User Guide SDMtoolbox

SDMtoolboxUserGuide
ByJasonL.Brown,TheCityCollegeofNewYork
Lastupdated:10/14/2014
TheSDMtoolboxconsistsofaseriesofpythonscriptsdesignedautomatecomplicatedArcGISanalyses
thatareoftentoodifficult/tediousfortheaverageGISusertoexecuteefficiently.Thistutorialgivesa
basicintroductiontouseSDMtoolboxforecologyandevolutionstudies.Alargesetofthetoolshereare
designedtocomplementMaxEntspeciesdistributionmodels(SDMs)ortoimprovethepredictive
performanceofMaxEntmodels.TheMaxEntprogramusesmaximumentropymodellingofspecies
geographicdistribution(Phillipsetal.2006)andhasbecomeoneofthemostprevalentmethodsdueto
itshighpredictedperformance,computationalefficiencyandeaseofuse.Manyoftheanalysesarealso
availableforuseonotherSDMmethods(see:SDMTools1.UniversalTools).
IfyouusetheSDMtoolboxpleaseremembertociteit.Bycitingthisyouencouragethedevelopment
ofmoretools.
Pleaseusethefollowingreference:
Brown,J.L.(2014)SDMtoolbox:apythonbasedGIStoolkitforlandscapegenetic,biogeographicand
speciesdistributionmodelanalyses.MethodsinEcologyandEvolution

TableofContents
GettingStarted.............................................................................................................................................5
Downloading.............................................................................................................................................5
Installation................................................................................................................................................5
Uninstallingorupdating..6
AFirstRun.................................................................................................................................................7
AnalysesGuide...........................................................................................................................................10
Chapter1.BiodiversityMeasurements.....................................................................................................12
EstimateRichnessandEndemicity(WEandCWE)................................................................................13
ARCGISSTEPBYSTEPGUIDE:...................................................................................................................13
SDMTOOLBOXSTEPBYSTEPGUIDE:.........................................................................................................14
Results.................................................................................................................................................15
Chapter2.LandscapeConnectivity...........................................................................................................18
LandscapeConnectivity..........................................................................................................................19
Results.................................................................................................................................................23
Chapter3.SpeciesDistributionModelingTools.......................................................................................24
CorrectingLatitudinalBackgroundSelectionBias................................................................................24
Solution1................................................................................................................................................25
Tool:1.BiasFileforCoordinateData(BFCD)inMaxEnt..................................................................25
ARCGISSTEPBYSTEPGUIDE:...............................................................................................................25
SDMTOOLBOXSTEPBYSTEPGUIDE:.....................................................................................................26
Tool:2a.BackgroundSelection:SamplebyBufferedMCP..............................................................27
Tool:3.ClipBFCDbyBSBiasFile.......................................................................................................28
Solution2................................................................................................................................................29
Tool:1.CSVtoEAP.MaxEntformatoutput(runsboth1aand1b).................................................29

Tool:2.ProjectClimateData(Raster)toEqualAreaProjection(Folder)........................................31
DistributionChangesBetweenBinarySDMs.........................................................................................32
Tool:CentroidChanges(Lines)..........................................................................................................32
Tool:DistributionChangesBetweenBinarySDMs...........................................................................34
Results.............................................................................................................................................35
OverpredictionCorrection:ClipModelsbyBufferedMinimumConvexPolygons...............................36
Tool:BinaryModels(folder)..............................................................................................................36
Results.............................................................................................................................................38
Tool:ContinuousModels(folder)......................................................................................................39
Results.............................................................................................................................................40
BackgroundSelectionviaBiasFiles.......................................................................................................41
Tool:BackgroundSelection:SamplebyBufferedMCP....................................................................42
Tool:BackgroundSelection:SamplebyDistancefromObs.Pts......................................................43
CreateFrictionLayer:InvertSDM..........................................................................................................44
Results.................................................................................................................................................46

SpatiallyRarefyOccurrenceData.45
ARCGISSTEPBYSTEPGUIDE:..46
SDMTOOLBOXSTEPBYSTEPGUIDE:....46
Chapter4.BasicTools:Raster,CSV&Shapefiletools..............................................................................50
Tool:CSVtoshapefile.............................................................................................................................50
Chapter5.RunningaSDMinMaxEnt:fromstarttofinish.....................................................................51
DataPreparation................................................................................................................................51
1.PreparingWorldclimData51
2.TestingAutocorrelationsofEnvironmentalData...54
3.PreparingOccurrenceData..55
4.CreationofBiasFiles..62
ModelCreation,CalibrationandEvaluation..64
5.SpatialJackknifing.64

GettingStarted
Downloading
Thelatestversionofthetoolboxisavailablefordownloadat:www.sdmtoolbox.org.Thissoftware
requiresArcMap10.1or10.2withanactiveSpatialAnalystlicense(www.ESRI.com).Thistoolboxis
programedspecificallyforArcMap10.1(andabove)andduetoaseriesofimprovementsinthisversion,
itisnotbackwardscompatiblewitholderreleasesofArcMap(i.e.ArcMap9.2).Thissoftwareconsists
ofanArcGIStoolboxandassociatedpythonscripts.
Installation
1.Download,unzipSDMtoolbox.zipandplaceallfilesinafolderonyourharddrivewhereyouwantthe
toolboxtobestored(e.g\Documents\ArcGIStoolboxes)
2.CloseallArcGISprograms
3.OpenArcCatalog10.1(aprogramintheESRIArcGISprograms,seeiconbelow)

Above:ArcCatalogIcon
4.Onceopen,activatetheArcToolboxwindow(ifnotalreadyvisible)byclickingtheredboxbelow

5.ThenrightclickArcToolboxWindow(seeimagebelow)selectAddToolbox.Thengotolocationof
downloadedtoolboxandselectSDMToolboxv1.0.tbx
6.ThetoolboxshouldappearinsidetheArcToolbox(seehighlightedtoolboxtoright).Ifthere,nowthe
toolboxisalmostinstalled.
7.Tofinishinstallationsimplyclosethe
ArcCatalogprogram.
8.NowstartArcMapandbeginusing
theSDMtoobox!

HowtoupdateoruninstallSDMtoolbox
1.CloseallArcGISprograms
2.OpenArcCatalog10(aprogramintheESRIArcGISprograms,seeiconbelow)

Above:ArcCatalogIcon
3.Onceopen,activatetheArcToolboxwindow(ifnotalreadyvisible)byclickingtheredboxbelow

4.ThenrightclickSDMtoollboxinArcToolbox
Window(seeImagetoright)andselectRemove.
5.Ifonlyuninstalling,thenyouaredone.If
installinganewversionofSDMtoolboxthenright
clickArcToolboxWindow(seeimagebelow)
selectAddToolbox.Thengotolocationof
downloadedtoolboxandselectSDMToolbox
v1.X.tbx
6.Thetoolboxshouldappearinsidethe
ArcToolbox(seehighlightedtoolboxtoright).If
there,nowthetoolboxisalmostinstalled.
7.TofinishinstallationsimplyclosetheArcCatalogprogram.
8.NowstartArcMapandbeginusingtheSDMtoobox!
AFirstRun
ManythingswillcausetheSDMtoolboxtonotrunthathavenothingtodowiththetoolboxitself.Upon
firstuse,thefollowingstepsshouldbeperformed:
1. OpenArcMap10.1andactivatetheArcToolboxwindow(ifnotalreadyvisible).Bottomimage
onthispageistheArctoolboxwindow.Ifnotvisible,clicktoolboxicon(seeimagebelow).

2. EnsureSpatialAnalystisEnabledinArcMap

A. Goto:CustomizeExtensionsB.Checktheboxnextto:SpatialAnalyst
(andGeostatisticalAnalystifavailable)

3. InstallallrelevantArcMap10.1or10.2PatchesandServicePacks.
ThebasereleaseofArcMap10.1/2hassomeseriousbugsthatcausemanyanalysestofail.The
onlywaytofixthesebugsistheinstallallrelevantpatchesandservicepacks.
A. Tosearchforthesegoto:
http://support.esri.com/en/downloads/patches
servicepacks/list?productid=160&productVersions=10.1&categoryTypes=5&categoryTypes=8
Or:http://support.esri.com/en/downloads/patchesservicepacks
B. OrusetheESRIsPatchFinderforWindowstoidentifypatches,thensearchforsuggested
patches/servicepacks(http://downloads2.esri.com/Support/downloads/other_/PatchFinder.exe)

4. EnableToolHelpandresizewindows.

OpentheBasicToolsRasterTools2a.Raster
toASCII(Folder)tool.DoubleClickthetool(see
imagetoright)

A. InthenewlyopenedtoolclickShowHelp(redboxabove)

B. Resizethewindowbydraggingthetwowindows(depictedbyredarrows)sothatthefinal
toolwindowisasbelow.NotetheSDMtoolboxIconshouldbefullyvisible.Resizingthe
helpwindowtothissizewillensurethatalldiagramsarecompletelyvisible.

Anoteonmapprojections
Mostuserreportederrorshavetodowithmapprojections.Asfollowsisachecklistofthingsyouneed
tocheckifyouhaveascriptfail.Inmostcasesyourdatashouldbeprojected,withtheprojection
specifiedintheGISfile.
1. Ifyouchangeordefinethemapprojectionafteropeningthemapdocument.YouNEEDto
saveallprojectedfiles,thenclosethemapdocumentandopenanewmapsession.Thefirst
fileopeninyournewsessionneedstobeoneofthenewlyprojectedfilesthisdefinesthemap
datum.Thisisparticularlyimportantifyouchangethespatialunitsastheresultofprojection,
e.g.decimaldegreestometers.Ifyoudonotdothis,oftenSDMtoolboxscriptswillfailorresult
ininaccurateresults.

2. IfthetoolrequiresaCSVofcoordinatesANDyouranalysesaregoingtobeinanother
projection,remembertoconvertinputcoordinates(orXYs)tothenew,andsame,datumprior
torunningtoolsorforuseinspeciesdistributionmodeling.
Formost,thequickestwaytodothisforCSVfiles(andothertables)isto:
1)ImporttheCSVtoashapefile(Table&ShapefileToolsCSVtoshapefiletool)
2)Defineinputprojectionofshapefileandthenprojecttothenewprojection(a.
ArcGISdefineprojectionandb.projecttools)
3)Addthenewcoordinates/XYstoShapefileusingtheArcGISAddXYstool
4)ExportshapefiletableasCSVfile(SDMtoolboxtheTable&ShapefileTools
ShapefiletoCSVtool)
IfusinganequalareasprojectionandinputdataareWGS1984coordinates,trythe
SDMtoolboxtoolthatwilldoalltheabovesteps:
SDMtools2.MaxEntToolsCorrectingLatitudinalBackgroundSelectionBiases
Solution2:ProjectInputDatatoEqualAreaProjection(EAP)1.CSVtoEAP.MaxEnt
formatoutput
3. Checkthatallyourinputdataareprojectedandinthesameprojection.Thisisthemost
commonerror.OftenreferenceASCIIfilesarenotprojectedatall.
4. Last,visualizeallGISfilestomakesuretheyareinfactproperlyprojected(allmapsshould
overlapetc.).Sometimesfilessaytheyareprojectedtothesameprojection,howeverinreality
somethingwasincorrect.
TochecktheprojectionofeachGISfile

ImportGISfiles,thenrightclickeachfileandselectProperties
SelecttheSourcetabandpagedownuntilyouseetheProjection.HeretheprojectionisLamberts
AzimuthalEqualArea

ToaccompanythisguideIhaveprovidedexampledataavailableatwww.sdmtoolbox.org.Download
this,thelatestversionoftheSDMtoolbox,andthisguidebeforebeginning.
ThisguidedoesnotcoverallthetoolsintheSDMtoolbox.However,asanoverview,theguidecovers
toolsfromallthemajorgroups.FormanytoolslackingaguideIhaveincludedexampledatatoexecute
eachanalysis.Theexampledatashouldbecontainedinafolderrespectivetothehierarchyofthe
toolbox.Forexample,forthetoolSDMtoolbox:BiodiversityMeasurementsInput:PointData
CalculateRichnessandEndemicity(WEandCWE),theexampledataareinthefolder
example_data\biodiversity_measurements\biodiversity_points
Lastly,eachtoolisannotatedandinstructionsshouldbecontainedwithineachtoolshelpfilefrom
withinArcGIS.Followsarethemajorgroupsofthetoolbox.Theguidetreatseachoneasaseparate
chapter.
ToolboxGuide
ChapterStructure
1. BiodiversityMeasurements
2. LandscapeConnectivity
3. SDMTools
4. BasicTools(BothCSV&ShapefiletoolsandRastertools)
5. RunningaSDMinMaxEnt:fromstarttofinish
Chapter1.BiodiversityMeasurements
ToolOverview
Thesetoolsestimatethreecommonbiodiversitymetrics:speciesrichness,weightedendemismand
correctedweightedendemism.Therearetwosetsofanalyseshere:analysesthatutilizepoint
occurrencedataandanalysesthatusebinarySDMs.
Asfollowsarethethreediversitymetrics:
1. SpeciesRichness(SR)issumofuniquespeciespercell.
SR=K(thetotalnumberofspeciesinagridcell)

2. WeightedEndemism(WE),whichisthesumofthereciprocalofthetotalnumberofcellseach
speciesinagridcellisfoundin.AWEemphasizesareasthathaveahighproportionofanimals
withrestrictedranges.
WE=1/C(Cisthenumberofgridcellseachendemicoccursin)
3. CorrectedWeightedEndemism(CWE).Thecorrectedweightedendemismissimplythe
weightedendemismdividedbythetotalnumberofspeciesinacell(Crisp2001).ACWE
emphasizesareasthathaveahighproportionofanimalswithrestrictedranges,butarenot
necessarilyareasthatarespeciesrich.
CWE=WE/K(Kisthetotalnumberofspeciesinagridcell)
Crisp,M.D.,Laffan,S.,Linder,H.P.,andMonro,A.2001.EndemismintheAustralianflora.Journalof
Biogeography28:183198.

EstimateRichnessandEndemicity(WEandCWE)
ARCGISSTEPBYSTEPGUIDE:
1. OpenafreshArcMapdocument
2. Importspecies_not_modeled.shpandmask.shp(Location:
\example_data\biodiversity_measurements\biodiversity_binary_SDMs)

A. Importeddata.B.NotethatthesedataunitsaremetersC.Tooltobeusedinthisguide

3. NextdoubleclicktheBiodiversityMeasurementsInputBinarySDMsOutput:Grid
EstimateRichnessandEdemicity(WEandCWE)tool
4. Continuetotoolinterfaceinstructions(followingpage)

EstimateRichnessandEndemicty(WEandCWE)toolinterface
SDMTOOLBOXSTEPBYSTEPGUIDE:
1. Selectexampledatafolder:
\example_data\biodiversity_measurements\biodiversity_binary_SDMs\Binary_SDMs

LeavetheInputsareASCIIfiles(.asc)unchecked.HeretheinputsareTIFFrasterfiles.

2. Inputdesiredoutputname.NotewhenthiscategoryishighlightedtheHelpboxdisplays
thetextintheboxtotheright.Iinput
Uruloke_spp,thismeansthattheoutputfiles
willbenamed:
Uruloke_spp_Estimated_Spp_Rich.tif,
Uruloke_spp_Est_Spp_Rich_Low_Res.tif,
Uruloke_spp_WE.tifandUruloke_spp_CWE.tif.

3. Selectoutputfolderlocation.Thisshouldbeanewemptyfolder.Ifnotempty,thiscan
causetheanalysistofail,particularlyiftemporaryfilesfromapreviousanalysiswerenot
properlyremoved(e.g.,thiscanhappenifanotherSDMtoolboxanalysisisterminatedearly).

4. HereIusedaresolutionof80,000m(or80km).Thedatausedhereareinmeters.Inthe
future,however,yourdatamightbeinginfeetordegrees.Thedistancevalueinputshould
belargeenoughtocapturelandscapeprocesses,butnottoolargewhereregional
differencesarelost.Irecommendstartingwithavalueequivalentto50or100km.Note1:
youractualvalueswillbeinthemapsunits(likelymeters,feetordecimaldegrees).Note2:
100km=~0.8983DDatEquator.
5. IpreferTIFFfilesasarasteroutputformatbecausetheyallowforlongerfilenames(vs.ESRI
gridfilesthatarelimitedto13characters)anddonthavetoomanyrawpartstoeachfile.
Thereis,however,aslightreductioninperformance(vs.ESRIgridfiles),thus,ifprocessing
thousandsofrastersthisshouldbetakenintoconsideration.
6. Apolygonmaskofacountryoutline.Thiswillcliptheedgesofpixelsbytheboundaryof
thismask.Thisproducesamuchmorevisuallypleasingoutput.Allbiodiversitymetricswill
beappendedtotheshapefiletableandcanbevisualizedinthefilesymbology.
NOTES:
ThisMUSTbeinthesameprojectionasotherinputdata(e.g.allprojectionsmustbe
WGS1984).
Agoodsourceforclippingmask(countryboundariesetc.)is:
http://www.divagis.org/Data
Again,besuretoprojectthefiletomatchyourinputrasters

7. Oftenduetolackingoccurrencedata,notallspeciescanbemodeled.Thisfeaturewill
includespeciesoccurrencesthatwerenotmodeledtobeincludedinthebiodiversity
estimates.
8. SelecttablefieldcorrespondingtospeciesID
9. Bufferdistance.Theinputpointswillbebufferedtothisdistance.HereIchose25,000m
(25km)thismeansacirclewitha25kmradiuswillbecreatedaroundeachpoint.
Results

Outputsfromanalyses.LefttoRight:EstimatedSpp.Richness,EstimatedSpp.Richness(low
resolution),WEandCWE

Tochangetheappearanceoftheoutputshapefile,rightclickthefileandselectProperties

ThenselecttheSymbologytab.IntheleftcolumnselectQuantities
Graduatedcolors,forFieldsValueselectanyofthethreebiodiversity
fields.HereIchosetouse10classesdefinedbyNaturalBreaks(Jenks).To
keepconsistentwiththeothercolorschemes,IusedtheRGBcolorramp
andinverteditsothatthehighestvaluesarered.Todothis,rightclickone
ofthecolors(seeabove)andselectFlipSymbols.Smallimagetorightis
theoutputfromthesesettings.
Extrabit:Foralittleextrapizazz,placeadigitalelevationmodelbelowthe
biodiversitylayer(useblacktowhitecolorramp)andmakethebiodiversity
layer1020%transparent.Thisgivesthemapalittletexture
correspondingtotopography.

Chapter2.LandscapeConnectivity
ToolOverview
Thistoolcreatesarasterofthesumofleastcostcorridorsandapolylineshapefileofleastcostpaths
betweenpopulationsthatsharehaplotypes.OftenasingleLCPbetweensitesoversimplifieslandscape
processes.Byusingcategoriesofcostpathsthatincludepathswithslightlymorecostlypathlengths
(relativetotheLCP),youcanbetterdepicthabitatheterogeneityanditsvaryingroleindispersal.For
eachcomparisonyoucanclassifythelowestcostpathsintothreecategories.Lastly,adensityanalysis
willproducearasterdepictingthefrequencythatLCPstraversethesamepath.
Formoreinformation,see:ChanLM,BrownJL,YoderAD(2011).Integratingstatisticalgeneticand
geospatialmethodsbringsnewpowertophylogeography.MolPhylogenetEvol59(2):52337.doi:
10.1016/j.ympev.2011.01.020.

LandscapeConnectivity
2. Importspecies_not_modeled.shpandmask.shp(Location:
\example_data\biodiversity_measurements\biodiversity_binary_SDMs)
3. NextdoubleclicktheLandscapeConnectivityGeneticSharedHaplotypesCalculated
LeastCostCorridorstool
4. Continuetothetoolinterfaceinstructions(followingpage)

Importeddata

CalculateLeastCostCorridorsandPathstoolinterface

1. Inputpointshapefilecontainingsites
andhaplotypestobeincludedinleast
costpathsandcorridors.Thisshapefile
musthavetwocolumns:onedepicting
sitenamesandanotherdepicting
haplotypeID.

Requiredgeospatialandhaplotypedataforanalysis
Tip.Ifyouneedtoconvertatabletoashapefileforusehere.Youneedtwoextracolumns
(latitudeandlongitude,seetableabove).ThenusethetoolCSV&ShapefileTools1.CSV
toShapefile
Avoidnonalphanumericcharactersinbothnames(e.g.,avoid:*:\/<>|"?[];=+&$,
etc.).
2. Tablefield(partofshapefile)depictinghaplotypeID
3. Tablefield(partofshapefile)depictingsiteID.Notethiscannotbeonlyanumber.Ifanumber
recodeasalphanumericID(e.g.change9to9a)
4. AfrictionLayer is a raster that depicts the ease of dispersal from each locality through the
landscape. In this analysis, the friction layer depicts
the output extent and spatial resolution of analysis.
If you want a larger extent or a lower spatial
resolution, increase both in your friction layer.
However, the larger both arethe longer the
analysis will take.
Creatingafrictionlayer.Oneprevalentwaytocreateafrictionlayerthatdoesntsufferfrom
applyingweightstohabitattypes(oftenassociatedwithcontributingtobiasesinresults)is
theuseofSDMs.AnSDMtoolboxtool(locationbelow)willinvertaSDMforuseasafriction
surface.Usingthismethod,areasofhighsuitabilitywillbeconvertedtoareasoflowdispersal
cost.

ToolPath:SDMTools1.UniversalToolsCreateFrictionLayerInvertSDM
5. Inputdesiredoutputname.NotewhenthiscategoryishighlightedtheHelpBoxdisplaysthe
textintheboxtotheright.IinputOplurus_cuvieri,thismeansthattheoutputfileswillbe
named:Oplurus_cuvieri_Dispersal_Network,Oplurus_cuvieri_LCPs.shp,
Oplurus_cuvieri_LCPs_Line_Density
6. Selectoutputfolderlocation.Thisshouldbeanewemptyfolder.Ifnotemptythiscancause
theanalysistofail,particularlyiftemporaryfilesfromapreviousanalysiswerenotproperly
removed(e.g.thiscanhappenifanotherSDMtoolboxanalysisisterminatedearly).
7. Outputfiletype.HereIselectedtheErdasImagine(.img)rasterformat.
Tip.IpreferTIFFfilesasoutputformatbecausetheyallowforlongerfilenames(vs.ESRIgrid
filesthatarelimitedto13characters)anddonthavetoomanyrawpartstoeachfile.There
is,however,aslightreductioninperformance(vs.ESRIgridfiles),thus,ifprocessing

8. Createleastcostpathlines.Leastcostpathanalysis(LCP)allowsresearcherstofindthe
cheapestwaytoconnecttwolocationswithinacostsurface(i.e.africtionlayer).
9. Therearetwomethodsforcalculatingtheleastcostcorridors(LCCs):
A.PercentageofLCPvalueisbasedontheLCPbetweeneachsite.Forexample,iftheLCPwas
5.0anda1%LCCclasscutoffwasselected,LCPswithvaluesbetween5.05.05wouldbe
includedinthatclass.ThisformulafocusesonlyontheLCPvalueandisnotaffectedbylarger
costpathvalues.
B.PercentageofCostPathValuesisbasedontherangeofcostpathvaluesacrosstheentire
landscapeforeachcomparison.Forexample,iftheleastandhighestcostpathswere5.0and
505,respectively,anda1%LCCclasscutoffwasselected,LCPswithvaluesbetween5.010.0
wouldbeincludedinthatclass.Thisformulafocusesonthetotalrangeofcostpathvaluesand
isgreatlyaffectedbythecostpathvaluesacross
thelandscape.
10. TheCalculateLeastCostCorridortoolcalculates
LCCsinthreeclasses:High,MidandLow.High
Cutoff.Costpathswithvaluesbetweenthisandthe
MidCutoffwillbeincludedintheHighClass.The
inputvaluesareintegersofthepercentage(e.g.1%
=1).Foroverviewseefigurebelow.
11. MidCutoff.CostpathswithvaluesbetweenthisandtheLowCutoffwillbeincludedintheMid
Class.
12. LowCutoff.CostpathswithvaluesbetweenthisandtheLCPwillbeincludedintheLowClass.
13. LCCweightvalues.BecauseallLCCsaresummedtocreateadispersalnetwork,weightedvalues
areplacedoneachcategoryofLCCs.TheinputinthisboxistheweightappliedtotheHighLCC
class.
14. WeightappliedtotheMidLCCclass.
15. WeightappliedtotheLowLCCclass.

Results
DispersalNetworks.A.LeastcostpathsandLCPlinedensities.WarmercolorsdepictLCPlines
traversedmorefrequently.B.HaplotypeDispersalNetworks.Warmercolorsdepictcostpaths
traversedmorefrequentlyandrepresentlikelyconnectionsinhabitat(duetocommonancestryamong
sharedhaplotypes).

Chapter3.SpeciesDistributionModelingAnalyses
CorrectingLatitudinalBackgroundSelectionBias
Solution1:BiasFiles
Solution2:ProjectInputDatatoEqualAreasProjection
DistributionChangesBetweenBinarySDMs
CentroidChanges(Lines)
OverpredictionCorrection:ClipModelsbyBufferedMinimumConvexPolygons
BinaryModels(folder)
ContinuousModels(folder)
BackgroundSelectionviaBiasFiles
SamplebyBufferedMCPs
SamplebyDistancefromObservedLocalities
CreateFrictionLayer:InvertSDM

CorrectingLatitudinalBackgroundSelectionBias
TOOLOVERVIEW
Ifyouareusingdatathatareinageographiccoordinatesystem(suchas,degreesminutessecondsor
decimaldegrees)forMaxEntanalyses(andmostotherbackgroundandpseudoabsencebasedSDM
methods)thenyouarebiasing
yourselectionofbackground Table1.AreaCoveredByaSquareDecimalDegreeatDifferent
points(orpseudoabsencepoints) Latitudes
anduniqueobservedlocalities N/Sor E/Wat E/Wat E/Wat
towardthepoles.Thelevelof Degrees2
E/Watequator 23N/S 45N/S 67N/S
biasdependsonthebreadthof
1.0 12392km2 11407km2 8762km2 4842km2
latitudesyouranalysescover.
Thereasonforthisisduetothe %AreaofEquator 100% 92.0% 70.7% 39.0%
areaoccupiedbytheseunits RelativeSampling
decreaseslatitudinally(asvalues Bias(1=none,2= 1 1.09 1.41 2.85
increase,seeTable1),withareas 2xsamplingbias)
largestatequatorandsmallest
atpoles.Thisinequalityresultsfromconvergenceofthemeridians(linesoflongitude)towardsthe
poles.
Therearetwosolutionstothisissue.Thefirstsolutioncorrectsthebiassamplingproblembycorrecting
howbackgroundvaluesanduniqueoccurrence
localitiesareselected.Thesecondsolutionfixesthe
problembyprojectingallthedataintoanequalareas
projection(EAP).Thelatteristhepreferredmethod,
howeverformanymodelers,thisrequires
MapLatitudesinTable1

considerableeffortandcanbeconfusingduetoissuesassociatedwithselectingthebestEAP.TheSDM
toolboxfacilitatesbothsolutions.
ThefirstsetoftoolsclipsaCoordinateBiasFile(downloadablefromwww.sdmtoobox.org)tothesizeof
yourMaxEntanalysisandthencalculatesaBFCDforthatarea.TheCoordinateBiasFileaccountsfor
backgroundsamplingbiasesassociatedwithlatitudinalchangesintheareaencompassedbydecimal
degreeunits.ThistoolconvertstheCoordinateBiasFiletotheproportionofareaoccupied(relativeto
thelargestvaluepresentinyouranalyses)tobeusedasabiasfileinMaxEnt.Avalueof2intheoutput
filedepictsa50%reductionincellarea(vs.cellvaluesof1).Thus,inabsenceofaBFCD,theprobability
ofcreatingabackgroundinthecellwithavalueof2istwiceashighasacellwithavalueof1.TheBFCD
allowsequalsamplingofbackgroundpointsthroughoutthelandscapeingeographicprojections.
InfoonthedownloadedCoordinateBiasFile:Unitsequalpercentofarearelativetosizeatequator
(wheresquaredecimaldegreesconstitutethelargestarea).Rawpercentageindownloadedfilewas
multipliedby10(reducingfilesizebysavingitasanintegerfile).Thusvalues01000reflect0.0to
100.0%ofareaoccupiedbyadecimaldegree(oranysubunitofthem)attheequator.
ThesecondsetoftoolsfacilitatetransformingclimateandspeciesoccurrencedatatoEAPforusein
MaxEnt(formattingoutputfordirectuse).
Solution1
QuickandEasySolution.CreatingaBiasfileinMaxEnttoaccountforbiases
Tool:1.BiasFileforCoordinateData(BFCD)inMaxEnt
2. ImportUruloke_eowynae.shpandbio_1.asc
(Location:\example_data\sdm_analyses\correcting_lat_BPs\soultion1\)
3. Importthedownloaded30arcsecondcoordinatebiasfile
4. NextdoubleclicktheSDMTools2.MaxEntToolsCorrectingLatitudinalBackground
SelectionSolution1:BiasFiles1.BiasFileforCoordinateData(BFCD)tool

ImportedData

1.BiasFileforCoordinateData(BFCD)inMaxEnttoolinterface
1. DownloadandunzipCoordinateBiasFilefromwww.sdmtoolbox.org(thismustmatchthe
resolutionofyourclimatedata)
2. Outputname.HereIusedU_eowynae.Note:_Coord_Bias_file_for_MaxEntwillbe
appendedtotheendoftheoutputname.
4. ClimatedatasizedtoextentofMaxEntModeling.HereusetheimportedBio_1.asclayer.Select
oneofyourclimatefilessizedtoyourmodelingextent(e.g.Bio1.asc).Thisfilewillbeusedto
matchthebiasfiletoproperextentandresolution(nochangewillbemadetothisfile).

CorrectingLatitudinalBackgroundSelectionBias:Solution1
Tool:2a.BSelection:SamplebyBufferedMCP
1. Thisanalysisiscontinuedfromprevious(thesameinputdataarerequired)
2. DoubleclicktheSDMTools2.MaxEntToolsCorrectingLatitudinalBackground
SelectionSolution1:BiasFiles2a.BackgroundPoints:SamplebyBufferedMCP
3. Continuetotoolinterfaceinstructions(below)

2a.BackgroundSelection:SamplebyBufferedMCPtoolinterface
1. Shapefileofspeciesoccurrence.
withlatitudeandlongitude.ThenusethetoolCSV&ShapefileTools1.CSVtoShapefile
etc.).
2. Thedistanceoutsideofminimumconvexpolygonincludedinbackgroundpointselection
3. Outputname.Note:_BP_Bias_file_for_MaxEntwillbeappendedtotheendoftheoutput
name.

Tool:3.ClipBFCDbyBackgroundSelectionBiasFile
1. Thisanalysisiscontinuedfromprevious(outputsfrombothstepsarerequired)
SelectionSolution1:BiasFiles3.ClipBFCDbyBSBiasFile
3.ClipBFCDbyBackgroundSelectionBiasFiletoolinterface
1. Outputfromtool:1.BiasFileforCoordinateData(BFCD)inMaxEnt
2. Outputfromtool:
2a.BackgroundSelection:SamplebyBufferedMCPToolInterface
2b.BackgroundSelection:SamplebyDistancefromPts.
3. Outputname.Note:_Both_Bias_file_for_MaxEntwillbeappendedtotheendoftheoutput
name.

Solution2
Bestpractice:Projectingalldataintoanequalareasprojection
Tool:1.CSVtoEAP.MaxEntformatoutput(runsboth1aand1b)
1. OpenafreshArcMapdocument.
SelectionSolution2:ProjectInputDatatoEqualAreaProjection(EAP)1.CSVtoEAP.
MaxEntformatoutput(runsboth1aand1b)tool

1. CSVtoEAP.MaxEntformatoutput(runsboth1aand1b)toolinterface
1. ImportUruloke_spp.csv
(Location:\example_data\sdm_analyses\correcting_lat_BPs\soultion2\)
ThisfileshouldmatchtheformatrequiredforMaxEnt(seetablelayoutbelow,savedas.csv
file).Notethistoolwillonlyacceptlatitudewrittenas:LATITUDE,latitude,Latitudeand
longitudewrittenas:LONGITUDE,latitude,Latitude.
2. Selectfieldcorrespondingtolatitude.
3. Selectfieldcorrespondingto
longitude.
4. OutputnameforprojectedCSVfile.
5. Selectoutputfolderlocation.This
shouldbeanewemptyfolder.Ifnot
empty,thiscancausetheanalysisto Table3.MaxEntInputSpeciesDataFormat:three
fail,particularlyiftemporaryfiles columnswithspecies,longitude,latitude.
fromapreviousanalysiswerenot
properlyremoved(e.g.thiscanhappenifanotherSDMtoolboxanalysisisterminatedearly).
6. SelectanappropriateEqualAreaProjection.Ifyourareaofextentiscenteredonasingle
continent,selectthatprojection.

HelpwithEqualAreaProjections:

GlobalProjections:EqualAreaCylindricalisbestforequatorialstudiescoveringseveral
continents;Mollweideisgreatforglobalstudieswithresolution>25km;LambertAzimuthal
EqualAreaisgreatformostregionalstudies.

Continental:AlbersEqualAreaProjectionisbestforstudiesatmidlatitudes(20Nand50N;
20Sand50S).Forregionscenteredonpoles,useLambertAzimuthalEqualArea.

Reminder.UsethesameprojectionforallrastersandCSVsinthestudy

Tool:2.ProjectClimateData(Raster)toEqualAreaProjection(Folder)
1. DoubleclicktheSDMTools2.MaxEntToolsCorrectingLatitudinalBackgroundSelection
Solution2:ProjectInputDatatoEqualAreaProjection(EAP)2.ProjectClimateData(Raster)
toEqualAreaProjection(Folder)tool

2.ProjectClimateData(Raster)toEqualAreaProjection(Folder)toolinterface
1. InputdataneedtobeanonASCIIrasterfilesandallfilesshouldbeinasinglefolder.IfASCII
files,firstusethe2b.ASCIItoRaster(folder)tool(partoftheBasicToolsRasterTools
group).
3. SelectanappropriateEqualAreaProjection.UsethesameprojectionselectedfortheCSV
speciesfile(pg.26step6).
4. Runtool.Thenusethe2a.RastertoASCII(folder)tool,partoftheRasterToolsgroup,to
convertnewlyprojectedrasterstoASCIIfiles(inputformatforuseinMaxEnt).

TOOLOVERVIEW
Acommonuseofspeciesdistributionmodelsistopredictdistributionalchangesduetoclimatechange.
HereIcreatedtwotoolsthathelpsummarizedistributionalchanges.Thefirsttoolcalculatesthe
distributionalchangesbetweentwobinarySDMs(e.g.currentandfutureSDMs).Outputisatable
depictingpredictedcontraction,expansion,andareasofnochangeinthespeciesdistribution.A
secondtoolalsocalculatesthedistributionalchangesbetweentwobinarySDMs(e.g.currentandfuture
SDMs),howeverthisanalysisisfocusedonsummarizingthecoredistributionalshiftsoftherangesof
manyspecies.Thisanalysisreduceseachspeciesdistributiontoasinglecentralpoint(knownasa
centroid)andcreatesavectorfiledepictingmagnitudeanddirectionofpredictedchangethroughtime.
Tool:CentroidChanges(Lines)
2. DoubleclicktheSDMTools2.MaxEntToolsDistributionChangesBetweenBinarySDMs
CentroidChangestool

CentroidChanges(Lines)toolinterface

1. InputFolder1:ThefoldercontainingcurrentbinarySDMs.
(Location:/example_data/sdm_analyses/distribtutionchanges/MaxEnt/current_binary_SDMs)
2. InputFolder2:ThefoldercontainingfuturebinarySDMs.
(Location:/example_data/sdm_analyses/distribtutionchanges/MaxEnt/future_binary_SDMs)
3. Inputrastertype.HeretheexampledataareASCII(.asc)rasterfiles.
4. Rasterfilenameassociations.Hereinput_2080_a1b_csiro.BecauseMaxEntnamesthefuture
andcurrentSDMsdifferently,youneedtoinputthedifferenceinfilenames.Forexample,if
thecurrentSDMforaspeciesAisnamedSpA_threshold.ascandthefutureisnamed
SpA_yr2080_threshold.asctheninput_yr2080.Note:Thesuffix_thresholdwill
automaticallybeaccountedforbythetool.IfyourSDMsdonothavethis,thenyoumustuse
thegenericCentroidChanges(Lines)tool[locatedat:SDMTools1.UniversalTools
CentroidChanges(Lines)],whichhasmoreflexibilityininputfilenames.
6. Outputname.Note:_centroid_changeand_cen_chg_densitywillbeappendedtotheend
oftheoutputname.
Results:Above.Outputfromexampledata.
Right.Exampleofamultispeciescomparison
todemonstratepowerofsuchanalysis.Inthe
northeastofMadagascarmanyspecieswill
respondsimilarlytoclimatechange

Tool:DistributionChangesBetweenBinarySDMs
2. DoubleclicktheSDMTools2.MaxEntToolsDistributionChangesBetweenBinarySDMs
DistributionChangesBetweenBinarySDMstool

DistributionChangesBetweenBinarySDMstoolinterface
1. InputFolder1:ThefoldercontainingcurrentbinarySDMs.
(Location:\example_data\sdm_analyses\distribtutionchanges\MaxEnt\current_binary_SDMs)
2. InputFolder2:ThefoldercontainingfuturebinarySDMs.
(Location:\example_data\sdm_analyses\distribtutionchanges\MaxEnt\future_binary_SDMs)
3. Rasterfilenameassociations.Hereinput_2080_a1b_csiro.BecauseMaxEntnamesthefuture
andcurrentSDMsdifferently,youneedtoinputthedifferenceinfilenames.Forexample,if
thecurrentSDMforspeciesAisnamedSpA_threshold.ascandthefutureisnamed
SpA_yr2080_threshold.asctheninput_yr2080.Note:Thesuffix_thresholdedwill
automaticallybeaccountedfor.IfyourSDMsdonothavethisthenyoumustusetheuniversal
DistributionChangesBetweenBinarySDMstool.[locatedat:SDMTools1.UniversalTools
DistributionChangesBetweenBinarySDMs],whichhasmoreflexibilityininputfilenames.

5. SelectanappropriateEqualAreaProjection.Ifyourareaofextentiscenteredonasingle
continent,selectthatprojection.

HelpwithEqualAreaProjections:

GlobalProjections:EqualAreaCylindricalisbestforequatorialstudiescoveringseveral
continents;Mollweideisgreatforglobalstudieswithresolution>25km;LambertAzimuthal
EqualAreaisgreatformostregionalstudies.

Continental:AlbersEqualAreaProjectionisbestforstudiesatmidlatitudes(20Nand50N;
20Sand50S).Forregionscenteredonpoles,useLambertAzimuthalEqualArea.

Reminder.UsethesameprojectionforallrastersandCSVsinthestudy

6. Checktosavetherasterfilesofresults(seebelow)
7. Outputfiletype.HereIselectedTiff(.tif)format.
Tip.IpreferTIFFfilesasoutputformatbecausetheyallowforlongerfilenames(vs.ESRIgrid
filesthatarelimitedto13characters)anddonthavetoomanyrawpartstoeachfile.There
is,however,aslightreductioninperformance(vs.ESRIgridfiles),thus,ifprocessing
Results
Results:CSVfileofareachangesandtoright,arasterofresults
(optional).

TOOLOVERVIEW
TolimitoverpredictionofSDMs,aproblemcommonwithmodelingspeciesdistributions,twotools
werecreatedthatclipSDMsbyabufferedminimumconvexpolygon(MCP)generatedfromtheinput
pointdataofeachspeciesfollowingtheapproachofKremenetal.(2008).Thismethodproducesmodels
thatrepresentsuitablehabitatwithinanareaofknownoccurrence(basedonabufferedMCP),
excludingsuitablehabitatgreatlyoutsideofobservedrangeandunsuitablehabitatthroughthe
landscape.
Kremen,C.,A.Cameron,A.Moilanen,S.J.Phillips,C.D.Thomas,H.Beentje,J.Dransfield,B.L.Fisher,F.
Glaw,T.C.Good,G.J.Harper,R.J.Hijmans,D.C.Lees,E.LouisJr.,R.A.Nussbaum,C.J.Raxworthy,
A.Razafimpahanana,G.E.Schatz,M.Vences,D.R.Vieites&M.L.Zjhra(2008):Aligning
conservationprioritiesacrosstaxainMadagascarwithhighresolutionplanningtools.Science320:
222226.
Tool:BinaryModels(folder)
2. Importpoints.shp
(Location:\example_data\sdm_analyses\overprediction_correction\)
3. Importbio_1.asc
(Location:\example_data\sdm_analyses\overprediction_correction\climate_data)
4. DoubleclicktheSDMTools2.MaxEntToolsOverpredictionCorrection:ClipModelsby
BufferedMCPsBinaryModels(Folder)tool

ImportedData

BinaryModels(folder)toolinterface
1. ApointshapefileofspeciesoccurrencescorrespondingtoinputSDMs.Note:speciesnamein
shapefilemustperfectlymatchinputoccurrencedataspeciesnames.
2. Fieldindicatingspeciesnames,here:SPECIES
3. Distancetobufferminimumconvexpolygons.Heretry:100km.
4. ThefoldercontainingbinarySDMstobeclipped.
(Location:\example_data\sdm_analyses\overprediction_correction\binary_SDMs)

Results

Tool:ContinuousModels(folder)
2. Importpoints.shp
(Location:\example_data\sdm_analyses\overprediction_correction\)
3. Importbio_1.asc
(Location:\example_data\sdm_analyses\overprediction_correction\climate_data)
4. DoubleclicktheSDMTools2.MaxEntToolsOverpredictionCorrection:ClipModelsby
BufferedMCPsContinuousModels(Folder)tool
5. Continuetotoolinterfaceinstructions

ContinuousModels(folder)toolinterface
1. ApointshapefileofspeciesoccurrencescorrespondingtoinputSDMs.Note.Speciesnamein
shapefilemustperfectlymatchinputoccurrencedataspeciesnames.
2. Fieldindicatingspeciesnames.HereSPECIES
3. Distancetobufferminimumconvexpolygons.Heretry100km.
4. ThefoldercontainingbinarySDMstobeclipped.
(Location:\example_data\sdm_analyses\overprediction_correction\binary_SDMs)

Results

TOOLOVERVIEW
Asubsetofpythonscriptscreatebiasfilesusedtofinetunebackgroundandoccurrencepointselection
inMaxent.Biasfilescontrolwherebackgroundpointsareselectedandthedensityofbackground
sampling.Properuseofbiasfilescanavoidsamplinghabitatgreatlyoutsideofaspeciesknown
occurrenceorcanaccountforbothcollectionsamplingbiasesandlatitudinalbiasesassociatedwith
coordinatedata.
Backgroundpoints(andsimilarpseudoabsencepoints)aremeanttobecomparedwiththepresence
dataandhelpdifferentiatetheenvironmentalconditionsunderwhichaspeciescanpotentiallyoccur.
Typicallybackgroundpointsareselectedwithinalargerectilineararea,withinthisareathereoftenexist
habitatthatisenvironmentallysuitable,butwasnevercolonized.Whenbackgroundpointsareselected
withinthesehabitats,thisincreasescommissionerrors(falsepositives).Asaresult,thebest
performingmodeltendstobeoverfit,becauseselectioncriterionfavoramodelthatfailtopredictthe
speciesintheuncolonizedclimaticallysuitablehabitat(Anderson&Raza2010,BarbetMassinetal.
2012).Thelikelihoodthatsuitableunoccupiedhabitatsareincludedinbackgroundsamplingincreases
withEuclidiandistancefromthespeciesrealizedrange.Thus,alargerstudyspatialextentcanleadto
theselectionofahigherproportionoflessinformativebackgroundpoints(BarbetMassinetal.2012).
Researchersshouldnotavoidstudyingspecieswithbroaddistributionsorthoseexistinginregionsthat
donotconformwelltorectilinearmaplayouts,rathertheysimplyneedtobemoreselectiveinthe
choiceofbackgroundpointsinMaxent(andpseudoabsencesinotherSDMmethods)(Barveetal.2011;
Merowetal.2013).
Tocircumventthisproblem,manyresearchershavebegunusingbackgroundpointandpseudoabsence
selectionmethodsthataremoreregional.SDMtoolboxcontainstwotoolstofacilitatemore
sophisticatedbackgroundselectionforuseinMaxent.TheSamplebyDistancefromObs.Pts.tool(see:
SDMTools2.MaxEntToolsBackgroundSelectionviaBiasFiles)usesacommonmethodthat
samplesbackgroundswithinamaximumradialdistanceofknownoccurrences(seeThuilleretal.2009).
TheSamplebybufferedMCPtoolrestrictsbackgroundselectionwithabufferedminimumconvex
polygonsbasedonknownoccurrences(seefollowingguide).
OnelimitationofpresenceonlydataSDMmethodsistheeffectofsampleselectionbiasfrom
samplingsomeareasofthelandscapemoreintensivelythanothers(Phillipsetal.2009).Maxent
requiresanunbiasedsamplingofoccurrencedataandspatialsamplingbiasescanbereducedbyusing
theGaussiankerneldensityofsamplinglocalitiestool.Thismethodproducesabiasgridthatupweights
presenceonlydatapointswithfewerneighborsinthegeographiclandscape.Todothisthetoolcreates
aGaussiankerneldensityofsamplinglocalities(Fig1n).Outputbiasvaluesof1reflectnosamplingbias,
whereashighervaluesrepresentincreasedsamplingbias.Dependingonthestudy,theinputpoints
couldbeallsamplinglocalitiesforalargertaxonomicgrouporsimplytheinputsamplinglocalitiesofa
focalspecies.Forexample,ifIwerestudyingasinglespeciesoffrogfromMadagascar,Icoulduse
either:i)1.onlytheoccurrencepointsfromthatspecies,orii)2.allsamplingpointsfromallamphibians
inMadagascar.Theformerfocusesonsamplingbiasesinthefocalspecies,wherethelatterfocuseson

widespreadspatialsamplingbiasesandlikelihoodofdetectionofyourspeciesinallsurveys(e.g.
samplingonlynearroads).
Anderson,R.P.&Raza,A.(2010)TheeffectoftheextentofthestudyregiononGISmodelsofspecies
geographicdistributionsandestimatesofnicheevolution:preliminarytestswithmontanerodents
(genusNephelomys)inVenezuela.JournalofBiogeography,37,13781393.
BarbetMassin,M.,Jiguet,F.,Albert,C.H.&Thuiller,W.(2012)Selectingpseudoabsencesforspecies
distributionmodels:how,whereandhowmany?MethodsinEcologyandEvolution,3,327338.
PhillipsSJ,DudkM,ElithJ,GrahamCH,LehmannA,LeathwickJ,FerrierS(2009)Sampleselectionbias
andpresenceonlydistributionmodels:implicationsforbackgroundandpseudoabsencedata.Ecological
Applications,19,181197.
Thuiller,W.,Lafourcade,B.,Engler,R.&Araujo,M.B.(2009)BIOMODaplatformforensemble
forecastingofspeciesdistributions.Ecography,32,369373.
Tool:BackgroundSelection:SamplebyBufferedMCP
2. ImportUruloke_eowynae.shpandbio_1.asc(Location:\example_data\sdm_analyses\
background_selection_via_bias_files)
3. DoubleclicktheSDMTools2.MaxEntToolsBackgroundSelectionviaBiasFiles
BackgroundSelection:SamplebyBufferedMCPtool
BackgroundSelection:SamplebyBufferedMCPtoolinterface

withlatitudeandlongitude.ThenusethetoolBasicToolsCSV&ShapefileTools1.CSV
toShapefile
etc.).
2. Thedistanceoutsideofminimumconvexpolygonincludedinbackgroundselection.
3. Outputname.
Tool:BackgroundSelection:SamplebyDistancefromObs.Pts.
2. ImportUruloke_eowynae.shpandbio_1.asc(Location:\example_data\sdm_analyses\
background_selection_via_bias_files)
3. DoubleclicktheSDMTools2.MaxEntToolsBackgroundSelectionviaBiasFilesSample
byDistancefromObs.Pts.

BackgroundSelection:SamplebyDistancefromObs.Pts.toolinterface

withlatitudeandlongitude.ThenusethetoolBasicToolsCSV&ShapefileTools1.CSV
toShapefile
etc.).
2. Themaximumdistanceawayfromtheobservedlocalitiestoincludeinbackgroundselection.
3. Outputname.
UNIVERSALSDMTOOLS
TOOLOVERVIEW
Theuseofleastcostpathsandalongpathdistancesoftendramaticallyimprovethecalculationof
geographicdistancefortestinghypotheses(suchas,isolationbydistance).However,fewstudieshave
accesstomeaningfulfrictionlandscapes.Someresearchers(i.e.Broquetetal.2006)generatefriction
landscapesfromclassifiedsatelliteimageswhereeachmajorhabitattyperepresentsadifferentvalue.
Aprimarydownfalltousinghabitatheterogeneityasafrictionlandscapeistheweighingofeachhabitat
classtorepresentrelevantfrictionvalues.Doingthisproperlyreliesheavilyonexpertlifehistory
knowledgeandwhendoneanalysislosessomeobjectivity.Forexample,Broquetetal.(2006)adjusted
thefrictionvaluesuntiltheysatisfiedpriorexpectations.Morerecentlyauthorsusedspecies
distributionmodels(SDMs)asfrictionlandscapes(Wangetal.2008,Chanetal.2011).Thismethodisa
moreobjectivealternativetoexpertknowledgeandthegenerationofhighqualitySDMscanbedone
withrelativeeaseformanyspecies.
Broquet,T.,Ray,N.,Petit,E.,Fryxell,J.M.&Burel,F.(2006)Geneticisolationbydistanceandlandscape
connectivityintheAmericanMarten(martesamericana).LandscapeEcology,21,877889
ChanLM,BrownJL,YoderAD(2011).Integratingstatisticalgeneticandgeospatialmethodsbringsnew
powertophylogeography.MolPhylogenetEvol59(2):52337.
Wang,Y.H.,Yang,K.C.,Bridgman,C.A.,Lin,L.K.(2008)Habitatsuitabilitymodellingtocorrelategene
flowwithlandscapeconnectivity.LandscapeEcology,23,9891000

Tool:InvertSDM
2. Importspecies_distribution_model.tif
(Location:\example_data\sdm_analyses\create_friction_layer\)
3. DoubleclicktheSDMTools1.UniversalToolsCreateFrictionLayerInvertSDM

Inputdata
InvertSDMtoolinterface
1. Inputspeciesdistributionmodel(SDM)

2. Nameofoutputfile.Note:_FrictionLayerwillbeappendedtotheendofoutputname.
4. Outputrasterformat.HerechoseERDASImagine(.img)
5. AreasofNoData(cellsthatlackSDMvalues,i.e.oceans)canbeconvertedtofrictionvalues.
Thisisparticularlyimportantifusingfrictionslayerstoconnectpopulationsisolatedonislands
andmainlandpopulations.
Results

InvertSDMtool.Right:InputSDM.Left:Outputfrictionlayer

UNIVERSALSDMTOOLS
TOOLOVERVIEW
SpatiallyRarefyOccurrenceData
MostSDMmethodsrequireinputoccurrencedatatobespatiallyindependenttoperformwell.
However,itiscommonforresearcherstointroduceenvironmentalbiasesintotheirSDMsfromspatially
autocorrelatedoccurrencepoints.Theeliminationofspatialclustersoflocalitiesisimportantformodel
calibratingandevaluation.Whenspatialclustersoflocalitiesexist,oftenmodelsareoverfittowards
environmentalbiases(reducingthemodelsabilitytopredictspatiallyindependentdata)andmodel
performancevaluesareinflated(Veloz2009;Hijimansetal.2012;Boriaetal.2014).Thespatiallyrarefy
occurrencedatatooladdressesthisissuebyspatiallyfilteringlocalitydatabyauserinputdistance,
reducingoccurrencelocalitiestoasinglepointwithinthespecifiedEuclidiandistance.Thistoolalso
allowsuserstospatiallyrarefytheirdataatseveraldistancesaccordingtohabitat,topographicor
climateheterogeneity(Table1d).Forexample,occurrencelocalitiescouldbespatiallyfilteredat5km2,
10km2and30km2inareasofhigh,mediumandlowenvironmentalheterogeneity,respectively.This
graduatedfilteringmethodisparticularusefulforstudieswithlimitedoccurrencepointsandcan
maximizethenumberofspatiallyindependentlocalities.
Veloz,S.D.(2009)Spatiallyautocorrelatedsamplingfalselyinflatesmeasuresofaccuracyforpresence
onlynichemodels.JournalofBiogeography,36,22902299.
Hijmans,R.J.(2012)Crossvalidationofspeciesdistributionmodels:removingspatialsortingbiasand
calibrationwithanullmodel.Ecology,93,679688.
BoriaR.A.,OlsonL.E.,GoodmanS.M.&AndersonR.A.(2014)Spatialfilteringtoreducesamplingbias
canimprovetheperformanceofecologicalnichemodels.EcologicalModeling,275,7377.
SpatiallyRarefyOccurrenceData
Tool:SpatiallyRarefyOccurrenceData
2. Importoccurrences.shpandclimate_hetero.tif
(Location:\example_data\sdm_analyses\rarefy\)
3. DoubleclicktheSDMTools1.UniversalToolsSpatiallyRarefyOccurrenceDataforSDMs
(reducespatialautocorrelation)tool

SpatiallyRarefyOccurrenceDatatoolinterface
1. Inputshapefileofspeciesoccurrencedata,hereselectoccurences.shp
2. Shapefilefieldcorrespondingtospeciesidentity,hereselectSPECIES
3. Shapefilefieldcorrespondingtolatitude,hereselectLATITUDE
4. Shapefilefieldcorrespondingtolongitude,hereselectLONGITUDE
5. Selectoutputfolderlocation.Thisshouldbeanewemptyfolder.Ifnotemptythiscan
6. Nameofoutputfile.Notethat"_rarefied_points"willbeappendedtofilename.
7. Thespatialresolutiontorarefythedata.Hereusethedefaultsettings.Notethatthisvalue
willNOTactuallybeusedherebecauseyouwillbeexecutingthemultidistanceoccurrence
datararefying.
8. PleaseselectContinent:AfricaEquidistantConic
9. Placingacheckmarkintheboxtoexecutethemultidistancedatararefying

10. Inputheterogeneityraster,heretheclimate_hetero.tifThisisrequireifusingthemulti
distancedatararefying
11. Thenumberofclasses,here5
12. Classificationtype,hereNATURAL_BREAKS
13. Themaximumdistance,here25Kilometers
14. Theminimumdistance,here2Kilometers

Chapter4.Raster,CSV&Shapefiletools
Tool:CSV,TXT,XLStoshapefile
2. ImportUruloke_spp.csv
(Location:\example_data\SDM_analyses\correcting_lat_BPs\soultion2\)
3. DoubleclicktheCSV&ShapefileTools1.CSVtoShapefile

CSVtoShapefiletoolinterface
1. InputCSVfilewithcolumnswithlatitudeandlongitude
2. Fieldwithlongitude
3. Fieldwithlatitude
4. Nameofnewshapefile
5. Selectoutputfolderlocation

Chapter5.RunningaSDMinMaxEnt:fromStarttoFinish
Belowisabriefoverviewofmyviewofthebestpracticesofcorrelativespeciesdistributionmodeling
andhowSDMtoolboxwillfacilitateachievingthem.ThisoverviewfocusesonmodelinginMaxEnt,but
manystepsareapplicabletoalltypesofdistributionmodeling.Foroverviewofmajorassumptionsand
otherconsiderations,seetableattheendofthisdocument.
Speciesdistributionmodelling(SDM)occursintwophases:1)Datacompilationand2)Modelcreation,
calibration,andvalidation
Datacompilation
Thisstepincludescollectingoccurrencerecordsofthefocalspeciesandenvironmentdataforitshabitats.
OccurrenceData
ThesinglemostimportantcomponentofanySDMistheinputoccurrencerecords.Extracareshouldgointo
selecting,andthenprocessing,thesepoints.Thequality,distributionandnumberofpointsaredirectlyrelated
totheaccuracyofthemodel.Useasmanyhighqualitylocalitypointsaspossible(e.g.GPSdatacollectedwith
confidenttaxonomicidentification)andtrytocollectoccurrencerecordsthatareevenlysampledthroughout
thespeciesrangeandavoidbiasesinthesamplingmethod(e.g.,samplingonlyfromroadtransects).Itis
bettertohaveonlyalimitednumberofpointsthatsatisfytheaboveconditionsthanmanypointsofvague
credence(e.g.beskepticalofpointsdownloadedfrominternetdatabases,particularlythosethatare
georeferencedfromlocalityinfo)(Chanetal.2011).
EnvironmentData
Theenvironmentdataprovidethelandscapeleveldatatoquantifythefocalspecies'ecologicaltolerances.
Includevariablesthatarelikelytobedirectlyrelevanttothespeciesbeingmodeled.Howeverdonotaddall
availableclimatedatawithoutregardtotheredundancyofthedata.Manyenvironmentalvariablesaretightly
correlatedmakingsomeredundant,thismakesinterpretingtheinfluencesofeachvariableinthemodel
difficult.Ifnotincludedinyourmodel,considertheeffectsofthefollowingitemsonthepresentdistributionof
yourspecies:firehistory,glaciations,contagiousdiseases,anthropogenicfactors,recentgeologicalchanges,
thespeciesmovementpotentialthroughthelandscapeorbioticinteractions.
1.PreparingWorldclimClimateDataforuseinMaxEntAnalyses
1A.PreparingWorldclimClimateData:Cliptherastertoareaofspeciesextent
Tools:ExtractbyMask(Folder)andRastertoASCII
2. DownloadESRIgridclimatedata(e.g.the30arcsecondbioclim)fromworldclim.org
3. OpenoneofthenewlydownloadedlayersinArcMap

4. Thereareseveralwaystodefinetheareatocliptheclimatedatainto.Oneoftheeasiestways
istosimplyzoomthedisplaywindowthedesiredextent(Imagebelow,whereIwantedto
reduceclimatedatatoMadagascar).OtherwaysincludedefiningthemaxminXYcoordinates(a
boundingbox)orusinganotherGISlayerasatemplates(suchas,acountrysboundary).Select
oneofthesemethodsandcontinue.Notetheareashouldencompassanareaabout50100km
(ca.0.51degree)greaterthantotaldistributionofallyourfocalspecies.Wewillthenusebias
filestolimitbackgroundselectionofeachspeciestomeaningfulareaswithinthisarea.

Zoomtool

Zoomtodesiredarea

5. DoubleclicktheBasicToolsRasterTools1.ExtractbyMask(Folder)
1. InputfoldercontainingthefullextentWorldclimdata,inputrastershouldbeESRIgridformat
2. ChecktheboxdepictingthattherastersareESRIgridformat.
4. Selecteitheramaskorselectextentandchoosetheappropriatemethodfordefiningthe
extent(hereIusedSameasDisplay).
5. Executetool

1B.PreparingWorldclimClimateData:ConvertrasterstoASCII
Tool:RastertoASCII
1. DoubleclicktheBasicToolsRasterTools2a.RastertoASCII(Folder)
1. InputfoldercontainingtheclippedWorldclimdataoutputfromprevioustool
2. SelectrastertypeTiff(.tif)
4. TheclimatedataarereadyforuseinMaxEnt
1C.PreparingWorldclimClimateData:DefineprojectionofASCIIclimatedata
Tool:3d.DefineProjectionasWGS84orArcMapssDefineProjection
IFinputdataarecoordinatesandWGS84then:
1. DoubleclicktheRasterTools3d.DefineProjectionasWGS84(folder)
1. InputfolderwithclippedASCIIworldclimdata.
2. Executetool
IFinputdataareanotherprojection,useArcMapstool:DefineProjection.

2.OptionalStep.WhichvariablesshouldIuse?TestingAutocorrelationsof
EnvironmentalData
Ifyouareinterestedinterpretinghoweachinputenvironmentalvariablecontributestoyour
speciesdistributionmodel,thenyouneedtoreduceautocorrelationofyourinput
environmentaldatabyremovinghighlycorrelatedvariables.Itiswidelyknownthatmany
climatevariablesarehighlycorrelatedwitheachother.Whileincludingallthesewillnotaffect
thepredictivequalityofyourMaxEntmodel,itdoesseriouslylimitanyinferenceofthe
contributionofanycorrelatedvariables(i.e.theMaxEntoutputsfromAnalysisofvariable
contributionsandtosomedegreeJackknifingenvironmentalvariables).Thisismainlybecause
whenamodelisbuiltinMaxEnt,ifahighlycorrelatedvariableisincludedinthemodel,this
oftenexcludesallotherhighlycorrelatedvariablesfrombeingincorporated.Thisisbecause
thesevariableslikelywouldcontributesimilarlytothemodels.Sincetheyarenotincluded,they
willnotbeproperlyrepresentedintheoutputAnalysisofvariablecontributions.
Tool:ExploreClimateData:RemoveHighlyCorrelatedVariables
1. DoubleclicktheBasicToolsSDMToolsUniversalSDMToolsExploreClimateData
RemoveHighlyCorrelatedVariables
1. SelectalltheclippedWorldclimdata(control+shiftwillallowyoutoselectallitemsinafolder).
Layersthatyouwishtoretain(vs.theothercorrelatedlayers)shouldbefirstinthelist.All
correlatedlayersthatoccurafterwillbeexcluded.Forinterpretinginfluenceofenvironmental
layersintheSDM,IprefertoplacelayersthatdepictmetricsfrequentlyusedinnonSDM
ecologyandevolutionstudies[suchas:BIO1=AnnualMeanTemperature,BIO2=MeanDiurnal
Range(Meanofmonthly(maxtempmintemp)),BIO12=AnnualPrecipitation].Furtherfor
simplicity,theselayersoftenbestrepresenttheoriginalinputclimatedata(astheydirectly
reflecttheactualmeasurements)andarenotderivedfromseverallayersorasubsetofthe
data.
2. Maximumcorrelationallowed.Multiplevaluescanbeinputseparatedbysemicolon(;).Input
avaluebetween01.Theabsolutevalueofthecorrelationcoefficientsrangefrom0to1.A
valueof1impliesthatalinearequationdescribestherelationshipbetweenXandYperfectly.A
valueof0impliesthatthereisnolinearcorrelationbetweenthevariables.
3. InputNoDataValue.Notethismustbethesameforallvaluesorelsecorrelationswillnotbe
accurate.SinceweusedonlyWorldclimhere,thisshouldnotbeanissues(asallvaluesarethe
same).TocheckNoDatavalues,importlayersintoArcGISandrightclickthelayerandselect
PropertiesandthengototheSourcetab.Alternatively,youcansimplyopenyour.ascfiles
inatexteditorandatthetopofheaderwillbetheNoDatavalue.
4. Selectoutputfolderlocation.Outputwillbetwotableswiththecorrelationcoefficientsamong
allcomparisonsandatablewiththefinallistofrasterstoincludeinyourmodel.

3.PreparingOccurrenceDataforuseinMaxEntAnalyses
3A.PreparingOccurrenceData:ImportSpeciesOccurrenceRecords
Tool:CSV,TXT,XLStoshapefile
2. ImportCSV,TXTorXLSfilewith
occurrencerecords.Tableofspecies
occurrencescontainingONLY:Species
ID,LongitudeandLatitude.Thefields MaxEntInputSpeciesDataFormat:threecolumns
mustbeinthatorder.ForspeciesID, withspecies,longitudeandlatitudeasordered
donotusenonalphanumeric here.
charactersinnames(e.g.,*:\/<>|
"?[];=+&$),replacespaces
with"_",andremoveperiods.
3. DoubleclicktheCSV&ShapefileTools1.CSVtoShapefile

CSVtoShapefiletoolinterface
1. InputCSVfilewithcolumnswithlatitudeandlongitude
2. Fieldwithlongitude
3. Fieldwithlatitude
4. Nameofnewshapefile

3B.PreparingOccurrenceData:Defineprojectionofoccurrencepointsshapefile
Tool:6b.DefineProjectionasWGS84orArcMapssDefineProjection
IFinputdataarecoordinatesandWGS84(ifnotseebelow):
1. DoubleclicktheCSV&ShapefileTools6b.DefineProjectionasWGS84
1. Inputnewlyimportedshapefilepoints
2. Executetool
IFinputdataareanotherprojection,useArcMapstool:DefineProjection.
3C.PreparingOccurrenceData:PCAofClimateVariablestoEstimateHeterogeneity
Tool:2a.CalculateClimateHeterogeneity:Step1PrincipalComponentAnalysis
1. DoubleclicktheSDMTools1.UniversalTools2a.CalculateClimateHeterogeneity:Step
1PrincipalComponentAnalysistool

2a.CalculateClimateHeterogeneity:Step1PrincipalComponentAnalysistoolinterface
1. Inputallyourclimaterastersthatdepictcontinuousdata.Note:holdshifttoselectmany
rastersatonce.

2. Selectoutputfolderlocation.Thisshouldbeanewemptyfolder.Ifnotemptythiscan
3. Nameofoutputfile.Notethat"_Climate_PCs"willbeappendedtofilename.

TovisualizeallthreebandsoutputfromthePCAtool,rightclicklayerandselectProperties.Then
selecttheSymbologytabandselectRGBComposite.Theoutputrasterdepictsclimatespace:the
moresimilarthecolorsthemoresimilarvalues.

3D.PreparingOccurrenceData:MeasureSpatialHeterogeneityofClimatePCs
Tool:2b.CalculateClimateHeterogeneity:Step2HeterogeneityCalculation
1. DoubleclicktheSDMTools1.UniversalTools2b.CalculateClimateHeterogeneity:Step2
HeterogeneityCalculationtool

2b.CalculateClimateHeterogeneity:Step2HeterogeneityCalculationtoolinterface
1. InputclimatesPCArasteroutputfrompreviousstep
2. Thisisthespatialscaleusedtocalculatethe
heterogeneityofthelandscape.E.g.,if3x3rectangle
andcellunitsareselected:heterogeneityvalueswillbe
calculatedfromeachrasterpixelandthe8cells OutputPCASummarytable
neighboringthefocalcell.
3. PercentofEigenValues
ofPC1.Thisvalueis
inputfromthe
"..._PCA_summary.txt"
file.Gotothebottom
ofthetextfiletothe
Sectionofthetablethatisnecessaryforinputintothistool
heading'PRECENTAND
ACCUMULATIVE

EIGENVALUES'andgototherowcorrespondingtoPC1andinputthevaluefromthe'Percent
ofEigenValues'.
4. PercentofEigenValuesofPC2.
5. PercentofEigenValuesofPC3.
6. OutputFolder
7. Outputfilename.Note:"_clim_hetero.tif"willautomaticallybeappended.

Above.Outputclimate
heterogeneityraster.Here
warmcolorsdepicthighareas
ofclimaticheterogeneity.

3E.PreparingOccurrenceData:GraduatedSpatialRarefying
AnUnbiasedSample:aNeedforSpatialRarefying

MostSDMmethodsrequireinputoccurrencedatatobespatiallyindependenttoperformwell.However,itis
commonforresearcherstointroduceenvironmentalbiasesintotheirSDMsfromspatiallyautocorrelated
occurrencepoints.Theeliminationofspatialclustersoflocalitiesisimportantformodelcalibratingand
evaluation.Whenspatialclustersoflocalitiesexist,oftenmodelsareoverfittowardsenvironmentalbiases
(reducingthemodelsabilitytopredictspatiallyindependentdata)andmodelperformancevaluesareinflated
(Veloz2009;Hijimansetal.2012;Boriaetal.2014).Thespatiallyrarefyoccurrencedatatooladdressesthis
issuebyspatiallyfilteringlocalitydatabyauserinputdistance,reducingoccurrencelocalitiestoasinglepoint
withinthespecifiedEuclidiandistance.Thistoolalsoallowsuserstospatiallyrarefytheirdataatseveral
distancesaccordingtohabitat,topographicorclimateheterogeneity(Table1d).Forexample,occurrence
localitiescouldbespatiallyfilteredat5km2,10km2and30km2inareasofhigh,mediumandlow
environmentalheterogeneity,respectively.Thisgraduatedfilteringmethodisparticularusefulforstudieswith
limitedoccurrencepointsandcanmaximizethenumberofspatiallyindependentlocalities.

Veloz,S.D.(2009)Spatiallyautocorrelatedsamplingfalselyinflatesmeasuresofaccuracyforpresence
onlynichemodels.JournalofBiogeography,36,22902299.
Hijmans,R.J.(2012)Crossvalidationofspeciesdistributionmodels:removingspatialsortingbiasandcalibrationwitha
nullmodel.Ecology,93,679688.
BoriaR.A.,OlsonL.E.,GoodmanS.M.&AndersonR.A.(2014)Spatialfilteringtoreducesamplingbiascanimprovethe
performanceofecologicalnichemodels.EcologicalModeling,275,7377.
Tool:SpatiallyRarefyOccurrenceData
1. DoubleclicktheSDMTools1.UniversalToolsSpatiallyRarefyOccurrenceDataforSDMs
(reducespatialautocorrelation)tool
1. Inputshapefileofspeciesoccurrencedata,hereselectoccurences.shp
2. Shapefilefieldcorrespondingtospeciesidentity,hereselectSPECIES
3. Shapefilefieldcorrespondingtolatitude,hereselectLATITUDE
4. Shapefilefieldcorrespondingtolongitude,hereselectLONGITUDE
6. Nameofoutputfile.Notethat"_rarefied_points"willbeappendedtofilename.
7. Thespatialresolutiontorarefythedata.Hereusethedefaultsettings.Notethatthisvaluewill
NOTactuallybeusedherebecauseyouwillbeexecutingthemultidistanceoccurrencedata
rarefying.
8. Pleaseselectproperequidistanceprojection.
9. Placingacheckmarkintheboxtoexecutethemultidistancedatararefying
10. Inputheterogeneityraster.
11. Thenumberofclasses,here5
12. Classificationtype,hereNATURAL_BREAKS

13. Themaximumdistance,here25Kilometers
14. Theminimumdistance,here2Kilometers
SpatiallyRarefyOccurrenceDatatoolinterface

4.CreationofBiasFiles

Asubsetofpythonscriptscreatebiasfilesusedtofinetunebackgroundandoccurrencepointselectionin
Maxent.Biasfilescontrolwherebackgroundpointsareselectedandthedensityofbackgroundsampling.
Properuseofbiasfilescanavoidsamplinghabitatgreatlyoutsideofaspeciesknownoccurrenceorcan
accountforcollectionsamplingbiaseswithcoordinatedata.
Backgroundpoints(andsimilarpseudoabsencepoints)aremeanttobecomparedwiththepresencedataand
helpdifferentiatetheenvironmentalconditionsunderwhichaspeciescanpotentiallyoccur.Typically
backgroundpointsareselectedwithinalargerectilineararea,withinthisareathereoftenexisthabitatthatis
environmentallysuitable,butwasnevercolonized.Whenbackgroundpointsareselectedwithinthese
habitats,thisincreasescommissionerrors(falsepositives).Asaresult,thebestperformingmodeltendstobe
overfitbecauseselectioncriterionfavoramodelthatfailtopredictthespeciesintheuncolonizedclimatically
suitablehabitat(Anderson&Raza2010,BarbetMassinetal.2012).Thelikelihoodthatsuitableunoccupied
habitatsareincludedinbackgroundsamplingincreaseswithEuclidiandistancefromthespeciesrealized
range.Thus,alargerstudyspatialextentcanleadtotheselectionofahigherproportionoflessinformative
backgroundpoints(BarbetMassinetal.2012).Researchersshouldnotavoidstudyingspecieswithbroad
distributionsorthoseexistinginregionsthatdonotconformwelltorectilinearmaplayouts,ratherthey
simplyneedtobemoreselectiveinthechoiceofbackgroundpointsinMaxent(andpseudoabsencesinother
SDMmethods)(Barveetal.2011;Merowetal.2013).
Tocircumventthisproblem,manyresearchershavebegunusingbackgroundpointandpseudoabsence
selectionmethodsthataremoreregional.SDMtoolboxcontainsthreetoolstofacilitatemoresophisticated
backgroundselectionforuseinMaxent.TheSamplebyDistancefromObs.Pts.tool(see:SDMTools2.
MaxEntToolsBackgroundSelectionviaBiasFiles)usesacommonmethodthatsamplesbackgrounds
withinamaximumradialdistanceofknownoccurrences(seeThuilleretal.2009).TheSamplebybuffered
MCPtoolrestrictsbackgroundselectionwithabufferedminimumconvexpolygonsbasedonknown
occurrences(seefollowingguide).
Anderson,R.P.&Raza,A.(2010)TheeffectoftheextentofthestudyregiononGISmodelsofspecies
geographicdistributionsandestimatesofnicheevolution:preliminarytestswithmontanerodents(genus
Nephelomys)inVenezuela.JournalofBiogeography,37,13781393.
BarbetMassin,M.,Jiguet,F.,Albert,C.H.&Thuiller,W.(2012)Selectingpseudoabsencesforspecies
distributionmodels:how,whereandhowmany?MethodsinEcologyandEvolution,3,327338.
PhillipsSJ,DudkM,ElithJ,GrahamCH,LehmannA,LeathwickJ,FerrierS(2009)Sampleselectionbiasand
presenceonlydistributionmodels:implicationsforbackgroundandpseudoabsencedata.Ecological
Applications,19,181197.
Thuiller,W.,Lafourcade,B.,Engler,R.&Araujo,M.B.(2009)BIOMODaplatformforensembleforecasting
ofspeciesdistributions.Ecography,32,369373.

Tool:BackgroundSelection:SamplebyBufferedMCP,SamplebyDistancefromObs.Pts.or
SamplebyBufferedLocalAdaptiveConvexHull
1. Decideifyouwanttorestrictbackgroundsamplingto:i)abufferedminimumconvexpolygon
basedonobservationlocalities,ii)aradialdistancefromalloccurrencepointsoran
intermediatebetweenthosetwoiii)usingthetool:SamplebyBufferedLocalAdaptiveConvex
Hull.
2. DoubleclickthecorrespondingtoolSDMTools2.MaxEntToolsBackgroundSelectionvia
BiasFilesBackgroundSelection:SamplebyBufferedMCPorBackgroundSelection:Sample
byDistancefromObs.Pts.orBackgroundSelection:SamplebyBufferedLocalAdaptive
ConvexHull
3. Continuetotoolinterfaceinstructions(BufferedMCPbelow)
BackgroundSelection:SamplebyBufferedMCPtoolinterface
1. CSVfileofspeciesoccurrences(fromprevioussteps)
2. Fieldcorrespondingtospeciesidentity
3. Filefieldcorrespondingtolongitude
4. Filefieldcorrespondingtolatitude
5. Thedistanceoutsideofminimumconvexpolygonincludedinbackgroundselection.
6. Selectoutputfolderlocation.Thisshouldbeanewemptyfolder.Ifnotemptythiscancausethe
analysistofail,particularlyiftemporaryfilesfromapreviousanalysiswerenotproperlyremoved
(e.g.thiscanhappenifanotherSDMtoolboxanalysisisterminatedearly).
7. ClimatedatasizedtoextentofMaxEntModeling.HereusetheBio_1.asclayer.Selectoneof
yourclimatefilessizedtoyourmodelingextent(e.g.Bio1.asc).Thisfilewillbeusedtomatchthe
biasfiletoproperextentandresolution(nochangewillbemadetothisfile).
Modelcalibrationandvalidation
5.SpatialJackknifingandindependenttestsofparameters
WhyuseSDMtoolboxforMaxEntmodeling:
I.SpatialJackknifing

Spatialjackknifing(orgeographicallystructuredkfoldcrossvalidation)testsevaluationperformanceof
spatiallysegregatedspatiallyindependentlocalities.SDMtoolboxautomaticallygeneratesalltheGISfiles
necessarytospatiallyjackknifeyourMaxEntModels.Thescriptsplitsthelandscapeinto35regionsbasedon
spatialclusteringofoccurrencepoints(e.g.if3:A,B,C).Modelsarecalibratedwithk1spatialgroupsandthen
evaluatedwiththewithheldgroup.Forexampleifk=3,modelswouldberunwithfollowingthreesubgroups:

1.ModeliscalibratedwithlocalitiesandbackgroundpointsfromregionABandthenevaluatedwithpoints
fromregionC
2.ModeliscalibratedwithlocalitiesandbackgroundpointsfromregionACandthenevaluatedwithpoints
fromregionB
3.ModeliscalibratedwithlocalitiesandbackgroundpointsfromregionBCandthenevaluatedwithpoints
fromregionA
II.IndependentTestsofModelFeatureClassesandRegularizationParameters
Equallyimportant,thistoolallowsfortestingdifferentcombinationsoffivemodelfeatureclasstypes(FC)and
regularizationmultiplier(s)(RM)tooptimizeyourMaxEntmodelperformance.Forexample,ifaRMwasinput
(here5),thistoolkitwouldrunMaxEntmodelsonthefollowingparametersforeachspecies:

1.RM:5&FC:Linear,2.RM:5&FC:LinearandQuadratic,3.RM:5&FC:Hinge,4.RM:5&FC:Linear,
QuadraticandHinge,5.RM:5&FC:Linear,Quadratic,Hinge,ProductandThreshold
III.AutomaticModelSelection
Finally,thescriptchoosesthebestmodelbyevaluatingeachmodel's:1.omissionrates(OR)*,2.AUC**,and
3.modelfeatureclasscomplexity.Itdoesthisinorder,choosingthemodelwiththelowestomissionrates
onthetestdata.IfmanymodelshavetheidenticallowOR,thenitselectsthemodelwiththehighestAUC.
LastlyifseveralmodelshavethesamelowORandhighAUC,itwillchoosethemodelwithsimplestfeature
classparametersinthefollowingorder:1.linear;2.linearandquadratic;3.hinge;4.linear,quadratic,and
hinge;and5.linear,quadratic,hinge,product,andthreshold.
Oncethebestmodelisselected,SDMtoolboxwillrunthefinalmodelusingalltheoccurrencepoints.If
desired,atthisstagemodelswillbeprojectedintootherclimates,environmentalvariableswillbejackknifed
tomeasureimportance,andresponsecurveswillbecreated.
*Foreachiteration,ORisweightedbythenumberofpointsintheevaluationsubgroup.Thisisnecessary
becausespatialgroupsmaynothaveidenticalnumberofpoints.Theweighinggivesequalcontributiontoall
pointsincludedinmodelevaluation.
**AUCiscalculatedfromthetotalstudyareaintheinputbiasfile(ifk=3,thenallgroups:ABC)
Forinfoandjustificationforeachofthesemethodssee:
Boria,R.A.,L.E.Olson,S.M.Goodman,andR.P.Anderson.2014.Spatialfilteringtoreducesamplingbiascanimprove
theperformanceofecologicalnichemodels.EcologicalModelling,275:7377.
Radosavljevic,A.andR.P.Anderson.2014.MakingbetterMaxentmodelsofspeciesdistributions:complexity,
overfitting,andevaluation.JournalofBiogeography.41:629643
Shcheglovitova,M.andR.P.Anderson.2013.Estimatingoptimalcomplexityforecologicalnichemodels:ajackknife
approachforspecieswithsmallsamplesizes.EcologicalModelling,269:917.
Tool:RunMaxEnt:SpatiallyJackknife
1. DoubleclicktheSDMTools2.MaxEntToolsModelinginMaxEntRunMaxEnt:Spatially
Jackknifetool
IMPORTANTNOTE1:noneoftheinputandoutputfilenames/filepathscanhavespacesinthem.If
thereareanyspaces,theoutputbatchscriptswilllikelyfailtoworkproperly.
IMPORTANT NOTE 2:Upon first use of this tool, due to its unique syntax, you need to specify the location
of the menu file. If you do not due this, the menu presented by ArcGIS will not make complete sense. For
a detailed overview of how to do this (it will take 30 seconds to do), go to:
http://www.sdmtoolbox.org/menu-fix-spatial-jackknife
1. FolderwiththeMaxEntprogram.Downloadablefrom:
http://www.cs.princeton.edu/~schapire/maxent/
2. CSVfileoutputfromspatialrarefiedoccurrencedata(outputfromstep3D)
3. CSVfieldcorrespondingtospeciesidentity
4. CSVfieldcorrespondingtolongitude
5. CSVfieldcorrespondingtolatitude
6. FolderwithclippedASCIIclimatedatafromstep3C.
7. Selectenvironmentallayersfromthisfolderthatdepictcategoricaldata.
8. Selectenvironmentallayerstoexcludefromanalyses(notlistinoutputfromstep2).
9. Foldercontainingbiasfilesfromstep4.
10. OutputfolderforGIS,pythonscriptsandMaxEntbatchfiles.OutputwillincludeallGISfiles
necessarytorunmodels.
11. ForspatialjackknifingthisformatoutputwillbeLogistic,regardlessofselection
12. ForspatialjackknifingthisformatoutputwillbeASCII,regardlessofselection

13. Creategraphsshowinghow
predictedrelativeprobability
ofoccurrencedependsonthe
valueofeachenvironmental
layer
14. Createanimageofeach
outputmodel
15. Measurevariableimportance
byjackknifingthevariables.
Eachvariableisexcludedin
turnandamodelcreatedwith
theremainingvariables.Then
amodeliscreatedusingeach
variableinisolation.
16. Thiswillskipthemodelifan
outputexists.
17. Thiswillsuppressany
warningsencounteredduring
modeling.Allwarningsare
alwayswrittentothelogfiles.
18. Thisisthebreadthofthe
model.Ahighernumbergives
amorespreadout
distribution.Inputmany
valuesseparatedbysemi
colons.

Forexample:
0.5;1;1.5;2;2.5;3;4;5

Thedefaultvalueis1.

Rememberthemorevalues
inputwillproducemoreSDMs
createdandrequiremore
computationtime.Foreach
regularizationmultiplier(RM),
15modelswillberun(5
featureclassgroupsand35
spatialjackknifegroups,
5x3=15to5x5=25).This
numberismultipliedforeach
replicateandeachspecies

modeled.Thus,ifyouhave2species,5RMsand2replicates;thiswouldresultin300or500
modelsrunfor3and5spatialjackknifegroups,respectively(2species*2replicates*5RM*15
25modelsperrun)
19. Applyathresholdtomakebinarymodel.Thiswillgeneratedabinarymodelinadditiontothe
continuousmodel.Innoneissupplied,SDMtoolboxwilluse10percentminimumtraining
presencetocalculatedomissionrates.Ifyoupreferanotherthreshold,pleaseselectithere.
20. ProjectionClimateLayers.FolderscontainingenvironmentaldataforprojectingtheMaxEnt
models(oftenarefuturearepastclimates).Toselectmultiplefoldersatonceholdtoshift.The
layersMUSTmatchtheinputenvironmentlayers,e.g.ifBio27isusedtobuildthemodelthen
theprojectionfoldermustcontainananalogvariableandhavetheidenticalname.Here
resolutionandspatialextentdonotneedtomatchinputenvironmentallayers.
21. Applyclampingwhenprojecting
22. Ifchecked,willnotpredictareasofclimatespaceoutsideoflimitsencounteredduringtraining
23. NumberofCPUstouseformodeling
24. ThiswillnotdisplaytheMaxEntGUIwhenrunningmodelspreferred
25. Checkthisboxtoperformalltheanalysesdescribedintotheinformationwindow.Ifnot
checkedthiswillrunthemodelingasifexecutedfromtheMaxEntGUI(nospatialjackknifingor
independentevaluationofRVorfeatureclasses).
26. Thisistheminimumnumberofpointstoexecutespatialjackknifing.Ifbelowthisvalue,the
modelswillbetrainedandevaluatedusingeithercrossvalidation,bootstrappingorsub
sampling(asspecifiedbelowinsteps:3032).Eachnonspatiallyjackknifedgroupisoptimized
withindependenttestsofdifferentcombinationsofthefivemodelfeatureclasstypes(FC)and
inputregularizationmultiplier(RM)values.
27. Replicatesofeachmodelparameterclassinspatialjackkniferuns
28. Numberofgroupstosubdividethelandscapeinto.Higherthenumberthemoremodelsrun,but
alsothemoretrainingpointsincludedineachmodelrun.
29. Ifselected:
Groupswillbespatiallysegregatedandnumbersofoccurrenceswithingroupsmaynotbe
equal.Thisanalysisismorefocusedonnaturalspatialgroups.Thismethodisbestif
projectingmodelsintootherclimates(i.e.currentorpast)andisparticularlyusefulfor
trainingandevaluatingmodelperformanceinpotentiallynonanalogousclimates.
Ifnotselected:
Spatialjackknifegroupswillbespatiallyrandomlyandnumbersofoccurrenceswithin
groupswillbeequal(+/1,duetounequalgroupsizesforsomecombinationsof
occurrencesrecordsandgroupnumber).Thismethodisbestifnotprojectingmodelsinto
otherclimates.
30. Replicatesofeachmodelparameterclassforspecieswithtoofewpointstospatiallyjackknife
31. ReplicateType.Ifreplicatesare>1,thenmultiplerunsareperformedbythistype:

Crossvalidate:MaxEntmakesknumberoffoldsofyouroccurrencedatatotrainandtestthe
data.HereyouarenotbeabletotellMaxEnthowmanyreplicatesyouwouldliketorunorthe
percentageofoccurrencedatayouwouldlikewithheldformodelvalidation(testoccurrences).
Optimalifyouhavealargenumberofspeciesoccurrences.

Bootstrap:Replicatessamplessetsarechosenbysamplingwithreplacement

Subsample:Replicatesamplesetsarechosenbyremovingtherandomtestpercentage(inputin
thefollowingwindow)withoutreplacement,thevariablesnotincludedarethenusedformodel
evaluation
32. Ifreplicatetypeis'boostrap'or'subsample,inputthepercentageofpointsusedfor
subsampling.
33. Additionalparametersnotusedinspatialjackknifing.
34. Runthetool.
35. Afterfilesarecreated,toexecutemodelsgotooutputfolder.Clickthebatchfile
"Step1_Optimize_MaxEnt_Model_Parameters.bat"thiswillrunallmodelsandsummarystats.
Knowthismaytakeseveralhours,orevendays(ifyouhavemanyspeciesandRV),tofinish.
36. OnceallthemodelsfromStep1arerun,the"Step2_Run_Optimized_MaxEnt_Models.bat"will
bepopulatedwiththebestmodelparameters.Runthisfiletogetfinalmodels.
37. Toseemodelranksforeachspecies,openthecorrespondingfolderandopenthe
species_name_SUMSTATS_RANKED_MODELS.csv.Herethebestmodelisthefirstrow.
Featurenumbercorrespondstofeatureclassgroupwith:1=linear;2=linear&quadratic;3=
hinge;4=linear,quadratic,andhinge;and5=linear,quadratic,hinge,product,andthreshold.
Finalremarks
GreatjobonlyasmallproportionofallpublishedpapersusingSDMs/ENMsaddressthefollowingbest
practicesofmodeling:
1.Usedspeciesspecificregionalbackgroundsampling
2.Spatiallyrarefiedoccurrencedata
3.SpatiallyjackknifedSDMstocalibratemodelparameters
4.Independentlyevaluatedfeatureclassparametersandregularizationmultiplier(s)
5.Reducedcorrelationofinputclimatevariablesforinterpretinginfluenceonmodel(optional
here)
NowconsiderthefollowingSDMtoolboxtoolsforfurtheranalyses:
Ifprojectingmodelsintofutureorpastclimates:
1. LimitDispersalinFutureSDMs
2. OverpredictionCorrection:ClipModelsbyBufferedMCPs
3. DistributionChangesBetweenBinarySDMs:
a. CentroidChanges(Lines)
b. DistributionChangesBetweenBinarySDMs
Tocreatebettersmodels:
4. CorrectingLatitudinalBackgroundSelectionBiases

5. Gaussiankerneldensityofsamplinglocalities
Toassesslandscapeconnectivity:
6. Amongallsitesorbetweensharedhaplotypes
7. Createfrictionlayers
TomeasurespatialbiodiversitypatternsofmanySDMs:
8. Calculatespeciesrichnessandendemism(weightedendemism&correctedweighted
endemism)

Nowgopublishyouresults!

SummaryofsomebasicconsiderationswhengeneratingSDMs
Tablemodifiedfrom:AlvaradoSerrano,D.F.andKnowles,L.L.(2014),Ecologicalnichemodelsinphylogeographicstudies:
applications,advancesandprecautions.MolecularEcologyResources,14:233248.Pleaseseepaperformoredetails.
AssumptionsthatmayaffectSDMs Specificconsiderations
Datacompilation effectsofspeciesnaturalhistory
occurrencerecords: geographic/environmentalbias
intraspecificvariability
Arespeciespresences(andabsence) positionaluncertainty
recordsrepresentativeoftheactual samplesize
distribution? samplingbias(e.g.towardsmoreaccessibleareas)
taxonomicaccuracy(e.g.subspeciesorraces)
temporalcoverageinrelationtoenvironmentaldata
Datacompilation dataqualityandbiases
Environmentalvariables: effectonspeciesdistribution
(directvs.indirect)
Doenvironmentalvariables resolutioninspaceandtime
accuratelycapturetheassociation spatialautocorrelation
betweenspeciessubsistenceand spatialextent
theenvironmentattherelevant temporalcoverageandstability
scale? type(categoricalvs.continuous)
Modelgenerationandcalibration algorithmassumptions
algorithmperformance
Isthemodellingalgorithm underdifferentscenarios
appropriategiventhedataavailable inputdatatype(e.g.presencesonlyvs.presence/absences)
andresearchquestion? outputgenerated(e.g.presence/absencevs.continuous
prediction)
sensitivitytomodelparameters
Modelgenerationandcalibration modelcomplexity
modelselectionprocedure
Isthemodelappropriately settingofmodelparameters
calibratedforthedataavailableand variableselectionstrategy
researchquestion?
Modelvalidation assumptions/limitationsofaccuracymeasurement
importanceofuseofmultiplemetrics
Isvalidationperformedontruly sensitivitytomodelparameters
independentdataandunder thresholdtransformationofcontinuouspredictions
appropriatesettings?
Modelprojection availabilityofvalidationdatainprojectedregions
likelihoodofnicheshifts
Isthespeciesenvironment modeluncertainty
relationshiplikelytobemaintained modeltransferability
inspaceand/ortime? risksofinterpolationandextrapolation

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