unmarked: Models for Data from Unmarked Animals

Fits hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling. Parameters governing the state and observation processes can be modeled as functions of covariates.

AuthorIan Fiske, Richard Chandler, David Miller, Andy Royle, Marc Kery, Jeff Hostetler, Rebecca Hutchinson
Date of publication2015-09-03 10:19:18
MaintainerAndy Royle <aroyle@usgs.gov>
LicenseGPL (>= 3)
Version0.11-0
http://groups.google.com/group/unmarked, https://sites.google.com/site/unmarkedinfo/home, http://github.com/ianfiske/unmarked, http://github.com/rbchan/unmarked

View on CRAN

Man pages

birds: BBS Point Count and Occurrence Data from 2 Bird Species

coef-methods: Methods for Function coef in Package 'unmarked'

colext: Fit the dynamic occupancy model of MacKenzie et. al (2003)

computeMPLElambdas: Compute the penalty weight for the MPLE penalized likelihood...

confint-methods: Methods for Function confint in Package 'unmarked'

crossbill: Detection/non-detection data on the European crossbill...

cruz: Landscape data for Santa Cruz Island

csvToUMF: Convert .CSV File to an unmarkedFrame

detFuns: Distance-sampling detection functions and associated density...

distsamp: Fit the hierarchical distance sampling model of Royle et al....

extract-methods: Methods for bracket extraction [ in Package 'unmarked'

fitList: constructor of unmarkedFitList objects

fitted-methods: Methods for Function fitted in Package 'unmarked'

formatDistData: Bin distance data

formatMult: Create unmarkedMultFrame from Long Format Data Frame

formatWideLong: Convert between wide and long data formats.

frogs: 2001 Delaware North American Amphibian Monitoring Program...

gdistsamp: Fit the generalized distance sampling model of Chandler et...

getB-methods: Methods for Function getB in Package 'unmarked'

getFP-methods: Methods for Function getFP in Package 'unmarked'

getP-methods: Methods for Function getP in Package 'unmarked'

gf: Green frog count index data

gmultmix: Generalized multinomial N-mixture model

gpcount: Generalized binomial N-mixture model for repeated count data

imputeMissing: A function to impute missing entries in continuous obsCovs

issj: Distance-sampling data for the Island Scrub Jay (_Aphelocoma...

jay: MHB European Jay data set

lambda2psi: Convert Poisson mean (lambda) to probability of occurrence...

linearComb-methods: Methods for Function linearComb in Package 'unmarked'

linetran: Simulated line transect data

mallard: Mallard count data

masspcru: Massachusetts North American Amphibian Monitoring Program...

modSel: Model selection results from an unmarkedFitList

multinomPois: Multinomial-Poisson Mixtures Model

nonparboot-methods: Nonparametric bootstrapping in unmarked

occu: Fit the MacKenzie et al. (2002) Occupancy Model

occuFP: Fit occupancy models when false positive detections occur...

occuPEN: Fit the MacKenzie et al. (2002) Occupancy Model with the...

occuPEN_CV: Fit the MacKenzie et al. (2002) Occupancy Model with the...

occuRN: Fit the occupancy model of Royle and Nichols (2003)

ovendata: Removal data for the Ovenbird

parboot: Parametric bootstrap method for fitted models inheriting...

pcount: Fit the N-mixture model of Royle (2004)

pcountOpen: Fit the open N-mixture models of Dail and Madsen and...

piFuns: Compute multinomial cell probabilities

pointtran: Simulated point-transect data

predict-methods: Methods for Function predict in Package 'unmarked'

ranef-methods: Methods for Function 'ranef' in Package 'unmarked'

SE-methods: Methods for Function SE in Package 'unmarked'

sight2perpdist: Convert sight distance and sight angle to perpendicular...

simulate-methods: Methods for Function simulate in Package 'unmarked'

SSE: Compute Sum of Squared Residuals for a Model Fit.

Switzerland: Swiss landscape data

unmarkedEstimate-class: Class "unmarkedEstimate"

unmarkedEstimateList-class: Class "unmarkedEstimateList"

unmarkedFit-class: Class "unmarkedFit"

unmarkedFrame: Create an unmarkedFrame, or one of its child classes.

unmarkedFrame-class: Class "unmarkedFrame"

unmarkedFrameDS: Organize data for the distance sampling model of Royle et al....

unmarkedFrameMPois: Organize data for the multinomial-Poisson mixture model of...

unmarkedFrameOccu: Organize data for the single season occupancy models fit by...

unmarkedFrameOccuFP: Organize data for the single season occupancy models fit by...

unmarkedFramePCO: Create an object of class unmarkedFramePCO that contains data...

unmarkedFramePCount: Organize data for the N-mixture model fit by pcount

unmarkedMultFrame: Create an unmarkedMultFrame, unmarkedFrameGMM,...

unmarked-package: Models for Data from Unmarked Animals

unmarkedRanef-class: Class '"unmarkedRanef"'

vcov-methods: Methods for Function vcov in Package 'unmarked'

Files in this package

unmarked
unmarked/inst
unmarked/inst/CITATION
unmarked/inst/csv
unmarked/inst/csv/distdata.csv
unmarked/inst/csv/frog2001pfer.csv
unmarked/inst/csv/frog2001pcru.csv
unmarked/inst/csv/alflCovs.csv
unmarked/inst/csv/widewt.csv
unmarked/inst/csv/alfl.csv
unmarked/inst/csv/alfl.capRecap.csv
unmarked/inst/bench
unmarked/inst/bench/bench.pcountOpen.R
unmarked/inst/bench/bench.occu.R
unmarked/inst/bench/bench.pcount.R
unmarked/inst/doc
unmarked/inst/doc/unmarked.R
unmarked/inst/doc/colext.R
unmarked/inst/doc/spp-dist.R
unmarked/inst/doc/cap-recap.Rnw
unmarked/inst/doc/unmarked.pdf
unmarked/inst/doc/cap-recap.R
unmarked/inst/doc/colext.pdf
unmarked/inst/doc/cap-recap.pdf
unmarked/inst/doc/distsamp.R
unmarked/inst/doc/spp-dist.Rnw
unmarked/inst/doc/colext.Rnw
unmarked/inst/doc/distsamp.pdf
unmarked/inst/doc/spp-dist.pdf
unmarked/inst/doc/unmarked.Rnw
unmarked/inst/doc/distsamp.Rnw
unmarked/inst/unitTests
unmarked/inst/unitTests/sim.distsamp.R
unmarked/inst/unitTests/runit.gpcount.R
unmarked/inst/unitTests/runit.unmarkedMultFrame.R
unmarked/inst/unitTests/runit.format.R
unmarked/inst/unitTests/sim.pcount.R
unmarked/inst/unitTests/runit.unmarkedFrame.R
unmarked/inst/unitTests/runit.occu.R
unmarked/inst/unitTests/runit.gmultmix.R
unmarked/inst/unitTests/sim.pcountOpen.r
unmarked/inst/unitTests/runit.ranef.R
unmarked/inst/unitTests/sim.colext.R
unmarked/inst/unitTests/runit.gdistsamp.R
unmarked/inst/unitTests/runit.utils.R
unmarked/inst/unitTests/sim.gdistsamp.R
unmarked/inst/unitTests/sim.gmultmix.R
unmarked/inst/unitTests/sim.gpcount.R
unmarked/inst/unitTests/runit.pcountOpen.R
unmarked/inst/unitTests/runit.colext.R
unmarked/inst/unitTests/sim.ranef.R
unmarked/inst/unitTests/runit.pcount.R
unmarked/inst/unitTests/runit.modSel.R
unmarked/inst/unitTests/runit.multinomPois.R
unmarked/inst/unitTests/runit.distsamp.r
unmarked/inst/unitTests/runTests.R
unmarked/inst/unitTests/runit.occuPEN.R
unmarked/inst/unitTests/runit.predict.R
unmarked/inst/unitTests/runit.nonparboot.R
unmarked/src
unmarked/src/hmm.c
unmarked/src/nll_pcount.h
unmarked/src/Makevars
unmarked/src/distr.cpp
unmarked/src/nll_pcountOpen.cpp
unmarked/src/nll_gpcount.h
unmarked/src/nll_occu.cpp
unmarked/src/nll_gpcount.cpp
unmarked/src/nll_occu.h
unmarked/src/detfuns.h
unmarked/src/nll_pcount.cpp
unmarked/src/nll_pcountOpen.h
unmarked/src/detfuns.cpp
unmarked/src/distr.h
unmarked/src/nll_occuPEN.cpp
unmarked/src/nll_distsamp.cpp
unmarked/src/Makevars.win
unmarked/src/nll_distsamp.h
unmarked/src/nll_occuPEN.h
unmarked/NAMESPACE
unmarked/NEWS
unmarked/data
unmarked/data/masspcru.RData
unmarked/data/Switzerland.RData
unmarked/data/gf.RData
unmarked/data/crossbill.rda
unmarked/data/cruz.rda
unmarked/data/ovendata.RData
unmarked/data/pointtran.RData
unmarked/data/linetran.RData
unmarked/data/frogs.RData
unmarked/data/issj.rda
unmarked/data/mallard.RData
unmarked/data/jay.rda
unmarked/data/birds.RData
unmarked/R
unmarked/R/gmultmix.R unmarked/R/classes.R unmarked/R/multinomPois.R unmarked/R/utils.R unmarked/R/pcount.R unmarked/R/unmarkedLinComb.R unmarked/R/unmarkedFit.R unmarked/R/mapInfo.R unmarked/R/occuRN.R unmarked/R/boot.R unmarked/R/colext.R unmarked/R/gpcount.R unmarked/R/pcountOpen.R unmarked/R/ranef.R unmarked/R/distsamp.R unmarked/R/unmarkedFitList.R unmarked/R/unmarkedEstimate.R unmarked/R/unmarkedFrame.R unmarked/R/getDesign.R unmarked/R/occuPEN.R unmarked/R/occu.R unmarked/R/occuFP.R unmarked/R/gdistsamp.R
unmarked/vignettes
unmarked/vignettes/colext-yearlysim.pdf
unmarked/vignettes/spp-dist-psi2.pdf
unmarked/vignettes/colext-gof.pdf
unmarked/vignettes/cap-recap.Rnw
unmarked/vignettes/ecology.bst
unmarked/vignettes/colext-cov.pdf
unmarked/vignettes/unmarked.bib
unmarked/vignettes/spp-dist.Rnw
unmarked/vignettes/colext.Rnw
unmarked/vignettes/unmarked.Rnw
unmarked/vignettes/distsamp.Rnw
unmarked/MD5
unmarked/README
unmarked/build
unmarked/build/vignette.rds
unmarked/DESCRIPTION
unmarked/man
unmarked/man/getB-methods.Rd unmarked/man/piFuns.Rd unmarked/man/gf.Rd
unmarked/man/backTransform-methods.rd
unmarked/man/unmarkedMultFrame.Rd unmarked/man/distsamp.Rd unmarked/man/SSE.Rd unmarked/man/occuPEN.Rd unmarked/man/simulate-methods.Rd
unmarked/man/unmarkedFitList-class.rd
unmarked/man/vcov-methods.Rd unmarked/man/unmarked-package.Rd unmarked/man/modSel.Rd unmarked/man/occuPEN_CV.Rd unmarked/man/unmarkedFrameMPois.Rd unmarked/man/SE-methods.Rd unmarked/man/gpcount.Rd unmarked/man/detFuns.Rd unmarked/man/lambda2psi.Rd unmarked/man/linearComb-methods.Rd unmarked/man/Switzerland.Rd unmarked/man/ranef-methods.Rd unmarked/man/frogs.Rd unmarked/man/mallard.Rd unmarked/man/fitted-methods.Rd unmarked/man/unmarkedRanef-class.Rd unmarked/man/pointtran.Rd unmarked/man/unmarkedFramePCO.Rd unmarked/man/multinomPois.Rd unmarked/man/imputeMissing.Rd unmarked/man/unmarkedFrameOccu.Rd unmarked/man/computeMPLElambdas.Rd unmarked/man/coef-methods.Rd unmarked/man/extract-methods.Rd unmarked/man/formatDistData.Rd unmarked/man/unmarkedFrame-class.Rd unmarked/man/gmultmix.Rd unmarked/man/formatWideLong.Rd unmarked/man/pcount.Rd unmarked/man/birds.Rd unmarked/man/unmarkedEstimate-class.Rd unmarked/man/confint-methods.Rd unmarked/man/linetran.Rd unmarked/man/crossbill.Rd unmarked/man/formatMult.Rd unmarked/man/unmarkedFramePCount.Rd unmarked/man/ovendata.Rd unmarked/man/unmarkedFit-class.Rd unmarked/man/csvToUMF.Rd unmarked/man/sight2perpdist.Rd unmarked/man/jay.Rd unmarked/man/colext.Rd unmarked/man/getP-methods.Rd unmarked/man/nonparboot-methods.Rd unmarked/man/unmarkedFrameDS.Rd unmarked/man/issj.Rd unmarked/man/pcountOpen.Rd unmarked/man/occu.Rd unmarked/man/occuFP.Rd unmarked/man/predict-methods.Rd unmarked/man/unmarkedFrame.Rd unmarked/man/cruz.Rd unmarked/man/unmarkedEstimateList-class.Rd unmarked/man/fitList.Rd unmarked/man/getFP-methods.Rd unmarked/man/masspcru.Rd unmarked/man/occuRN.Rd unmarked/man/gdistsamp.Rd unmarked/man/parboot.Rd unmarked/man/unmarkedFrameOccuFP.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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