occupancy in presence

7/29/2019 occupancy in presence

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EstimationofWildlifePopulations 95

Lecture26EstimatingOccupancywithProgramPRESENCE

ProgramPRESENCEwasdevelopedspecificallytofitmodelsandestimateparameters

associatedwithoccupancy(detection/nondetectiondata). Thedeveloperstriedtomakethe

learningcurvelesssteep,comparedtoProgramMARK.

Therearemanysimilaritiesbetweenthetwoprograms(modelsarefitusingmaximum

likelihood,comparedwithAIC,etc.),buttherearealsosomedifferences(dataformat,layoutof

theDM,windowswithintheprogram,etc.).

Dataformatting,input,andfiletypesDatafilesinPRESENCEhavea.paoextensionandtheresultsfilesendin.pa2. AswithMARK,

thedatafilehasaparticularformat. ThesefilescanbecreatedoutsideofPRESENCEand

importedorinputdirectlyintoPRESENCE.

OnceyouhavestartedPRESENCE,inthemenubar,selectFile>NewProject.

IntheEnterSpecificationsforPRESENCEAnalysisdialogwindow,selectthelargeInput

DataFormbuttoninthebottomleftcorner. Thiswillopenadatainputinterfacewindow

thatallowsyoutocopyandpasteyourdataintoPRESENCEfromaspreadsheetpackage.

Thedataorcovariatesareenteredintotherespectivegridcellsandthefivetextboxesnear

thetopofthewindowdefinethevariousdimensionsofthespreadsheet:

thenumberofrows(samplingunits)

numberofcolumns(repeatedsurveys)

numberofsurveyoccasionsperseason

numberofsitespecificcovariates

numberofsamplingorsurveyspecificcovariates

Openthedatafileinthespreadsheetprogram,selectandcopythedatainthefile. Then

returntotheInputDataFormandselectEdit>Paste>PasteValuesfromtheEditmenuto

pastethedataintoPRESENCE.

Blueridgetwolinedsalamanders

Wellusetheblueridgetwolinedsalamanderdataagain(salamander.csv)39sites,

surveyed5times.

Notice

that

there

are

39

rows

and

5columns

in

the

data

set,

with

no

covariatesincludedhere.

Besuretospecifytheappropriatevaluesinthe5textboxesintheInputDataFormso

yourPRESENCEdatafilecontainsallofthedata.


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SavethedatafilebyselectingFile>SaveAs.Whenyoudoso,amessageboxwillappear

askingwhetheryouwanttousethelastcolumnofthedetectiondataasfrequencydata

(numberoftimeseachencounterhistorywasobserved). SelectNo. Noticethatthe.pao

extensionisincludedonthePRESENCEdatafile.

YoucannowclosetheDataInputFormandreturntotheEnterSpecificationswindow.

HittheClicktoselectfilebutton,browseforandthenselectthedatafileyouvejust

saved. Youllseethefullfilenameanddetailsforyourdata. Besureallofthisinformation

iscorrectandfeelfreetolookatthe.paofiletoseehowPRESENCEcodesthedata. Once

youaresureeverythingiscorrect,selectOK.

YounowhaveaResultsBrowserwindow,similartowhatyousawinMARK. Ifyoudonot

seethiswindow,youllhavetostartover,asthedatafilewasnotcreated.

Buildingmodelsandgeneratingestimates Torunasingleseasonanalysis,inthemainPRESENCEwindowselectRun>Analysis:single

season.ThiswillbringuptheSetupNumericalEstimationRun(SNER)window. Thissame

windowisusedforallanalyses,onlytheModelboxvariesbetweenthedifferenttypesof

analyses.

Withinthemodelbox,thereare2options,PredefinedorCustom.

Thepredefinedoptionisselectedbydefault,whichprovidesalistof6predefinedmodels

thatuserscanselecttolearnhowtousePRESENCE,butgenerallywillbeoflimitedusefora

fullblowndataanalysis. Torunthese,highlightthemodelofinterestandhittheOKto

Runbutton. YoullthenseeadialogboxsimilartoMARK,askingyoutoconfirmthatyouwanttheseresultsaddedtotheprojectfile.

YoucanrunanymodelusingtheCustomoption. Selectingthisoptionbringsupthe

DesignMatrixwindow. UnlikeProgramMARK,inPRESENCE,thedesignmatrixforeach

parametertypeisgivenaseparatesheet,andinthesingleseasonmodelthereare2

parametertypes:OccupancyandDetectionprobabilities.

AswithMARK,eachrowofthedesignmatrixrepresentsarealparameter,e.g.,occupancy

anddetectionprobabilities. Thecolumnsrepresentthebetaparameters: theparameters

thatareactuallyestimated thecoefficientsintheregressionequation. Ifacovariatename

isenteredintoagridcell,thevalueofthatcovariateisusedintheregressionequation.

FitthepredefinedmodelsandthenbuildthesamemodelswiththeCustomoption.

Ensurethattheresultsarethesame.


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Toviewtheresultsforanyofyourmodels,clickonthemodelnametoselectit,thenright

clicktoopenapopupmenuandthenselectViewmodeloutput.

Theoutputbeginswiththemodelname,followedbysomesummaryinformationaboutthe

datafile,thenumberofparametersusedtofitthemodel,twicethenegativeloglikelihood

valueevaluatedatthemaximumlikelihoodestimates(whichisusedtocalculateAICvaluesorcouldbeusedinlikelihoodratiotests),theAICvalueforthemodel,andthenave

estimateofoccupancy(uncorrectedfordetectionprobability). Theestimatedvaluesfor

andpfromthemodel(andthestandarderrors)arealsoprovided. Forcustommodels,the

outputalsoincludesanestimateofaderivedparametertheprobabilitythataunitis

occupiedgiventhatthespeciesisneverdetected.

Howdothesemodels/estimates/inferencescomparetowhatyoufoundwithProgram

MARK?

AICvs.AICc NoticethattheResultsBrowserprovidesAICanddeltaAICvalues,insteadofAICcanddelta

AICc. YoucanchangeAICtoAICcbyspecifyingtheeffectivesamplesize(ESS)(Underthe

ToolsmenuinPRESENCE).

However,determiningwhatvaluetousefortheeffectivesamplesizehasbeenupfor

discussion. OnarecentpostonthePRESENCEdiscussionforum,DarrylMacKenzie

suggested4potentialoptions:

Numberofsamplingunits

Numberofdetections(equivalenttonumberofreleasesinCJS)

Numberofsurveysat'occupied'units

Somethingelse

Hesaidthislistisrankedinorderfromconservative >liberal,meaningthatwithoption1,

you'regoingtogetthegreatestpenaltyformorecomplicatedmodels. Thiswillresultinthe

simplermodelsgettingrankedtoohighiftherealESSisactuallysomethingbigger. Further,

hetendstosuggestthatpeopletryacoupleofoptionsifthey'reconcernedandseehow

thataffectsfinalinferences.

Forthepurposesofthisclass,ifyoudecidetousePRESENCE,youcanjustusetheAICvalues.


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Buildingmodelswithcovariates AswithMARK,PRESENCEcanincorporatecategoricalandcontinuouscovariates. These

maybesite orsurveyspecific. Surveyspecificcovariateschangeoverthesamplingseason,

sothesecovariateswillhavespreadsheetsthathavethesamenumberofrowsandcolumns

asthedataset. YoucanaddlabelstothecovariatesbyselectingEdit>RenameCovariate.

Surveyspecificcovariateshavemissingvaluesinthesameplacesasthedataset. These

missingcovariatevaluesareokay,aslongasthesurveydataisalsomissing.Missingvalues

forsitespecificcovariatesarenotallowed.

Mahoenuigiantweta

Wellalsousethewetadataagain(weta.xls)72sites,surveyed35times,with

informationastowhetherthesitewasbrowsedbyferalgoats.

Noticeafewthings:

Thisspreadsheet

has

several

worksheets

included

one

for

the

detection

histories,oneforthecovariate,and3moresheetswithinformationonsurvey

specificcovariatesdenotingwhich1of3differentobserversconductedthe

occupancysurveys. (Ididntprovidethesurveyspecificcovariatesintheinitial

dataset.)

Whereasitewasnotsurveyedonagivenday,thisisdenotedasainsteadofa

.asinMARK.

Thesitespecificcovariate(browsedandunbrowsed)iscodedas2columns.

Startanewproject,repeatingthestepsyoudidaboveforthesalamanderdata. Wenow

have2site

specific

covariates

(browsed

and

unbrowsed)

and

3survey

specific

covariates.

Asyouchangesthesevaluesintheinitialsetup,additionaltabsarecreatedintheData

InputForm.

Besuretosavethedataonceyouhaveinputallofthedataandcovariates.

Trybuildingthefollowingmodels(feelfreetotryothersaswell):

Psi(.)p(.)

Psi(.)p(time)

Psi(.)p(observer)

Psi(browsed)p(.)

Psi(browsed)p(time)

Psi(browsed)p(observer)


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Modelaveraging Atthemoment,modelaveragingisnotavailableinProgramPRESENCE. Youcancompute

weightedaveragesforestimatesbyhand,butcomputationsfortheappropriatestandard

errorsarealittletrickier.

Predictingoccupancy Onceamodelhasbeenfittothedata,theresultingregressionequationofspecies

occurrencecanbeusedtopredicttheprobabilityofoccupancyatotherunitsbasedupon

thevaluesofthecovariatesinthemodelmeasuredattheotherunits.

Addtherequirednumberofrowstothebottomofthedetectiondata,withallsurveys

indicatedasmissing.Bydoingso,thiswillhavenoeffectontheestimationofthe

parametervalues.Thesitespecificcovariatevaluesforthesephantomunitscanbe

enteredasnormal,andthesurveyspecificcovariatescouldalsobeenteredasmissing

values.

WhenthemodelisfitwithinPRESENCE,avalueforthepredictedoccupancyprobabilitywill

beoutputtedfortheseotherunitsalongsidetheestimatesfortheunitsthatwereactually

surveyed.

occupancy in presence

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