├── .Rbuildignore ├── .gitattributes ├── .github ├── .gitignore └── workflows │ ├── R-CMD-check.yaml │ └── build-mac-binary.yaml ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── NEWS.md ├── R ├── IDS.R ├── RcppExports.R ├── boot.R ├── classes.R ├── colext.R ├── deprecated_sim_power.R ├── distsamp.R ├── distsampOpen.R ├── gdistremoval.R ├── gdistsamp.R ├── getDesign.R ├── gmultmix.R ├── goccu.R ├── gpcount.R ├── makePiFun.R ├── mapInfo.R ├── mixedModelTools.R ├── multinomPois.R ├── multmixOpen.R ├── nmixTTD.R ├── occu.R ├── occuCOP.R ├── occuFP.R ├── occuMS.R ├── occuMulti.R ├── occuPEN.R ├── occuRN.R ├── occuTTD.R ├── pcount.R ├── pcount.spHDS.R ├── pcountOpen.R ├── piFun.R ├── plotEffects.R ├── posteriorSamples.R ├── power.R ├── predict.R ├── ranef.R ├── simulate.R ├── unmarkedCrossVal.R ├── unmarkedEstimate.R ├── unmarkedFit.R ├── unmarkedFitList.R ├── unmarkedFrame.R ├── unmarkedLinComb.R ├── utils.R ├── vif.R └── zzz.R ├── README.Rmd ├── README.md ├── _pkgdown.yml ├── data ├── MesoCarnivores.rda ├── Switzerland.RData ├── birds.RData ├── crossbill.rda ├── cruz.rda ├── frogs.RData ├── gf.RData ├── issj.rda ├── jay.rda ├── linetran.RData ├── mallard.RData ├── masspcru.RData ├── ovendata.RData └── pointtran.RData ├── inst ├── CITATION ├── bench │ ├── bench.occu.R │ ├── bench.pcount.R │ └── bench.pcountOpen.R ├── csv │ ├── alfl.capRecap.csv │ ├── alfl.csv │ ├── alflCovs.csv │ ├── csv_factor_test.csv │ ├── distdata.csv │ ├── frog2001pcru.csv │ ├── frog2001pfer.csv │ └── widewt.csv └── shinyPower │ ├── server.R │ └── ui.R ├── man ├── IDS.Rd ├── MesoCarnivores.Rd ├── SE-methods.Rd ├── SSE.Rd ├── Switzerland.Rd ├── backTransform-methods.rd ├── birds.Rd ├── coef-methods.Rd ├── colext.Rd ├── computeMPLElambdas.Rd ├── confint-methods.Rd ├── crossVal.Rd ├── crossbill.Rd ├── cruz.Rd ├── csvToUMF.Rd ├── detFuns.Rd ├── distsamp.Rd ├── distsampOpen.Rd ├── extract-methods.Rd ├── fitList.Rd ├── fitted-methods.Rd ├── formatDistData.Rd ├── formatMult.Rd ├── formatWideLong.Rd ├── frogs.Rd ├── gdistremoval.Rd ├── gdistsamp.Rd ├── getB-methods.Rd ├── getFP-methods.Rd ├── getP-methods.Rd ├── gf.Rd ├── gmultmix.Rd ├── goccu.Rd ├── gpcount.Rd ├── imputeMissing.Rd ├── issj.Rd ├── jay.Rd ├── lambda2psi.Rd ├── linearComb-methods.Rd ├── linetran.Rd ├── makePiFuns.Rd ├── mallard.Rd ├── masspcru.Rd ├── modSel.Rd ├── multinomPois.Rd ├── multmixOpen.Rd ├── nmixTTD.Rd ├── nonparboot-methods.Rd ├── occu.Rd ├── occuCOP.Rd ├── occuFP.Rd ├── occuMS.Rd ├── occuMulti.Rd ├── occuPEN.Rd ├── occuPEN_CV.Rd ├── occuRN.Rd ├── occuTTD.Rd ├── optimizePenalty-methods.Rd ├── ovendata.Rd ├── parboot.Rd ├── pcount.Rd ├── pcount.spHDS.Rd ├── pcountOpen.Rd ├── piFuns.Rd ├── plotEffects.Rd ├── pointtran.Rd ├── posteriorSamples.Rd ├── powerAnalysis.Rd ├── predict-methods.Rd ├── randomTerms.Rd ├── ranef-methods.Rd ├── shinyPower.Rd ├── sight2perpdist.Rd ├── sigma.Rd ├── simulate-methods.Rd ├── unmarked-package.Rd ├── unmarkedEstimate-class.Rd ├── unmarkedEstimateList-class.Rd ├── unmarkedFit-class.Rd ├── unmarkedFitList-class.rd ├── unmarkedFrame-class.Rd ├── unmarkedFrame.Rd ├── unmarkedFrameDS.Rd ├── unmarkedFrameDSO.Rd ├── unmarkedFrameGDR.Rd ├── unmarkedFrameMMO.Rd ├── unmarkedFrameMPois.Rd ├── unmarkedFrameOccu.Rd ├── unmarkedFrameOccuCOP.Rd ├── unmarkedFrameOccuFP.Rd ├── unmarkedFrameOccuMS.Rd ├── unmarkedFrameOccuMulti.Rd ├── unmarkedFrameOccuTTD.Rd ├── unmarkedFramePCO.Rd ├── unmarkedFramePCount.Rd ├── unmarkedMultFrame.Rd ├── unmarkedPower-class.Rd ├── unmarkedPowerList.Rd ├── unmarkedRanef-class.Rd ├── vcov-methods.Rd └── vif.Rd ├── src ├── Makevars ├── Makevars.win ├── RcppExports.cpp ├── TMB │ ├── compile.R │ ├── tmb_IDS.hpp │ ├── tmb_distsamp.hpp │ ├── tmb_gdistremoval.hpp │ ├── tmb_goccu.hpp │ ├── tmb_keyfun.hpp │ ├── tmb_multinomPois.hpp │ ├── tmb_occu.hpp │ ├── tmb_pcount.hpp │ ├── tmb_pifun.hpp │ ├── tmb_utils.hpp │ └── unmarked_TMBExports.cpp ├── detfuns.cpp ├── detfuns.h ├── distprob.cpp ├── distprob.h ├── distr.cpp ├── distr.h ├── get_lik_trans.cpp ├── get_mlogit.cpp ├── hmm.c ├── nll_distsamp.cpp ├── nll_distsampOpen.cpp ├── nll_gdistremoval.cpp ├── nll_gdistsamp.cpp ├── nll_gmultmix.cpp ├── nll_gpcount.cpp ├── nll_multinomPois.cpp ├── nll_multmixOpen.cpp ├── nll_nmixTTD.cpp ├── nll_occu.cpp ├── nll_occuCOP.cpp ├── nll_occuMS.cpp ├── nll_occuMulti.cpp ├── nll_occuPEN.cpp ├── nll_occuRN.cpp ├── nll_occuTTD.cpp ├── nll_pcount.cpp ├── nll_pcountOpen.cpp ├── pifun.cpp ├── pifun.h ├── tranprobs.cpp ├── tranprobs.h ├── utils.cpp └── utils.h ├── tests ├── testthat.R └── testthat │ ├── test_IDS.R │ ├── test_colext.R │ ├── test_crossVal.R │ ├── test_distsamp.R │ ├── test_distsampOpen.R │ ├── test_fitList.R │ ├── test_formatInputs.R │ ├── test_gdistremoval.R │ ├── test_gdistsamp.R │ ├── test_gmultmix.R │ ├── test_goccu.R │ ├── test_gpcount.R │ ├── test_linearComb.R │ ├── test_makePiFun.R │ ├── test_modSel.R │ ├── test_multinomPois.R │ ├── test_multmixOpen.R │ ├── test_nmixTTD.R │ ├── test_nonparboot.R │ ├── test_occu.R │ ├── test_occuCOP.R │ ├── test_occuFP.R │ ├── test_occuMS.R │ ├── test_occuMulti.R │ ├── test_occuPEN.R │ ├── test_occuRN.R │ ├── test_occuTTD.R │ ├── test_parboot.R │ ├── test_pcount.R │ ├── test_pcount.spHDS.R │ ├── test_pcountOpen.R │ ├── test_plotEffects.R │ ├── test_powerAnalysis.R │ ├── test_powerAnalysis_deprecated.R │ ├── test_predict.R │ ├── test_ranef_predict.R │ ├── test_simulate.R │ ├── test_simulate_deprecated.R │ ├── test_unmarkedFrame.R │ ├── test_utils.R │ └── test_vif.R └── vignettes ├── README.txt ├── cap-recap.Rmd ├── colext-data-1.png ├── colext-est-1.png ├── colext-gof-1.png ├── colext-pred-1.png ├── colext.Rmd ├── colext.Rmd.orig ├── contributing_to_unmarked.Rmd ├── distsamp.Rmd ├── ecology.csl ├── occuMulti.Rmd ├── powerAnalysis-figures ├── pa50-1.png ├── pl-1.png └── pl2-1.png ├── powerAnalysis.Rmd ├── powerAnalysis.Rmd.orig ├── simulate.Rmd ├── spp-dist.Rmd ├── unmarked.Rmd └── unmarked.bib /.Rbuildignore: 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