maxent原版英文说明复习进程Word格式文档下载.docx

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Spring2010

Lab6MaximumEntropy

Assigned:

MondayMarch1

Due:

MondayMarch8

20points

ThislabexercisewasprimarilywrittenbyStevenPhillips,MiroDudikandRobSchapire,withsupportfromAT&

TLabs-Research,PrincetonUniversity,andtheCenterforBiodiversityandConservation,AmericanMuseumofNaturalHistory.Thislabexerciseisbasedontheirpaperanddata:

StevenJ.Phillips,RobertP.Anderson,RobertE.Schapire.

Maximumentropymodelingofspeciesgeographicdistributions.

EcologicalModelling,Vol190/3-4pp231-259,2006.

MygoalistogiveyouabasicintroductiontouseoftheMaxEntprogramformaximumentropymodelingofspecies’geographicdistributions.

TheenvironmentaldataconsistofclimaticandelevationaldataforSouthAmerica,togetherwithapotentialvegetationlayer.ThesamplespeciestheauthorsusedwillbeBradypusvariegatus,thebrown-throatedthree-toedsloth.

NOTEontheMaxentsoftware

Thesoftwareconsistsofajarfile,maxent.jar,whichcanbeusedonanycomputerrunningJavaversion1.4orlater.Itcanbedownloaded,alongwithassociatedliterature,fromwww.cs.princeton.edu/~schapire/maxent.IfyouareusingMicrosoftWindows（asweassumehere）,youshouldalsodownloadthefilemaxent.bat,andsaveitinthesamedirectoryasmaxent.jar.Thewebsitehasafilecalled“readme.txt”,whichcontainsinstructionsforinstallingtheprogramonyourcomputer.

Thesoftwarehasalreadybeendownloadedandinstalledonthemachinesin317Percival.

ð

Firstgototheclasswebsiteanddownloadthemaxent-tutorial-data.zipfile.Extractittothec:

/tempfolderwhichwillcreateac:

/temp/tutorial-datadirectory.

Findthemaxentdirectoryonthec:

/driveofyourcomputerandsimplyclickonthefilemaxent.bat.Thefollowingscreenwillappear:

Toperformarun,youneedtosupplyafilecontainingpresencelocalities（“samples”）,adirectorycontainingenvironmentalvariables,andanoutputdirectory.Inourcase,thepresencelocalitiesareinthefile“c:

\temp\tutorial-data\samples\bradypus.csv”,theenvironmentallayersareinthedirectory“layers”,andtheoutputsaregoingtogointhedirectory“outputs”.Youcanentertheselocationsbyhand,orbrowseforthem.Whilebrowsingfortheenvironmentalvariables,rememberthatyouarelookingforthedirectorythatcontainsthem–youdon’tneedtobrowsedowntothefilesinthedirectory.AfterenteringorbrowsingforthefilesforBradypus,theprogramlookslikethis:

Thefile“samples\bradypus.csv”containsthepresencelocalitiesin.csvformat.Thefirstfewlinesareasfollows:

species,longitude,latitude

bradypus_variegatus,-65.4,-10.3833

bradypus_variegatus,-65.3833,-10.3833

bradypus_variegatus,-65.1333,-16.8

bradypus_variegatus,-63.6667,-17.45

bradypus_variegatus,-63.85,-17.4

Therecanbemultiplespeciesinthesamesamplesfile,inwhichcasemorespecieswouldappearinthepanel,alongwithBradypus.Othercoordinatesystemscanbeused,otherthanlatitudeandlongitude,aslongasthesamplesfileandenvironmentallayersusethesamecoordinatesystem.The“x”coordinateshouldcomebeforethe“y”coordinateinthesamplesfile.

Thedirectory“layers”containsanumberofasciirastergrids（inESRI’s.ascformat）,eachofwhichdescribesanenvironmentalvariable.Thegridsmustallhavethesamegeographicboundsandcellsize.MAKESUREYOURASCIIFILESHAVETHE.ascEXTENSION!

!

Oneofourvariables,“ecoreg”,isacategoricalvariabledescribingpotentialvegetationclasses.Youmusttelltheprogramwhichvariablesarecategorical,ashasbeendoneinthepictureabove.

Doingarun

Simplypressthe“Run”button.Aprogressmonitordescribesthestepsbeingtaken.Aftertheenvironmentallayersareloadedandsomeinitializationisdone,progresstowardstrainingofthemaxentmodelisshownlikethis:

The“gain”startsat0andincreasestowardsanasymptoteduringtherun.Maxentisamaximum-likelihoodmethod,andwhatitisgeneratingisaprobabilitydistributionoverpixelsinthegrid.Notethatitisn’tcalculating“probabilityofoccurrence”–itsprobabilitiesaretypicallyverysmallvalues,astheymustsumto1overthewholegrid.Thegainisameasureofthelikelihoodofthesamples;

forexample,ifthegainis2,itmeansthattheaveragesamplelikelihoodisexp

（2）≈7.4timeshigherthanthatofarandombackgroundpixel.Theuniformdistributionhasgain0,soyoucaninterpretthegainasrepresentinghowmuchbetterthedistributionfitsthesamplepointsthantheuniformdistributiondoes.Thegainiscloselyrelatedto“deviance”,asusedinstatistics.

Therunproducesanumberofoutputfiles,ofwhichthemostimportantisanhtmlfilecalled“bradypus.html”.Partofthisfilegivespointerstotheotheroutputs,likethis:

Lookingata