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.

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
URLs

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