs N for the 3n Rechtschaffner designs with k factors is:
N = 1 + 2k + k(k - 1)/2
It is recommended to add 3 to 4 center points to these designs.

RED-MUP designs
The RED-MUP designs are custom designs developed for the use with 96 well plates
(see figure below) and larger (384, 1536, etc.). These are widely used platforms for
experimentation in biochemistry, microbiology, pharmaceutical development, etc.,
with some special properties (buildable and extendable to other factor intervals). The
RED-MUP designs consist of two sub-designs corresponding to the vertical and
horizontal directions of the plates, i.e., 8 and 12, respectively, for 96-well plates. The
total design is made by multiplying the two sub-designs together. Hence, this total
design supports a model with all interactions between the factors in the sub-designs,
plus from each sub-design, the main effects, and when these sub-design so support,
interactions, and quadratic effects.
The RED-MUP designs are well suited for the RSM objective with up to 5 or 6 factors.
The intent with these designs is to get a precise model that can be used for optimization
and for detailed understanding.
The maximum number of “RSM factors” depends on the sizes of the sub-designs. An 8
run sub-design, e.g., a Doehlert design with 2 center points, supports 2 “RSM factors”
(1 constant, 2 linear, two quadratic, and one interaction terms), and a 12 run sub-
design, e.g., a three level Rechtschaffner design with 2 center points, supports 3 “RSM
factors” (1 constant, 3 linear, 3 quadratic, and 3 interaction terms) for a total of 5
“RSM factors” for a 96-well plate.
Mixed objective
Since the RED-MUP designs are constructed from two sub-designs, one of these can
be an RSM design and the other a screening design. In such a case the objective is said
to be mixed.

261
User Guide to MODDE

Special designs
When selecting to create a RED-MUP design, there are special designs for the 96 well
plates (8 x 12) which aim to fill up the plate.

Doehlert designs
The Doehlert designs are quadratic RSM designs with some special properties
(buildable and extendable to other factor intervals). They allow the estimation of all
main effects, all first order interactions, and all quadratic effects without confounding.
They are saturated designs with similar properties to the CCF and CCC designs.
Geometrically they are polyhedrons based on hyper-triangles (simplexes), with a
hexagon in the simplest two-factor case.
Doehlert design in 2 factors with 6 runs + center points, can be extended to a new
design by adding 3 experiments. Usually also one or two new center points are added
in the new design (i.e., in the figure the right-most point in the old design).

The Doehlert designs are well suited for the RSM objective with up to 5 or 6 factors
(respectively 33 and 45 runs with 3 center points). The intent with these RSM designs
is to get a precise model that can be used for optimization and for detailed
understanding.
The required number of runs N, except for replicated center points, for the quadratic
Doehlert designs with k factors is:
N = 1 + k + k2
It is recommended to add 3 to 4 center points to these designs.

262
 Appendix B: Designs

Designs for mixture factors

In a mixture experiment the responses of interest depend only on the relative
proportions of the components (called mixture factors) that make up the mixture or
formulation. Hence, the sum of all the mixture factors is a constant T, usually equal to
1 when no mixture factors are kept constant.

Mixture and process factors

Mixture factors are expressed as the fraction of the total amount of the formulation.
Their experimental ranges lie between 0 and 1.
Regular factors (i.e., temp, pH, etc.) that are not part of the mixture or formulation are
referred to as process factors. These are expressed as amounts or levels, and can be
either quantitative (measured on a continuous scale) or qualitative (have only
discrete values).
MODDE supports both mixture and process factors in the same experiment.

Mixture factors definition

A mixture factor can be a formulation factor or a filler factor. Only one mixture factor
can be defined as filler.

Formulation factor
Formulation factors are the usual mixture factors used in formulations with specifically
defined experimental ranges. Most mixture experiments have only formulation factors.

Filler factor
The presence of filler is typical of certain types of simple mixture experiments. For
example in a synthesis the solvent is typical filler, as is water in a juice punch. A filler
is a mixture component, usually of little interest, making up a large percentage of the
mixture, and added at the end of a formulation to bring the mixture total to the desired
amount.
It is recommended to define a mixture factor as filler when all three conditions below
are fulfilled:
• The factor is always present in the mixture.
• The factor accounts for a large percentage of the mixture and there is no
restriction on its range. It is added at the end to bring up the mixture total to
the desired amount (usually 1 when no mixture factors are kept constant).
• You are not interested in the effect of the filler per se.
When you specify a filler factor, MODDE checks that these conditions are met and
defaults to a slack variable model, with the filler factor omitted from the model.

Use
All mixture factors are controlled or constant. The Uncontrolled option is unavailable
for both formulation and filler factors.
Formulation factors can be defined as Constant when you want to keep them constant
in the experiment.

263
User Guide to MODDE

When mixture factors are constant, the mixture total T = 1 - Sum (constant mixture
factors). When no formulation factors are defined as constant, the mixture total has to
be equal to 1. MODDE issues an error message and stops whenever the mixture total is
not equal to T or 1.

Note: A filler factor cannot be Constant.

Scaling
Mixture factors are always unscaled when you fit the model with MLR. When you fit
the model with PLS, all mixture factors are scaled to unit variance.

Note: When the mixture region is regular, mixture factors are first
transformed to pseudo components, and then scaled with PLS models.

Mixture constraint
In a mixture experiment the mixture total (i.e. the sum of all the mixture factors in the
experiment) is equal to a constant T. The mixture Total T is generally equal to 1 when
no mixture factor is kept constant. This mixture constraint implies that the mixture
factors are not independent, and this collinearity has implications on the mixture
experimental region, the mixture designs, and the mixture model formulation.

Mixture experimental region

When all mixture factors vary from 0 to T (the mixture total), the shape of the
experimental region is a Simplex. With constraints on their ranges, the experimental
region is usually an irregular polyhedron inside the simplex. In some constrained cases,
as for example, with lower bounds constraints only, the experimental region is a small
simplex inside the original simplex. See Crosier (1984).
MODDE checks for consistent bounds, and computes:
RU = ∑Ui - T
RL = T - ∑Li
Li and Ui are the lower and upper bound of the ith mixture factors.
From RL, RU and Ri (the range of every formulation factor) MODDE determines if the
experimental region is a Simplex (the L simplex oriented as the original one, or the U
simplex with opposite orientation) or an irregular polyhedron.

Regular region pseudo components transformations

When the mixture region is the L or U simplex, MODDE defaults to transforming the
mixture factors to pseudo component to make all their ranges vary between 0 and 1.
This is very similar to orthogonal scaling of process factor, to make their ranges vary
between -1 and +1.
With a regular mixture region, MODDE uses classical mixture designs.
The design is expressed in pseudo components and the worksheet is of course always
displayed in original units.
The analysis is performed on the mixture factors transformed to pseudo
component, as the coefficients of the Cox model can then be directly interpreted as the
mixture factors effects.

264
 Appendix B: Designs

Note: You can select to have the analysis done on the mixture factors
expressed in original unit under the Analysis menu.

Region is the L simplex

When the mixture region is the L simplex, the L pseudo component transformation is
defined as:
Pi =(Xi - Li)/(RL)
The transformed mixture factors Pi vary from 0 to 1.

Region is the U simplex

When the mixture region is the U simplex, the U pseudo component transformation is
defined as:
Pi =(Ui - Xi)/(RU)
The transformed mixture factors Pi vary from 0 to 1, but in this case the new simplex in
the P's has an opposite orientation to the original simplex in X, that implies that effects
in P are reversed from those in X.

Classical mixture designs

When all factors are mixture factors and the shape of the region is a simplex, the
designs available in MODDE are the following classical mixture designs (all classical
mixture designs are displayed in pseudo components in the design matrix, and by
default the analysis is done with the formulation factors transformed to pseudo
components).

Screening designs
MODDE provides three variants of the axial design. Axial designs locate all the
experimental points on the axis of the simplex and are recommended for screening, see
Snee (references).
Standard Axial (AXN)
The standard axial design includes the following 2*q +m runs (q = number of mixture
factors, m centroid points as specified by user).
1. All the q vertex points. The coordinates of the ith Vertex point is
xi = (0, 0, 0..1, 0, 0..).
2. All q interior points of the simplex. The coordinates of the ith Interior point is
xi = (1/2q, 1/2q, 1/2q,..(q+1)/2q, 1/2q, 1/2q..).
3. The overall centroid of the simplex with coordinates
x = (1/q, 1/q,....., 1/q..) replicated (m-1) times.

265
User Guide to MODDE

Extended Axial (AXE)

The extended axial design includes the following 3*q +m runs (q = number of mixture
factors, m specified by user).
1. All the q vertex points. The coordinates of the ith Vertex point is xi = (0, 0,
0..1, 0, 0..).
2. All q interior points of the simplex. The coordinates of the ith Interior point is
xi = (1/2q, 1/2q, 1/2q,..(q+1)/2q, 1/2q, 1/2q..).
3. All the q End points. The coordinates of the ith End point is
xi = (1/(q-1), 1/(q-1), 1/(q-1), 0, 1/(q-1), 1/(q-1)..).
4. The overall centroid of the simplex with coordinates
x = (1/q, 1/q,....., 1/q..) replicated (m-1) times.
Reduced Axial (AXR)
The reduced axial design includes the following (q+m) (specified by user) points:
1. All the q vertex points.
2. A subset or none (specified by user) selected from the q interior points.
3. The overall centroid replicated as desired.

RSM
MODDE provides 2 variants of the quadratic model designs, one special cubic and one
cubic. The simplex centroid design has all the experimental points on the vertices, and
on the center of the faces of consecutive dimensions.
Modified simplex centroid (SimM)
The modified simplex centroid design supports a quadratic model and includes the
following:
1. The q vertex points. The coordinates of the ith Vertex point is
xi = (0, 0, 0..1, 0, 0..).
2. The (q (q-1))/2 Edge centers. The coordinates of the ijth edge point is xij = (0,
0, 1/2, 1/2 0, 0..).
3. The q Interior check points. The coordinates of the ith interior point is xi =
(1/2q, 1/2q, (q+1)/2q, 1/2q, 1/2q..).
4. The overall centroid with coordinates x = (1/q, 1/q,...1/q), replicated as
desired.

266
 Appendix B: Designs

Modified simplex centroid Face center (SimF)

The modified simplex centroid face center design supports a quadratic model and
includes the following:
1. The q vertex points. The coordinates of the ith Vertex point is
xi = (0, 0, 0..1, 0, 0..).
2. The (q (q-1))/2 Edge centers. The coordinates of the ijth edge point is xij = (0,
0, 1/2, 1/2 0, 0..).
3. The q Face centers of dimension (q-1). The coordinates of the ith face center
is: (1/q-1, 1/q-1,..,0, 1/q-1..1/q-1).
4. The q Interior check points. The coordinates of the ith interior point is xi =
(1/2q, 1/2q, (q+1)/2q, 1/2q, 1/2q..).
5. The overall centroid with coordinates x = (1/q, 1/q,...1/q), replicated as
desired.
Simplex centroid Special Cubic (SimSC)
The simplex centroid special cubic design supports a special cubic model and includes
the following:
1. The q vertex points. The coordinates of the ith Vertex point is
xi = (0, 0, 0..1, 0, 0..).
2. The (q (q-1)) 1/3, 2/3 Edge points. The coordinates of the ijth edge point is
xij = (0, 0, 1/3, 2/3, 0, 0..), xji = (0, 0, 2/3, 1/3, 0, 0..).
3. The q(q-1)(q-2)/6 Face centers of dimension 2. The coordinates of the ith
face center is (0, 0, 0, 1/3, 1/3, 1/3..0, 0, ).
4. The q Interior check points. The coordinates of the ith interior point is xi =
(1/2q, 1/2q, (q+1)/2q, 1/2q, 1/2q..).
5. The overall centroid with coordinates x = (1/q, 1/q,...1/q), replicated as
desired.
Simplex Centroid Cubic (SimC)
The simplex centroid cubic design supports a cubic model and includes the following:
1. The q vertex points. The coordinates of the ith Vertex point is
xi = (0, 0, 0..1, 0, 0..).
2. The (q (q-1)) 1/3, 2/3 Edge points. The coordinates of the ijth edge point is
xij = (0, 0, 1/3, 2/3, 0, 0..), xji = (0, 0, 2/3, 1/3, 0, 0..).
3. The q(q-1)/2 Edge centers. The coordinates of the ith edge center is xi = (0, 0,
0, 1/2, 1/2, 0...0).
4. The q(q-1)(q-2)/6 Face centers of dimension 2. The coordinates of the ith
face center is (0, 0, 0, 1/3, 1/3, 1/3..0, 0, ).
5. The q Interior check points. The coordinates of the ith interior point is xi =
(1/2q, 1/2q, (q+1)/2q, 1/2q, 1/2q..).
6. The overall centroid with coordinates x = (1/q, 1/q,...1/q), replicated as
desired.

267
User Guide to MODDE

D-Optimal designs
What are D-Optimal designs?
D-Optimal designs are computer generated designs, tailor made for a specific
problem. They allow great flexibility in the specifications of your problem. They are
particularly useful when you want to constrain the region and no classical design
exists.
“D-Optimal” means that these designs maximize the information in the selected set of
experimental runs with respect to a stated model.
For a specified regression model Y = X*β + ε where:
Y is a (N x 1) vector of observed responses,
X is a (N x p) extended design matrix, i.e. the n experimental runs extended with
additional columns to correspond to the p terms of the model (i.e., the added columns
are for the constant term, interaction terms, square terms, etc..)
β (beta) is a (p x 1) vector of unknown coefficients to be determined by fitting the
model to the observed responses.
ε (epsilon) is a (N x 1) vector of residuals (the differences between the observed and
predicted values of the response y). They are assumed to be independent of each other,
normally distributed and with constant variance σ2
The D-Optimal design maximizes the determinant of the X'X matrix, which is an
overall measure of the information in X. Geometrically; this corresponds to
maximizing the volume of X in a p dimensional space.

Candidate set
D-Optimal designs are constructed by selecting N runs from a candidate set. This
candidate set is the discrete set of “all potential good runs”.
MODDE generates the candidate set as follows:
I) For a regular process region, the candidate set consists of one or more of the
following sets of points (depending on your model and the number of factors):
• The full factorial for up to 10 factors, reduced factorial for up to 32 factors.
• Centers of edges between hyper-cube corners
• Centers of the faces of the hyper-cube.
• Overall centroid
II) For constrained regions of mixture or/and process factors, the candidate set consists
of one or more of the following set of points:
• The extreme vertices of the constrained region
• The centers of the edges. If these exceed 200, the center of the 200 longest
edges
• The centers of the various high dimensional faces
• The overall centroid.
MODDE has implemented an algorithm to compute the extreme vertices, center of
edges, center of faces etc. as described by Piepel (1988).

268
 Appendix B: Designs

D-Optimal algorithm
D-Optimal designs have been criticized for being too dependent on an assumed model.
To reduce the dependence on an assumed model, MODDE has implemented a
Bayesian Modification of the K-Exchange algorithm of Johnson and Nachtsheim
(1983), as described by W. DuMouchel and B. Jones in “A Simple Bayesian
Modification of D-Optimal designs to reduce dependence on an Assumed Model”,
Technometrics (1994).
With this algorithm one can add to the “primary terms” i.e. the terms in the model,
“potential terms”, i.e. additional terms that might be important. The objective is to
select a D-Optimal design, rich enough to guard for potential terms, and enable the
analysis to detect possibly active ones.
In order not to increase the number of runs N, and to avoid a singular estimation, one
assumes that the coefficients of the potential terms are likely to have a mean of 0 and a
finite variance (tau, τ)2.

Implementation of the D-Optimal algorithm in MODDE

K-exchange algorithm
The k-exchange algorithm is a compromise between the exchange algorithm of Wynn
(1972) with k=1 and the Federov algorithm with k = N (the selected number of runs).
In MODDE k is set to 3, that is at every iteration of the procedure, the algorithm
considers an exchange between k = 3 points in the design with the smallest prediction
variance and points in the candidate set. If any exchange increases the determinant, the
point(s) (up to 3) are exchanged.

Variance of the coefficients of the potential terms

As recommended by W. DuMouchel, tau, τ, is set to 1 in MODDE.

Potential terms
Potential terms are higher order terms not included in the model but taken into account
during the creation of the candidate set. Potential terms are default added but can be
removed by clearing the Use potential terms box.
Depending on the number of factors, the objective and the model, MODDE adds the
following potential terms:

Process Factors with constraints

Screening
Factors Model Potential terms

2 - 12 Linear All interactions

2 - 12 Linear + interactions All squares

RSM
Factors Model Potential terms

2-8 Quadratic All cubes

269
User Guide to MODDE

Process Factors without Constraints

Screening
Factors Model Potential terms

2 - 20 Linear All interactions

21 - 32 Linear Interactions between the first 20 factors

2 - 17 All interactions All squares

RSM
Factors Model Potential terms

2-6 Quadratic All cubes

7 - 12 Quadratic None

Mixture Factors and irregular regions

Screening
Factors Model Potential terms

2 - 20 Linear All squares + interactions

RSM
Factors Model Potential terms

2 - 12 Quadratic All cubes

Note: No potential terms are added for investigations with all factors defined
as qualitative.

270
 Appendix B: Designs

Design evaluation
To evaluate and compare D-Optimal designs, MODDE computes the following
criteria:

LogDetNorm
The log of the determinant of X'X normalized for number of terms in the model p, and
number of runs N.
This is the criterion used, by default, to select the best design. MODDE selects the
design with the largest value (closest to 0) of LogDetNorm.
LogDetNorm = Log10 [ Det(X'X)1/p / N]
The maximum value of LogDetNorm, for an orthogonal design, is 0.

LogDet
The Log of the determinant of the X'X matrix

Condition No
The condition number of the X design matrix coded orthogonal, and extended
according to the model.

G efficiency
G efficiency is a lower bound on D efficiency, which compares the efficiency of a D-
Optimal design to a fractional factorial.
G efficiency is defined as:
Geff = (100*p)/(n*d)
Where
p = number of terms in the model
n = number of runs in the design
d = Maximum relative prediction variance v over the candidate set, where the
prediction variance v = x(X'X)-1x'

Inclusions and design augmentation

MODDE allows you to specify a set of experimental runs as Inclusions specified
under Design | Inclusions. If you enter experiments in Inclusion before creating your
design these runs are default a part of the resulting D-Optimal design.
Inclusions are useful for design augmentation. If you already have performed a few
experiments, and want to add M additional experiments, add the old experiments in
Inclusions, ask for N+M runs and state the desired model. The M runs are selected D-
Optimally from the candidate set with respect to your model.
For more on design augmentation see the Complement design section in the File
chapter.

Note: All of these statistics are computed from the runs selected D-optimally
and do not include the possible center points added to the worksheet.

271
User Guide to MODDE

Irregular region
Screening
When the mixture region is an irregular polyhedron, MODDE computes the extreme
vertices (corners) delimiting the region. These extreme vertices constitute the candidate
set and the centers of the high dimensional faces are added to support potential
terms. The design is a D-optimal selection of N (specified by user) runs from the
candidate set.

RSM
MODDE computes the extreme vertices, 1/3, 2/3 centers of edges, centers of faces of
dimension (q-1) and the overall centroid of the experimental region. When there are
too many extreme vertices, only the center of the 25% longest edges is computed.
These experimental points constitute the candidate set.
The design is a D-Optimal selection of N runs (specified by the user) from the
Candidate set.

Pseudo component transformation

You can always select to have the mixture factors expressed in pseudo components for
the analysis. MODDE uses the L pseudo component transformation when RL ≤ RU and
the U pseudo component when RU < RL.
Pseudo component transformation is the MODDE default when the method of fit is
MLR as it stretches the experimental region and alleviates the problem of ill
conditioning.

Note: All mixture designs are displayed in pseudo components.

Mixture models
Because of the mixture constraint, (the mixture factors are not independent) the
analysis of mixture data with multiple regression requires a special model form.
The traditional approaches have been:
• Defining the model omitting one mixture factor, hence making the others
independent. This is the Slack Variable approach.
• Omitting some terms from the model, so that the terms remaining in the
model are independent. This is Scheffé model, with the constant term
removed from the linear model and the quadratic terms removed from the
quadratic model.
• Using the complete model including all the mixture terms, but putting
constraints on the coefficients to make them estimable. This is the Cox
reference model, and the constraints on the coefficients are defined with
respect to a standard reference mixture. This standard reference mixture
serves the same function as the centering constant with process variables
models.

272
 Appendix B: Designs

Process and mixture factors together

When you have both process and mixture factors, you can select to treat them as one
model, or to specify separate models for the mixture factors, and the process factors.
With both mixture and process factors, the only model form available is the Cox
reference mixture model.
When the model obeys mixture hierarchy, the PLS coefficients are expressed relative
to a stated standard reference mixture. The following constraints are imposed on the
coefficients:
For linear models
∑bksk = 0
For quadratic models
∑bksk = 0 (1)
∑ckjbkjsk = 0 for k = 1,,,,q (1) and for j = 1,,,,q (2)
Here ckj = 1 when j ≠ k and ckj = 2 when k = j.
and sk are the coordinates of the standard reference mixture.

If γ (gamma) are the coefficients of the interactions between the process and mixture
factors:
∑γksk = 0

Note: When the model contains terms of order 3, or contains qualitative and
formulation factors, the PLS coefficients are not adjusted relative to a stated
standard mixture.

273
User Guide to MODDE

D-Optimal Onion designs

Onion designs can be created for regular process factors, using an imported candidate
set, and using scores from SIMCA-P as design variables. When importing scores, the
scores are automatically loaded from the SIMCA-P usp-file, and the candidate set for
the Onion design is comprised of all objects (rows) in the workset of the SIMCA-P
model selected as the basis of the Onion design.
The design is made in a number of layers (shells), with a separate D-optimal design for
each layer. Typically the number of layers is two or three.
D-Optimal onion designs are similar to space filling designs in that design points are
situated also in the interior of the design space.
D-Optimal onion designs are available in MODDE only when the factors are
quantitative.
Observations in the candidate set are sorted by their distance to the center of the
multivariate space, expressed as percentiles from the center.
The candidate set is then divided into layers, by default three, layer one being the
innermost layer and layer three the outermost layer.
A D-Optimal design is then performed on each layer separately and the final design
and worksheet includes all the runs selected D-Optimally in each layer. This makes the
selected runs fill the multivariate design space.
The model and the number of runs in each layer as well as the percentile of
observations included in each layer can be specified by the user.
The D-Optimal onion design selects runs from each layer separately, ensuring that the
design will have points that fill the space.

Screening onion designs

When the objective is screening, two D-Optimal Onion design are available. The
recommended design has a full interaction model in the outer layer. The second choice
is with a linear model in the outer layer.
The default number of layers (three when the candidate set allows it) can be changed
from the Layer box. The outer layer is the last layer, and the innermost layer is number
1. The maximum allowed number of layers is default 10. You can change the Max
number of layers in Onion Design in View | General Options, tab General.
For more see the D-Optimal chapter.

RSM onion designs

When the objective is RSM, the quadratic D-Optimal Onion design is available. The
recommended design has a full quadratic model in the outer layer.
The default number of layers (three when the candidate set allows it) can be changed
from the Layer box. The outer layer is the last layer, and the innermost layer is number
1. The maximum allowed number of layers is default 10. You can change the Max
number of layers in Onion Design in View | General Options, tab General.
For more see the D-Optimal chapter.

274
Appendix C: Optimizer

Introduction
The optimizer works according to a given set of specifications. The specification of the
factors and responses are selected according to the desired result. A drawback with this
strategy can be that the best possible solution might not be reached. With unrealistic
response specifications it will be impossible for the optimizer to do a good job. With a
good strategy and by using complementary tools such as contour plots, DPMO
estimates, sweet spot plots and Design Space estimates, a good understanding for the
possibilities can be obtained.
The optimizer is used to find an experimental setpoint that fulfills various criteria. The
optimizer uses a search function to find the best possible solution to an equation
system given a number of operating criteria. The optimizer starts with a number of
criteria set in the optimizer window.
This appendix describes the possibilities and limitations of the optimizer function. The
first part is a description of how the optimizer works and the second part discusses how
different objectives can be reached by selecting different start criteria for the
optimization.

Search function
The optimizer works with a desirability function (f(ds)) that searches for the best
possible combination of factor settings that predicts a result inside the response
specifications and as close as possible to the target(s). When searching for one solution
with many criteria, the result will be a compromise. This compromise is based on a
summary function that is a measure of the distance to target for all results. It is
expressed as f(ds).
How f(ds) works depends on the weight for each response and the limit and target
specifications: the optimizer objective.

275
User Guide to MODDE

Optimizer objectives
The optimizer can be set up for different objectives:
1. Limit optimization – where the objective is to reach a solution where all
responses are within the specification limits. This is default in MODDE.
2. Target optimization – where the objective is to reach a solution where all
responses are as close to target as possible. For the target optimization it is
necessary that all responses can be optimized close to or to reach the target.
Otherwise you may end up with an unacceptable solution.
3. Focus optimization – where the objective is to favor one or several responses
over the others using individual weights.
To control the optimization criteria the weight function has a key role, as well as
reasonable limits and targets for the responses. The optimizer works with a desirability
function, f(ds), and will strive to reach the lowest possible value. The shape of the
function is controlled by the weight and the settings of criteria (Min, Target, Max) for
each response. In the following pictures two desirability functions are shown, the first
with weight=1 and the second with weight=0.2.
With the weight 1 the lowest possible f(ds) is -100 and with a weight of 0.2, the lowest
possible f(ds) is -20.

Limit optimization
With weight=1 the desirability function decreases rapidly close to the limit and then
flattens out. As consequence it will be easier to reach a compromise where all
responses are inside the specification limits but maybe not as close to target as
possible.

Weight = 1. The desirability function reached the lowest possible value, -100, just
inside the specification limit. This will work well to find a compromise when many
responses strive to get inside the specification limits. Note that in this plot the 'weight
scaled limit' and the 'limit' are displayed on top of each other.

276
 Appendix C: Optimizer

Target optimization
If all weights are set to 0.2, the optimizer will search for a target solution for all
responses if that is possible. If that is not possible, the optimizer might find a solution
that will predict some responses very close to target and some outside the specification
limits.

Weight = 0.2. The desirability function will reach the lowest possible value, -20, close
to the target. If the weight is set to 0.2 for all responses it will go for a target solution
due to the slope of the function. This solution might be unacceptable if a common
target solution isn’t present.

Focus optimization
If the weights are set differently for different responses, responses with higher weights
take priority in the search for a solution inside the specifications. The overall
optimization criterion is to reach the lowest sum of f(ds). With the weight 1 the lowest
possible f(ds) is -100 and with a weight of 0.2, the lowest possible f(ds) is -20.

Define optimizer specifications

To open the optimizer, click Optimizer on the Prediction menu. MODDE opens a
window with 3 spreadsheets. For detailed information about the optimizer window,
see the Optimizer section in the Prediction chapter.
The start specifications are from the initial factor and response definitions. If no
response specification for Min, Target, and/or Max exists the default criteria is
‘Predict’.
Reaching an optimal result is in many cases an iterative process. If the response
specifications are impossible to reach the criteria will probably have to be reevaluated.
With the help of some raw data analysis and some initial model analysis, you can get a
reasonable understanding of the possibilities.

277
User Guide to MODDE

Response specification example in the optimizer

In this example we want to minimize the NOx emission with an upper specification
limit (Max) of 25. Setting the target to 0 might seem logical but it is not possible for
the optimizer function to reach in the experimental region investigated. An inspection
of the raw data, see Replicate Plot below, shows that all NOx data are between 10 and
30. Therefore it should be impossible to get a prediction close to 0 for the current
experimental region. A more reasonable target in this case is NOx=15. The target and
max limit values are supported in the plots that follow.

Replicate Plot: All values for NOx can be found between 10 and 35.
The response Soot is minimized while the response Fuel is set to Target for
illustrational purposes. Generally we also want to minimize the Fuel consumption.

278
 Appendix C: Optimizer

Optimizer result
The optimizer will search for a solution to the specifications from 8 different starting
points using a Nelder-Mead Simplex algorithm trying to minimize the desirability
value f(ds). The result is expressed as a normalized distance to target Log(D) and
DPMO (Defects Per Million Opportunities outside specifications).
For more information about the calculations, see the Optimizer section in the
Statistical appendix.
After running the optimizer the best proposal (lowest Log(D)) is selected. A Log(D) <
-1 means that all results should be safely within specification limits. The optimal value
of Log(D) is -10; then all response predictions are on target. DPMO gives information
about robustness to small disturbances introduced by the Sensitivity Range specified
for the factors.

In the run list above, row 6 has a DPMO = 0 meaning that with disturbances + 5% on
the factor settings will give a solution inside the specifications. Row 1 has
approximately the same Log(D) but a DPMO = 7000 indicating that a small
disturbance in the factor settings from this point will result in some hits outside the
specifications. Therefore row 6 is preferable.
The result from the optimizer can be evaluated with three main tools:

• Contour Plot Wizard generates a plot around the factor settings of the
selected row, showing the dynamics around the selected point, e.g. if it is a
flat region or very sensitive to small changes. The selected run is displayed
in the plot as lines from the axes with arrows pointing toward the position of
the selected run.

• Sweet Spot Plots Wizard generates an overlay of contour plots where

the common region within specifications is shown in green. The selected run
is displayed in the plot as lines from the axes with arrows pointing toward
the position of the selected run.

• Analyze Design Space displays how the factor settings can be varied
around the selected point (optimum) and still fulfill the response criteria. We
can make an estimation of a safe DS region with Monte Carlo simulations on
the factor settings.

279
Appendix D: Design Space

Introduction
The calculation of the design space is a search function that expands the possible factor
ranges from a setpoint (optimum) to the largest possible range where all response
predictions are still within the specifications.
Predictions in the design space are done with Monte Carlo simulations. The resulting
distribution of predictions simulates a real situation with a random combination of
factor setting disturbances within a given range.
There are two Design Space features in MODDE:
• Predictive Design Space Estimation for optimization.
• Design Space Validation for robustness testing.
This chapter gives further insight to these features.

Predictive Design Space Estimation

The basis for good quality estimates is the use of a proper experimental design. The
Design Space function available by clicking the Analyze Design Space button in the
Optimizer provides:
• A good overview of where the selected point is located in the design region.
• An estimate of the largest possible factor variation that still results in
predictions within specification.
……………………
The “International Conference on Harmonisation (ICH); Draft Guidance: Q8(R1)
Pharmaceutical Development Revision
1” (http://www.fda.gov/cber/ich/ichguid.htm) has outlined quality by design (QbD)
principles for pharmaceutical development which introduced the concept of Design
Space (DS). ICH Q8 defines DS as “the multidimensional combination and interaction
of input variables (e.g. material attributes) that have been demonstrated to provide
assurance of quality”.
……………………

281
User Guide to MODDE

The predictive DS estimate shows the factor settings of the selected run in the
optimizer and the accepted variability around these settings that still result in
predictions in the accepted response region.

We can make an estimation of a safe DS region with Monte Carlo simulations on the
factor settings. MODDE will perform a search to identify the largest possible range for
each factor (faded region) that can be used and still meet all response requirements.
The default target is 1000 (0.1%) hits outside the limits (DPMO) for one response. In
this case the limiting response will be Soot, the final predictions will give 0.17% of the
predictions outside the upper limit.

Monte Carlo simulations

The Monte Carlo simulations are:
• random factor settings according to the selected distribution,
• around their optimum value but within the Low and High limits,
• followed by predictions of the responses. In this case 100 000 predictions are
performed. The distribution as well as the number of simulations and the
range can be changed by the user.
The resulting distributions can be presented as a histogram, one for each response.

282
 Appendix D: Design Space

Evaluate the results and make necessary adjustments.

If the result in some way is not satisfactory, one option can be to change the starting
point for the DS search (optimum factor setting). Another option is to lock some factor
ranges where setting tighter specifications won’t be a problem. See the Design Space
Validation for robustness testing section later in this chapter.
For alternative start points it can be preferable to step back to the optimizer and select
another start point based on Log(D), DPMO and Sweet Spot evaluation. The modeling
results, e.g. Coefficient Plot, can also be an information source to finding
alternatives. All settings can be changed in the DS estimation table for a user
controlled search in order to find the most appropriate solution.
Previously in this section we showed the results of a DS estimate starting from row 6
in the optimizer. We will now show you how selecting a different starting point can
affect the outcome of the estimation.
An alternative selection of starting point from the optimization can give
approximately the same result but a more extreme factor setting. See the following DS
estimate from the optimizer proposal of row 1. Note that in this design space
estimation we have chosen to not use the model error for a more visual illustration of
the different results. The suggested factor settings are much closer to a limit and likely
represent a less stable point of operations.

These settings give results within specifications but with a combination of factor
settings that is more extreme and close to the experimental limits. Another
consequence is that the accepted region of variability for the proposed factor settings is
narrower than the previous proposal starting from row 6.

How to find the best Design Space

1. Develop the best model for each response.
2. Find the optimal settings for the factors that comply with the response
criteria.
3. Check if the proposed optimal factor settings are critical (close to a limit) or
in a safe region.
4. Make an estimation of the safe region with Monte Carlo simulation on the
factor settings.
5. Evaluate the results and make necessary adjustments.
6. Set your preferred factor specifications.
7. Document the final results.

283
User Guide to MODDE

Design Space Validation for robustness testing

According to the FDA: “VALIDATION OF ANALYTICAL PROCEDURES:
Definition and terminology. The robustness of an analytical procedure is a measure of
its capacity to remain unaffected by small, but deliberate variations in method
parameters and provides an indication of its reliability during normal usage.”
Design Space validation is a way to test if the system investigated is robust against
disturbances in the investigated region.
The aim of robustness testing is to evaluate if a process, or a system, performs
satisfactory even when some influential factors are allowed to vary. In other words, we
want to investigate the system’s sensitivity (or preferably lack of sensitivity) to
changes in certain critical factors. The advantages of a robust process or system
include simpler process control, a known range of applicability and an ensured quality
of the product or process.
A robustness test is usually carried out before the release of an almost finished product,
or analytical system, as a test to ensure quality. Umetrics recommends the use of DoE
for robustness testing and such a design is usually centered on the factor combination,
which is currently used for running the analytical system, or the process. We call this
the setpoint. The setpoint may have been found through a screening design, an
optimization design, or some other identification principle, such as written quality
documentation. The aim of robustness testing is, therefore, to explore robustness close
to the chosen setpoint.
In Design Space Validation we use Monte Carlo simulations on the regression model
and simulate random disturbances within the investigated range of operation for all
factors. The regression model originates from a low resolution design supporting linear
models since we assume that small disturbances have mainly linear effects. Fractional
factorial resolution III and Placket Burman designs are recommended.

Design Space Validation example

In this example we show that the DoE strategy in combination with Monte Carlo
simulations here gives a proper estimate of the system's robustness.
The investigation chosen to illustrate the Design Space Validation feature originates
from a pharmaceutical company. It represents a typical analytical chemistry problem
within the pharmaceutical industry. In analytical chemistry, the HPLC method is often
mounted for routine analysis of complex mixtures. It is therefore important that such a
system will work reliably for a long time, and be reasonably insensitive to varying
chromatographic conditions. For details about this example, see the tutorial
"Robustness testing".

284
 Appendix D: Design Space

Evaluation
The Prediction | Design Space Validation tests the robustness by making a large
number of random disturbances (Monte Carlo Simulation) in the specified region. In
this example the specified region is the Experimental Region. In the DS window
(shown below) the factor part shows the original investigation settings with a specific
selection for the qualitative factor Column. ColA was manually selected as this column
gave the worst results (See Tutorial example for more information about the specific
example). The result is shown as a distribution of random samples including model
prediction errors and it is well within the specification limits for some responses. The
result can be expressed in general statistics as well as capability indexes Cpk or DPMO
= Defects Per Million Opportunities outside specifications.

A description of the details of this window is found in the Design Space window
section in the Design Space chapter.

Factor spreadsheet
All factors are varied within the design limits with Monte Carlo simulations according
to a Normal distribution. These are the default settings.

Response spreadsheet
The result for response k1 is optional; there are no specific demands for this response.
The result for response k2 is partially outside the specification limits.
The result for response Res1 is above the low specification limit.
The result for response PlateN(2) is above the low specification limit
From the above we conclude that this system is robust against disturbances in the
factors for Res1 and PlateN(2). k2 is not robust against disturbances in the factors.

285
User Guide to MODDE

Final adjustments
Design Space can be used to estimate the maximum accepted variability in factors that
still predict all results within the specifications.
The problem in the described example is response k2. The requirement for k2 is that
less than 0.1%, corresponding to DPMO = 1000, of the predictions may be outside the
specification limits.
There are constraints when handling this type of situation;
• Which factors affect the result?
• How can we adjust the factor limits without causing too much problems in
the normal use of the procedure?
First we have to check the model to understand which factors are the most influential.
The model has to be significant for an adjustment in factor ranges to have affect on the
result distribution.
In this example the model for k2 is very significant and the most important factor is
Acetonitrile (ACN).

286
 Appendix D: Design Space

Assuming that the factor Temperature is easy to control with a narrower range we start
with this factor by adjusting temperature to +/- 0.5 °C. At the same time we can open
the Role for ACN to 'Free'. This instruction together with the specification limit for k2
(DPMO = 1000) will give an estimate of a range for ACN where we can predict that
the system is robust according to the specifications. The picture below displays the
result of the settings.

The proposed settings for ACN are now 25.51 to 26.49 and the estimated distribution
for k2 is 1410 hits outside the specification limits.
A final step might be to make an adjustment of the factor settings to some practical
new specification within the range for ACN, for instance 25.5 to 26.5. The result
shown below implies that the critical response k2 will have 0.16% of future predictions
outside the specifications.

287
User Guide to MODDE

Result statistics for k2

To open the response histogram, click the Create Histogram button in the Design
Space window.
In the Response box on the Standard toolbar, select which responses to display.

To view statistics, right-click the Design Space window, and then click Design Space
Statistics.

A more detailed description of this example is found in the tutorial named “Robustness
Testing”.

288
References

1. R.A. Fisher, “Statistical methods, experimental design, and scientific

inference”, A re-issue (J. H. Bennett, Ed.), Oxford University Press, Oxford,
England, (1990).
2. G.E.P.Box, W. G. Hunter, and J. S. Hunter, “Statistics for experimenters”,
Wiley, New York, (1978).
3. G.E.P. Box, The collected works, Vol 1. (G.C. Tiao, Ed.), Wadsworth
Advanced Books and Software, Belmont, CA, 1985.
4. Morgan, Chemometrics: Experimental Design, ACOL, London, and Wiley,
New York, (1991).
5. Wold, “Soft modeling, The basic design and some extensions”, In Vol. II of
K-G. Jöreskog and H. Wold, Ed.s. Systems under indirect observation, Vol.s
I and II, North-Holland, Amsterdam, (1982).
6. Wold, A. Ruhe, H. Wold and W. J. Dunn III, “The Collinearity Problem in
Linear Regression. The Partial Least Squares Approach to Generalized
Inverses”, SIAM J. Sci. Stat. Comput. 5, 735-743, (1984).
7. Höskuldsson, “PLS Regression Methods”, J.Chemometrics, 2, 211-228,
(1988).
8. Wold. “Cross validatory estimation of the number of components in factor
and principal components models”, Technometrics 20, 397, (1978).
9. Draper and Smith, “Applied Regression Analysis”, Second Edition, Wiley,
New York.
10. Cornell, “Experiments with Mixtures”, New York: Wiley, (1990).
11. Cox, “A Note on Polynomial Response Functions for Mixtures”, Biometrica,
58, 155-159, (1971).
12. Crosier, “Mixture Experiments: geometry and Pseudo components”,
Technometrics, 26, 209-216, (1984).
13. Kettaneh-Wold, “Analysis of mixture data with partial least squares”,
Chemometrics and Intelligent laboratory Systems, 14, 57-69, (1992).
14. Rechtschaffner R.L., Saturated fractions of 2n and 3n factorial designs,
Technometrics, 1967, Vol.9, N°4, 569-575.
15. Ing-Marie Olsson, Erik Johansson, Martin Berntsson, Lennart Eriksson,
Johan Gottfries, and Svante Wold, “Rational DOE-protocols for 96 well
plates”, Chemometrics and Intelligent Laboratory Systems, 2006.
16. Doehlert, D.H., “Uniform shell designs”, Journal of the Royal Statistical
Society, 1970, Serie C, N°19, 231-239.
17. Snee, “Test Statistics for Mixture Models”, Technometrics, Nov. 1974.

289
User Guide to MODDE

18. Nordfelth, R., et al., 2005 Small-Molecule Inhibitors Specifically Targeting

Type III Secretion, Infection and Immunity, 73, 3104-3114.
19. Design space; ICH Q8(R1) Pharmaceutical Development Revision 1,
http://www.ich.org/cache/compo/276-254-1.html.
20. Quality by Design; http://en.wikipedia.org/wiki/Quality_by_Design

290

Index
2  Organization ................................... 133
2D contour ................................... 167, 187
3  Analysis phase ......................................... 2
3D
Labels..............................................216
Onion plots......................................115
Rotation response surface .................41
Scatter ............................. 115, 126, 176
Surface ............................................172
Zoom and rotate ................ 41, 214, 220
4 
4D
Contour ...........................................169
Sweet spot .......................................177
A  Axes ............................................ 174, 207
Abbreviation .................................... 65, 75
Absolute Limits ...................................181
Accelerators ......... 30, 31, 45, 64, 221, 224
Activation ............................................229
Add
Command to Favorites ......................46
Experiments ....................................131
Factor .......................................... 27, 65
Inclusions ..........................................90
Response ..................................... 32, 75
Row ...................................................32
Squares and interactions.............. 34, 38
Terms ................................................34
To Favorites ......................................51
To Report .................................. 51, 228
Add to Favorites ....................................51
Add to Report ........................................51
Adjust according reference .......... 174, 243
Alpha level ............................................54
Analysis
Fit............................................ 136, 137
Menu ......................................... 15, 133
Of variance ............................. 150, 238
Phase ............................................... 2, 9
Wizard ............................................ 135
Analysis Advisor ................................... 45
Analysis menu
Select Fit Method ............................ 136
Analysis of Variance ................... 150, 238
Analysis Wizard .................................. 135
Arrow .................................................... 41
Audit trail .............................................. 53
Augmenting designs .............................. 23
Auto update predictions....................... 176
Auto, MLR, PLS, Scheffé ................... 137
Automatic fit ......................................... 59
Automatic update .......................... 59, 205
Autoscale modifier ................................ 77
Axial designs ....................................... 265
AXN .................................................... 265
AXR .................................................... 265
B 
Balanced ...................................... 106, 257
Block
Blocking............................................ 56
Blocks ....................................... 95, 102
BlockV ............................................ 131
D-Optimal designs .......................... 252
Interactions ............................. 102, 250
Mark ................................................. 41
Orthogonal ...................................... 250
Random..................................... 56, 253
RSM designs ................................... 252
Screening designs ........................... 251
Box Behnken designs .......................... 260
Box Whisker........................................ 128
Box-Cox plot ............................... 147, 243
291
User Guide to MODDE
Buttons
Command menu bar ........................222
Format bar .......................................226
Generate report bar .........................226
Optimizer buttons............................185
Plot bar ..............................................41
Spreadsheet bar .................................41
Standard bar ......................................39
Status bar ..........................................44
Window bar.......................................44
C  Candidate set..................................... 89
Candidate runs .....................................112
Candidate set
Constraints in qualitative and
multilevel ..........................................89
Created by MODDE .......................268
Imported ..........................................111
Max size ............................................59
Candidate set section ...........................107
Case sensitivity ......................................10
CCC
Design .............................................260
Settings .............................................99
CCF .....................................................260
Central Composite design
Circumscribed
Design .............................................260
Settings .............................................99
Centroid ................................. 34, 265, 272
Classical mixture designs ....................265
Coding qualitative factors....................241
Coefficients ................... 55, 152, 240, 241
Collinearity ..........................................264
Color
Scatter plot ......................................176
Sweet spot plot ................................177
Worksheet .......................................131
Color by variable .................................176
Command menu bar ..............................13
Compatibility .......................................111
Complement design
Doehlert ............................................27
D-Optimal .........................................25
Estimate square term .........................24
General..............................................23
Inclusions .................................. 90, 271
292
PBSS to PB ..................................... 258
Screening to RSM Rechtschaffner .... 28
Condition Number ............................... 236
Confidence interval for predictions ..... 242
Confidence level
Changing ........................................... 56
Used in .... 145, 149, 150, 173, 175, 176
Confoundings .............................. 152, 202
Constraint
Constraints supported ....................... 86
Defining ................................ 85, 86, 87
Mixture ........................................... 264
Modifying graphically ...................... 88
Qualitative or multilevel ................... 89
Why .................................................. 85
Continue Edit Report With .......... 222, 226
Contour
Customize ............................... 213, 214
From Optimizer .............................. 187
Insert text .......................................... 41
Labels ............................................. 214
Levels ............................................. 214
Options............................................ 214
Plot .................................. 167, 169, 187
Wizard .................................... 166, 187
Contour levels ..................................... 214
Controlled.............................................. 68
Convention ............................................ 10
Coordinate Reader ................................. 41
Copy .................................................... 188
Correlation................... 129, 162, 163, 232
Correlation matrix ......................... 60, 129
Correlation plot ................................... 129
Cross-validation rules .......................... 234
Cubic centroid ................................. 6, 265
Cubic model .................................. 34, 260
Cubic terms ......................................... 234
Curvature ............................................. 125
Customize
Contour plot ............................ 213, 214
Header and footer............................ 209
Properties of the axes ...................... 207
Properties of the plot area ............... 210
Scatter plot ...................................... 216

Toolbars, commands, options ..... 39, 61
D  to target ........................................... 186
Decimal ......................................... 71, 207
Default options ......................................52
Default plot settings.............................206
Default template .......................... 222, 226
Degrees of freedom .............................239
Delete investigation ...............................21
Deleted Studentized Residuals .... 146, 241
Derived responses
Defining ............................................78
Operators...........................................81
Qualitative factors .............................82
Sets of variables ................................80
Syntax ...............................................81
Description button ...............................101
Descriptive Statistics ...........................128
Design
Advanced designs .............................18
Import design from file .....................21
Traditional designs ............................18
Design augmentation ...........................271
Design Region ............................. 201, 202
Design Runs .......................... 97, 104, 112
Design Runs Span ...............................106
Design Space
Buttons ............................................194
Estimation ............................... 190, 191
Statistics .................................. 197, 254
Validation .......................................284
Window...........................................192
Design Wizard ............................... 64, 117
Desirability ..........................................248
Detect curvature .......................... 124, 125
Determinant
Criteria .................................... 106, 271
D-Optimal design maximizes ..........268
Log .......................................... 109, 271
Normalized Log ..............................109
DF residuals.........................................134
DFresid ................................................239
Diagnostic part ....................................152
Diagnostics .................................. 125, 143
Index
Distance
to model .......................................... 146
DModY ............................................... 146
Dockable Windows ............................... 44
Doehlert ......................................... 27, 262
D-Optimal
Algorithm........................................ 269
Complement...................................... 25
Onion design ........................... 113, 274
Pages ....................................... 108, 122
Results ............................................ 108
Summary ......................................... 203
What ....................................... 103, 268
When....................................... 103, 272
E 
Edge ............................................ 203, 265
Edit menu .............................................. 31
Edit model ............................... 34, 99, 104
Effects ................................................. 155
E-format ................................................ 52
Eigenvalues ................................. 134, 236
Email ..................................................... 22
Encrypt .................................................. 29
Estimate squares .................................... 23
Evaluate ............................... 109, 134, 271
Evaluation plot .................................... 184
Exclude button ...................................... 41
Exclude tool .......................................... 41
Execute folder ....................................... 46
Exit ........................................................ 30
Experiment Name .......................... 52, 131
Experiment Number ...................... 52, 131
Experimental cycle .................................. 1
Experimental design .......................... 5, 10
Exporting Favorites configuration ......... 50
Extended................................ 57, 200, 204
Extended Axial .................................... 265
External variability ...................... 124, 250
Extreme Vertices ................................. 203
293
User Guide to MODDE
F  Full factorial design ..................... 257, 260
Factor
Add ...................................................32
Advanced page ..................................69
Definition ..........................................65
Max number ......................................67
Mixture and process ........................ 263
Modifying .........................................73
Name .................................................10
Qualitative................................. 82, 241
Scaling ...................................... 70, 235
Setting ...............................................67
Spreadsheet .......................................72
Transformation..................................70
Types ................................................67
Use ....................................................68
Factorial designs .......................... 257, 260
Favorites
Add command ...................................46
Add to Favorites................................51
Button ...............................................39
Create a new folder ...........................46
Restore ..............................................61
Window....................................... 45, 46
F-distribution ............................... 149, 150
Filler ................................................ 67, 68
Fit
Goodness of ....................................239
Lack of ............................ 140, 149, 150
Model ...................................... 136, 137
Multiple Linear Regression (MLR).231
Partial Least Squares (PLS) ............232
Summary .........................................139
Fit methods .............................. 7, 231, 232
Fold over ......................................... 23, 24
Folder .............................................. 45, 46
Footer .......................................... 209, 214
Format
Axes ................................................207
Bar in report ....................................226
Header/Footer .................................209
Menu in report ................................225
Plot area ..........................................210
Formulation ............................. 67, 68, 263
Fractional factorial
Complement ......................................23
Design .............................................257
Free Mark ..............................................41
294
Full Factorial Mixed ............................ 257
Full Screen ...................................... 44, 51
G 
G-efficiency......................... 108, 112, 203
General Options
General page ..................................... 59
List presentation................................ 57
Restore .............................................. 61
General page.................................... 59, 66
Generate D-Optimal button ................. 107
Generate new ............................... 107, 186
Generate Report bar ............................ 226
Generate Report window ..................... 222
Generators ................................. 37, 38, 99
Grab Plot ..................................... 224, 226
Graeco-Latin square ............................ 258
Gridlines ...................................... 207, 212
H 
Hat matrix ........................... 239, 241, 242
Header ......................................... 209, 214
Help ............................................. 226, 229
Help menu ........................................... 229
Help-button ......................................... 229
Hierarchy ............................................. 234
High Limit ........................................... 181
Histogram ............................................ 127
Hypercube ........................................... 260
Hyperlink ............................................ 224
Hyper-triangles .................................... 262
I 
Image................................................... 224
Import
Candidate set............................. 18, 111
Design from file ................................ 21
Favorites configuration ..................... 50
Scores ....................................... 18, 111
Worksheet to inclusions .................... 92

Inclusions
Added to the worksheet.....................90
Design augmentation ......................271
Editing inclusions..............................92
Generating.........................................92
Part of the design ..............................91
vs. complement design ......................90
Increment.............................................207
Insert Image .........................................226
Insert Rows.............................. 32, 92, 176
Installation ...............................................1
Interactions .............................. 34, 99, 158
Interior points ......................................265
Interpreting the model .........................152
Investigation Options.............................52
Irregular region ....................................272
L  Hierarchy ........................................ 243
Labels ..................................................176
Lack of Fit
Alpha level ........................................54
ANOVA ..........................................238
DF ...................................................134
Model validity .................................140
Plot ..................................................149
Latent structures ..................................232
Layers .................... 59, 112, 258, 261, 274
Layers overlap .....................................112
L-designs ................................... 5, 18, 258
Legend ......................................... 210, 214
Line style .............................................210
Linked responses ...................................82
List presentation ....................................57
Loading plot ................................ 162, 163
Lock
Contour levels .................................213
Investigation......................................29
Log
Determinant ............................ 109, 271
In audit trail.......................................53
LogDet.................................................271
LogdetNorm ................................ 109, 271
Low Limit............................................181
Index
M 
Main Effect.................................... 58, 157
Manage licenses .................................. 229
Maximum runs .................................... 199
Menu item ............................................. 10
Mid-range ...................... 70, 235, 236, 240
Minimum ..................................... 207, 248
Mip-file ................................................. 11
Missing ................................................ 237
Mixture
and process factors .................. 247, 263
Constraint........................................ 264
Contour plot wizard ........................ 166
Data................................................. 243
Designs ........................................... 263
Experimental region ........................ 264
Factor definition.............................. 263
Irregular region ............................... 272
Models ............................................ 243
Prediction plot wizard ..................... 173
MLR scaling .................... 70, 77, 235, 236
MLR solution from PLS ...................... 234
MODDE .................................... 1, 11, 230
Model
Distance .......................................... 146
Fit............................................ 136, 137
Hierarchy ........................................ 234
Individual ........................................ 134
Interpret .......................................... 152
List .................................................. 204
Saturated ......................................... 142
Select .......................................... 38, 95
What is ................................................ 5
Model bar .............................................. 44
Model predictive power....................... 233
Model validity ..................................... 140
Multilevel factor .................................... 67
Multiple Linear Regression ............. 7, 231
Multiplots ...................................... 39, 206
Multivariate ................................... 18, 232
N 
Network installation ............................ 229
New ......................................... 11, 17, 226
295
User Guide to MODDE
New From Default Template ...............226
New worksheet from file .......................21
Next Component
Analysis menu......................... 137, 138
Extract .............................................138
MLR solution from PLS .................234
No Mark ................................................41
Non-English ........................................214
Normal probability ...................... 143, 156
Normalized coefficients................. 55, 152
Normalized Log Determinant ..............109
Number format ................................ 52, 60
Number of decimals ...................... 71, 207
N-value ................................................237
O  Overall distance to target ..................... 184
Objective ................................... 5, 94, 199
Observed vs Predicted ................... 41, 148
Office 2003.............................. 59, 61, 224
Older MODDE versions ........................11
Onion
Candidate set ...................................111
Design ............................. 258, 261, 274
Generate .................................... 18, 113
Layers max........................................59
Plots ................................................115
Onion D-Optimal ......................... 112, 113
Open All Items ......................................46
Open investigation .................................21
Operators ...............................................81
Optimization criteria............................181
Optimizer
Copy to prediction list .....................188
Definition ........................................248
Generate new ..................................186
Generating the start runs .................185
Lists ........................................ 181, 183
Log ..................................................183
Play button ......................................186
Running the Optimizer ....................186
Optimizer buttons ................................185
Optimizer runs .....................................186
296
Options
Customize ......................................... 61
Default .............................................. 52
General.............................................. 58
List .................................................... 60
Scaling .............................................. 70
Options button ..................................... 169
Organization .................................. 12, 133
Orthogonal
Blocking.................................. 102, 250
Correlation ...................................... 129
Scaling .............................. 70, 235, 236
Scaling by MODDE ................ 111, 264
Settings ........................................... 200
Outliers ........................ 143, 146, 162, 232
Output.............................................. 50, 59
Overlay prediction ....................... 173, 174
P 
Partial Least Squares ....................... 7, 232
Password protect ................................... 29
Paste Design .......................................... 94
Paste unformatted ................................ 224
PBSS ................................................... 258
Percent......................................... 113, 177
Placeholders ........................ 224, 226, 227
Plackett Burman .................................. 258
Plackett Burman Super-Saturated........ 258
Plate-Size ...................................... 18, 259
Plot area....................................... 210, 214
Plot bar .................................................. 41
Plot Labels............................................. 52
Plot Loadings .............................. 163, 242
Plot options.................................. 166, 213
Plot Settings
3D scatter ........................................ 216
Axis................................................. 207
Header and footer............................ 209
Plot area .......................................... 210
Plots....................................... 16, 205, 228
PLS plots ............................. 162, 163, 242
PLS Scaling ............................. 71, 77, 235

PLS summary list ................................142
PLS Summary plots ..................... 139, 141
Potential terms ............................. 203, 269
Prediction
Copy from optimizer .......................188
Derived responses .............................78
Formula ...........................................242
Linked responses ...............................82
Plot wizard ......................................173
Response prediction plot .................175
Scatter plot ......................................176
Sweet spot plot ................................177
Prediction List .....................................176
Prediction plot wizard..........................173
Predictivity ..............................................4
PRESS/SSY .............................................7
Print .......................................................30
Print format dialog.................................30
Print preview ................................... 30, 39
Print setup..............................................30
Print-button............................................30
Process and mixture factors .................263
Product ID ...........................................229
Program limits ............................... 59, 107
Properties window in report ................228
Property page............................... 205, 213
Protect investigation ..............................29
Pseudo components ..................... 137, 200
Pseudo-resolution ................................250
Pure error ..................................... 134, 150
Q  Report/template ................................... 226
Q2 ................................................ 140, 239
Qualitative factors ................... 67, 82, 241
Quantitative ............................. 67, 69, 263
Quantitative multilevel .............. 67, 68, 69
R  Residuals ....................... 58, 144, 145, 241
R2 .................................. 57, 139, 142, 239
Random ................................... 56, 61, 253
Index
Range
Contour level range ......................... 214
Curvature ................................ 124, 125
Factor ........................................ 67, 181
Recalculate Scale button ..................... 207
Rechtschaffner design ................. 259, 261
Recommended designs .................. 95, 274
RED-MUP ....................... 18, 59, 259, 261
Reduced Axial ..................................... 265
Reduced CCC ...................................... 260
Reduced CFF ....................................... 260
Reference mixture ......................... 34, 204
Regions................................................ 214
Register ............................................... 229
Regression ........................................... 231
Regular presentation ...................... 57, 200
Regular responses .................................. 77
Remove
All Placeholders .............................. 225
Button ................................. 32, 34, 214
Encryption ........................................ 29
or add header/footer ........................ 209
Placeholder ............................. 225, 226
Terms ................................................ 34
Rename...................................... 46, 61, 82
Repetitions................................... 106, 112
Replicate plot ...................................... 130
Replicate tolerance ................ 59, 130, 201
Replicated experiments . 97, 130, 134, 150
Report Generator ........................... 22, 221
Report Generator FAQ window .......... 226
Reproducibility ............................ 140, 141
Reset button........................................... 34
Residual Standard Deviation ............... 237
Residual types ..................................... 146
Residuals plots .................................... 144
Resolution III ................................ 23, 257
Resolution IV designs ......................... 257
297
User Guide to MODDE
Response
Add ........................................... 32, 119
Box............................................ 39, 206
Definition .................................... 75, 83
Exclude using modifier .....................77
Manipulations ...................................84
Name .................................................10
Regular..............................................77
Spreadsheet .......................................83
Sweet spot .......................................177
Response box................................. 39, 206
Response Surface Modeling ...... 6, 94, 260
Response value label .............................41
Restore...................................................61
Revert ....................................................22
Rich Text Format...................................50
Robustness ................................... 192, 284
Role .....................................................181
Rotate ............................................ 41, 220
Rotation ................................. 41, 207, 220
RSD ............................................. 237, 239
RSD*sqrt .............................................150
RSM Objective ................................ 94, 95
Run list ................................................183
Run Optimizer ............................. 185, 186
Run order ....................... 52, 124, 131, 144
Runs....................................... 97, 186, 268
S  Select fit method.................................. 137
Safe Region ................................. 190, 191
Saturated Models .................................142
Save
Audit trail ..........................................53
Button ....................................... 39, 226
Inclusions ..........................................90
Investigation......................................21
Plot or list .................................. 21, 205
Plot settings ............................. 206, 212
Save As.......................................... 21, 205
Save Format dialog ................................21
Save List As .................................. 21, 205
Save Plot As .................................. 21, 205
Save Settings ............................... 206, 212
298
Save Settings button ............................ 206
Scale
Contour plot ............................ 213, 214
Options.............................................. 70
Scale XY ............................................... 41
Scaled coefficients............................... 240
Scatter plot
3D or 2D ......................... 115, 126, 176
Loading ................................... 162, 163
Onion .............................................. 115
Plot settings..................................... 216
Score ............................................... 162
Scheffé ........................................ 137, 236
Scientific ....................................... 52, 207
Score ............................. 18, 111, 162, 274
Score column plot................................ 162
Score vectors ....................................... 162
Screening ....................................... 94, 257
Screening complemented ...................... 23
ScreenTips ............................................. 61
SD ............................................... 149, 150
SD Regression ..................................... 150
SD-LoF................................................ 149
SD-pe .................................................. 149
SD-pe*sqrt........................................... 149
SDY..................................................... 141
Select all ................................................ 31
Send by e-mail....................................... 22
Set Run Order ................................ 15, 124
Settings
Button ............................................... 38
Copy factor settings ........................ 188
D-Optimal ....................................... 122
Factor ................................................ 67
Investigation ..................................... 59
Plot .................. 206, 207, 209, 210, 214
Restore .............................................. 61
Saving ..................................... 206, 212
Show ............................................... 200
Shaded ................................................. 214
Shortcut menu ..................................... 205

Show
All Placeholders ..............................225
Details button ....................................58
Menu .................................................16
Placeholder...................... 225, 226, 227
ScreenTips on toolbars ......................61
SimC ....................................................265
SIMCA-P............................... 18, 111, 274
SimF ....................................................265
SimM ...................................................265
Simplex ...............................................264
SimSC .................................................265
Slack variable ......................................272
Slide.......................................................61
Sort ................................................ 32, 155
Special Cubic Model ...........................265
Split objective .................................. 94, 99
Spreadsheet................................ 41, 72, 83
Square terms ..........................................95
SS ........................................ 139, 140, 238
SS explained ........................................232
Standard bar...........................................39
Standardized residuals ................. 146, 241
Star Distance .........................................99
Start runs .............................................185
Status bar ....................................... 44, 224
Stdev................................................ 80, 81
Styles ...................................................225
Summary D-Optimal ...........................203
Summary List .............................. 141, 142
Summary plot .............................. 139, 141
Surface......................................... 172, 214
Sweet Spot Plot ........................... 177, 189
Symbol Style .......................................210
Syntax for derived responses .................81
System default .......................................61
T  Predictions ...................................... 176
Tagushi ....................................................5
Target in Optimizer ..................... 181, 248
T-button ................................. 41, 167, 169
Index
Templates ............................ 222, 224, 226
Text file ................... 21, 92, 107, 111, 224
Theme.................................................... 59
Tile Windows ........................................ 44
Time .................................................... 207
Time stamp .......................................... 209
Title ............................................. 207, 209
Toolbars
Command menu in report ............... 222
Customize ......................................... 61
Format bar in report ........................ 226
Generate report bar in report ........... 226
Model ................................................ 44
Plot .................................................... 41
Reset ................................................. 61
Spreadsheet ....................................... 41
Standard ............................................ 39
Status ................................................ 44
Window ............................................ 44
Tools menu .......................................... 225
Traditional designs ................................ 18
Transformations .............. 70, 77, 147, 264
Treat folder as item ............................... 46
Txt ........................... 21, 92, 107, 111, 224
U 
Uncentered .......................................... 236
Uncentered coefficient ........................ 240
Unconfound ........................................... 99
Uncontrolled .................................. 68, 237
Undo .................................. 31, 34, 39, 226
Unfold ................................................... 61
Unit Variance .......................... 70, 71, 235
Unit variance coding ................... 137, 236
Unit variance scaling ..................... 70, 235
Units ................................................ 65, 75
Update
Constraint-button .............................. 88
Placeholder button .......................... 227
Placeholders .................... 225, 226, 227
Report ....................................... 22, 225
URL..................................................... 224
Use True Type ..................................... 214
299
User Guide to MODDE

Usp-file .......................................... 18, 111 Worksheet

Add experiment ................................ 32
V  Copy ................................................. 31
Variable importance ............................161 Description...................................... 131
Design matrix.................................. 200
View menu .................................... 14, 224 Menu ............................................... 123
View/Hide Toolbars ..............................14 Missing data .................................... 237
Open ................................... 39, 41, 123
W  Sort ................................................... 32
WC plots...................................... 163, 242
X 
Weight ......................................... 163, 181
X Mark .................................................. 41
Window
X'X
Bar ....................................................44
Condition number ........................... 236
Dockable ...........................................44
Eigenvalues ............................. 134, 236
Menu .................................................16
Matrix ..................... 258, 260, 268, 271
Toolbar..............................................44
Wizard Y 
Analysis Wizard ..............................135
Y Mark .................................................. 41
Contour plot wizard ........................166
Design wizard ...................................64 Y-miss ................................................. 237
Prediction plot wizard .....................173
Z 
Workset ....................................... 111, 274
Zoom ............................................. 41, 220

300