├── README.md └── RMark ├── DESCRIPTION ├── NAMESPACE ├── NEWS ├── R ├── PIMS.R ├── RMark-package.R ├── TransitionMatrix.R ├── add.design.data.R ├── adjust.chat.R ├── adjust.parameter.count.R ├── cleanup.R ├── collect.model.names.R ├── collect.models.R ├── compute.design.data.R ├── compute.link.R ├── compute.links.from.reals.R ├── compute.real.R ├── convert.inp.r ├── convert.link.to.real.r ├── covariate.predictions.r ├── create.mark.mcmc.R ├── create.model.list.R ├── deltamethod.r ├── deriv.inverse.link.R ├── export.MARK.r ├── export.chdata.R ├── export.model.r ├── extract.mark.output.R ├── fill.covariates.R ├── find.covariates.R ├── get.link.R ├── get.real.R ├── import.chdata.R ├── inverse.link.R ├── make.design.data.R ├── make.mark.model.R ├── make.time.factor.r ├── mark.R ├── mark.wrapper.R ├── mark.wrapper.parallel.r ├── mata.wald.r ├── merge.design.covariates.r ├── merge.mark.r ├── model.average.R ├── model.average.default.r ├── model.average.list.r ├── model.average.marklist.R ├── model.table.R ├── popan.r ├── predict_real.R ├── print.mark.R ├── print.summary.mark.R ├── process.ch.R ├── process.data.R ├── read.mark.binary.R ├── release.gof.R ├── remove.mark.r ├── rerun.mark.R ├── run.mark.model.R ├── run.models.R ├── setup.model.R ├── setup.parameters.R ├── splitCH.r ├── store.r ├── summary.ch.r ├── summary.mark.R ├── utility.r ├── valid.parameters.R ├── var.components.R ├── var.components.reml.r └── zzz.R ├── data ├── Blackduck.rda ├── Density.r ├── Density.txt ├── Donovan.7.rda ├── Donovan.8.rda ├── IELogitNormalMR.rda ├── LASP.rda ├── LogitNormalMR.rda ├── NSpeciesOcc.rda ├── NicholsMSOccupancy.rda ├── Paradise_shelduck.rda ├── PoissonMR.rda ├── Poisson_twoMR.rda ├── RDOccupancy.rda ├── RDSalamander.rda ├── brownie.rda ├── crdms.rda ├── deer.rda ├── dipper.rda ├── edwards.eberhardt.rda ├── example.data.rda ├── killdeer.rda ├── mallard.rda ├── mstrata.rda ├── robust.rda ├── salamander.rda ├── weta.rda ├── wwdo.09.rda └── wwdo.10.rda ├── inst ├── CITATION ├── DerivedPar.txt ├── MarkModels.pdf ├── README.txt ├── extdata │ ├── MSJS.inp │ ├── MSJS3state.inp │ ├── RDMultScalOcc.sampledata.csv │ ├── aa.inp │ ├── adult.inp │ ├── age-transients-full.inp │ ├── age.inp │ ├── age_ya.inp │ ├── blackduck.txt │ ├── blckduck.inp │ ├── brownadt.inp │ ├── brownie.inp │ ├── capsid.inp │ ├── chase.inp │ ├── cjs3grp.inp │ ├── clogit_demo.inp │ ├── deer.inp │ ├── dipper.inp │ ├── dipper.txt │ ├── donovan.7.inp │ ├── donovan.8.inp │ ├── ed.inp │ ├── ed_males.inp │ ├── edwardsandeberhardt.inp │ ├── edwardsandeberhardt.txt │ ├── effect_size.inp │ ├── effect_size3.inp │ ├── example.data.txt │ ├── f_age.inp │ ├── huggins.inp │ ├── indcov1.inp │ ├── indcov2.inp │ ├── interval.inp │ ├── island.inp │ ├── killdeer.inp │ ├── killdeer.txt │ ├── ld1.inp │ ├── linear.inp │ ├── m_age.inp │ ├── mallard.txt │ ├── mallardnestexample.inp │ ├── mixed_closed1.inp │ ├── ms_cjs.inp │ ├── ms_directional.inp │ ├── ms_gof.inp │ ├── ms_rdsimple1.inp │ ├── mssurv.inp │ ├── mstrata.txt │ ├── multi_group.inp │ ├── nicholsmsoccupancy.inp │ ├── pass3mstrata5.inp │ ├── plover_mark.inp │ ├── rd_complex1.inp │ ├── rd_simple1.inp │ ├── rdsalamander.inp │ ├── recruit-ms.inp │ ├── robust.inp │ ├── robust.txt │ ├── salamander.inp │ ├── simple_closed1.inp │ ├── skagit.txt │ ├── staggered.inp │ ├── transient.inp │ ├── weta.txt │ ├── yngadt.inp │ └── young.inp ├── models.txt └── parameters.txt └── man ├── ABeginnersGuide.Rd ├── Blackduck.Rd ├── Burnham.Rd ├── Density.Rd ├── Donovan.7.Rd ├── Donovan.8.Rd ├── HidMarkov.Rd ├── IELogitNormalMR.Rd ├── LogitNormalMR.Rd ├── MSJollySeber.Rd ├── MS_popan.Rd ├── MStruncate.Rd ├── NSpeciesOcc.Rd ├── NicholsMSOccupancy.Rd ├── PIMS.Rd ├── Paradise_shelduck.Rd ├── PoissonMR.Rd ├── Poisson_twoMR.Rd ├── RDMultScalOcc.Rd ├── RDOccupancy.Rd ├── RDSalamander.Rd ├── TransitionMatrix.Rd ├── Whatsnew.Rd ├── add.design.data.Rd ├── adjust.parameter.count.Rd ├── adjust.value.Rd ├── brownie.Rd ├── cleanup.Rd ├── coef.mark.Rd ├── collect.model.names.Rd ├── collect.models.Rd ├── compute.design.data.Rd ├── compute.link.Rd ├── compute.links.from.reals.Rd ├── compute.real.Rd ├── convert.inp.Rd ├── convert.link.to.real.Rd ├── covariate.predictions.Rd ├── crdms.Rd ├── create.mark.mcmc.Rd ├── create.model.list.Rd ├── deer.Rd ├── deltamethod.special.Rd ├── deriv_inverse.link.Rd ├── dipper.Rd ├── edwards.eberhardt.Rd ├── example.data.Rd ├── export.MARK.Rd ├── export.chdata.Rd ├── export.model.Rd ├── extract.indices.Rd ├── extract.mark.output.Rd ├── fill.covariates.Rd ├── find.covariates.Rd ├── get.link.Rd ├── get.real.Rd ├── import.chdata.Rd ├── inverse.link.Rd ├── killdeer.Rd ├── larksparrow.Rd ├── load.model.Rd ├── make.design.data.Rd ├── make.mark.model.Rd ├── make.time.factor.Rd ├── mallard.Rd ├── mark.Rd ├── mark.wrapper.Rd ├── mark.wrapper.parallel.Rd ├── mata.wald.Rd ├── merge.mark.Rd ├── merge_design.covariates.Rd ├── model.average.Rd ├── model.average.list.Rd ├── model.average.marklist.Rd ├── model.table.Rd ├── 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