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CLIMATELINKAGEMAPPERUSERGUIDECLIMATELINKAGEMAPPERUSERGUIDEVERSION10UPDATEDJANUARY2014DARRENKAVANAGH1,TRISTANNUEZ2,ANDBRADMCRAE31ADZEINFORMATICS2UNIVERSITYOFCALIFORNIA,BERKELEY3THENATURECONSERVANCYACKNOWLEDGEMENTSCLIMATELINKAGEMAPPERBUILDSUPONTHEPYTHONCODEDEVELOPEDBYTRISTANNUEZASPARTOFHISMASTERSWORKNUEZ2011,NUEZETAL2013WEAREGRATEFULTOOURCOLLABORATORSINTHECLIMATECHANGESUBGROUPOFTHEWASHINGTONWILDLIFEHABITATCONNECTIVITYWORKINGGROUPFORTHEIRFEEDBACKANDASSISTANCE,ANDTOJENNYMCGUIREFORTESTINGANDSUGGESTINGIMPROVEMENTSTOTHEUSERGUIDESOFTWAREREQUIREMENTSANDLICENSINGCLIMATELINKAGEMAPPERRUNSONTHEWINDOWSPLATFORMONLYITREQUIRESGRASSGISANDARCGISDESKTOP100OR101ARCINFOLICENSEWITHTHESPATIALANALYSTEXTENSIONTHETOOLANDITSSOURCECODEAREPROVIDEDFREEOFCHARGEUNDERAGNUGENERALPUBLICLICENSEMOREDETAILSCANBEFOUNDONTHELINKAGEMAPPERWEBSITEHTTP/CODEGOOGLECOM/P/LINKAGEMAPPER/,WHERETHECODEISHOSTEDPREFERREDCITATIONKAVANAGH,DM,TANUEZ,ANDBHMCRAE2013CLIMATELINKAGEMAPPERCONNECTIVITYANALYSISSOFTWARETHENATURECONSERVANCY,SEATTLEWAAVAILABLEATWWWCIRCUITSCAPEORG/LINKAGEMAPPERTABLEOFCONTENTS1INTRODUCTION32INSTALLATION33USINGCLIMATELINKAGEMAPPER331INPUTDATAREQUIREMENTS332RUNNINGFROMAPYTHONSCRIPT533PROCESSINGSTEPS54CLIMATELINKAGEMAPPERDEMO65EXTRAHINTS751BACKGROUNDPROCESSING752CHANGINGLINKAGERULESWITHOUTRESTARTINGFROMSCRATCH76SUPPORT77LITERATURECITED71INTRODUCTIONCLIMATELINKAGEMAPPERISPARTOFTHELINKAGEMAPPERTOOLKIT,WHICHINCLUDESLINKAGEMAPPERMCRAEANDKAVANAGH2011ANDOTHERMODULESDESIGNEDTOSUPPORTREGIONALWILDLIFEHABITATCONNECTIVITYANALYSESTHETOOLISDESIGNEDTOCREATELINKAGESBETWEENDESIGNATEDCOREAREASTHATFALLALONGACLIMATICGRADIENTEGTEMPERATUREMOREDETAILSONCLIMATECORRIDORTHEORYANDAPPROACHESTOMODELINGCLIMATECORRIDORSCANBEFOUNDINNUEZ2011ANDNUEZETAL2013,WASHINGTONWILDLIFEHABITATCONNECTIVITYWORKINGGROUPWHCWG2011ANDWHCWG2012FORPROJECTNEWSANDTOOLUPDATESPLEASEVISITTHEPROJECTWEBSITEHTTP/CODEGOOGLECOM/P/LINKAGEMAPPER/AND/ORJOINTHEUSERGROUPHTTP/GROUPSGOOGLECOM/GROUP/LINKAGEMAPPER2INSTALLATION1DOWNLOADANDINSTALLLINKAGEMAPPERDOWNLOADANDINSTALLTHELINKAGEMAPPERTOOLBOXFROMHTTP/CODEGOOGLECOM/P/LINKAGEMAPPER/OPENTHEZIPARCHIVEANDPLACETHETOOLBOXDIRECTORYWITHALLITSCONTENTSONYOURCOMPUTERPLACETHEDEMODIRECTORYINAFOLDERTHATHASNOSPACESORSPECIALCHARACTERSINITSPATHTOINSTALLTHETOOLBOXFOLLOWTHEINSTRUCTIONSINTHELINKAGEMAPPERUSERGUIDEMCRAEANDKAVANAGH2011,WHICHISALSOINCLUDEDINTHEDOWNLOAD2DOWNLOADANDINSTALLGRASSGISVERSION65ORLATERTHEREAREMANYVERSIONS,OFGRASS,BUTTHISONEHASBEENSHOWNTOWORKWITHCLIMATELINKAGEMAPPERHTTP/TINYURLCOM/GRASS70DEVELOPMENTVERSIONSCHANGEDAILY,SOITISPOSSIBLETHATOTHERVERSIONSMAYNOTWORKWITHCLIMATELINKAGEMAPPERTOINSTALLGRASSGISRUNTHEDOWNLOADEDINSTALLATIONFILEANDFOLLOWTHEONSCREENINSTRUCTIONS3USINGCLIMATELINKAGEMAPPERTOSTARTCLIMATELINKAGEMAPPERSELECTTHELINKAGEMAPPERTOOLBOXSEEFIGURE1INARCGIS,ANDCLICKONCLIMATELINKAGEMAPPERTHEDIALOGILLUSTRATEDINFIGURE2SHOULDAPPEARADESCRIPTIONOFEACHPARAMETERFOLLOWSBELOW31INPUTDATAREQUIREMENTSAMODELINPUTSAPROJECTFOLDERTHISISTHEWINDOWSFOLDERWHERETHEFINALOUTPUTWILLBESAVEDITISALSOUSEDBYTHETOOLTOSTORETEMPORARYOUTPUTSTHISFOLDERSHOULDBEINASHALLOWTREEANDHAVEASHORTNAMESOMETHINGLIKECANBO,IDEALLYONALOCALDRIVEFOROPTIMUMPROCESSINGSPEEDANDRELIABLYTHENAMEOFTHEDIRECTORYWILLALSOBEUSEDASAPREFIXFORFINALLINKAGEMAPPERFIGURE1LINKAGEMAPPERTOOLKITOUTPUTFILESEGANBO_LCPSTHERESHOULDBENOSPACESORSPECIALCHARACTERSANYWHEREINTHEFOLDERPATHBCOREAREAFEATURECLASSENTERTHEPOLYGONFEATURECLASSEGSHAPEFILETHATCONTAINSTHECOREAREASTHEPOLYGONSTHATWILLBECONNECTEDWITHLINKAGESCCOREAREAFIELDNAMETHISDROPDOWNLISTWILLLISTALLATTRIBUTEFIELDSINTHECOREFEATURECLASSTHESELECTEDFIELDMUSTCONSISTOFPOSITIVEINTEGERSFID1DCLIMATERASTERENTERTHECLIMATEEGTEMPERATURESURFACEHERETHISCANBEINANYSTANDARDRASTERFORMATTHATARCGISACCEPTSERESISTANCERASTEROPTIONALTOOPTIONALLYINCORPORATEOTHERIMPEDIMENTSTOMOVEMENT,INADDITIONTOCLIMATICVARIABILITY,ARESISTANCERASTERCANBEENTEREDHERESEETHELINKAGEMAPPERUSERGUIDEMCRAEANDKAVANAGH2011FORTIPSONCREATINGARESISTANCERASTERBOPTIONSAGRASSGISINSTALLATIONFOLDERFORTHETOOLTOWORKCORRECTLYYOUMUSTTELLITWHEREGRASSGISISINSTALLEDONWINDOWS764BITTHEDEFAULTFOLDERISCPROGRAMFILESX86GRASSGIS65SVNBMINIMUMDISTANCEBETWEENCOREPAIRSENTERTHEMINIMUMEDGETOEDGELINKAGEDISTANCETHATSHOULDSEPARATEONECORETOANOTHERLINKAGESLESSTHANTHISDISTANCEWILLNOTBECREATEDTHEDISTANCEUNITISTHATOFTHEINPUTSPATIALLAYERSCMAXIMUMDISTANCEBETWEENCOREPAIRSENTERTHEMAXIMUMEDGETOEDGELINKAGEDISTANCETHATSHOULDSEPARATEONECORETOANOTHERLINKAGESGREATERTHANTHISDISTANCEWILLNOTBECREATEDTHEDISTANCEUNITISTHATOFTHEINPUTSPATIALLAYERSNOTELEASTCOSTCORRIDORSCANSTILLBELONGERTHANTHISDISTANCE,ASTHEYWILLTYPICALLYBECONSIDERABLYLONGERTHANTHEEDGETOEDGEDISTANCEBETWEENTHECOREPAIRSTHEYARECONNECTINGDCLIMATETHRESHOLDAPOSITIVENUMERICVALUE,INTHESAMEUNITSASTHECLIMATERASTER,THATLIMITSCOREPAIRSBASEDONCLIMATECOREAREASWILLONLYBECONNECTEDIFTHEDIFFERENCEBETWEENTHELOWESTCLIMATEVALUESISGREATERTHANTHETHRESHOLDTOAVOIDOUTLIERS,THISVALUEISTWOSTANDARDDEVIATIONSBELOWTHEMEANOFTHECORESEENUEZ2011ANDNUEZETAL2013FORMOREDISCUSSIONONTHISTOPICECLIMATEVARIABLECOSTTHISISTHEDISTANCETOCLIMATERATIO,INCOSTDISTANCEUNITSPERUN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