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.

Author | Ian Fiske, Richard Chandler, David Miller, Andy Royle, Marc Kery, Jeff Hostetler, Rebecca Hutchinson |

Date of publication | 2015-09-03 10:19:18 |

Maintainer | Andy Royle <aroyle@usgs.gov> |

License | GPL (>= 3) |

Version | 0.11-0 |

http://groups.google.com/group/unmarked, https://sites.google.com/site/unmarkedinfo/home, http://github.com/ianfiske/unmarked, http://github.com/rbchan/unmarked |

**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'

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? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.