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.

Install the latest version of this package by entering the following in R:
AuthorIan Fiske, Richard Chandler, David Miller, Andy Royle, Marc Kery, Jeff Hostetler, Rebecca Hutchinson
Date of publication2017-04-16 19:21:55 UTC
MaintainerAndy Royle <aroyle@usgs.gov>
LicenseGPL (>= 3)
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...

pcount.spHDS: Fit spatial hierarchical distance sampling model

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'


birds Man page
bup Man page
bup,unmarkedRanef-method Man page
catbird Man page
catbird.bin Man page
coef,linCombOrBackTrans-method Man page
coef-methods Man page
coef,unmarkedEstimate-method Man page
coef,unmarkedFit-method Man page
coef,unmarkedModSel-method Man page
colext Man page
computeMPLElambda Man page
confint-methods Man page
confint,unmarkedBackTrans-method Man page
confint,unmarkedEstimate-method Man page
confint,unmarkedFit-method Man page
confint,unmarkedLinComb-method Man page
confint,unmarkedRanef-method Man page
coordinates Man page
coordinates,unmarkedFrame-method Man page
coords Man page
crossbill Man page
cruz Man page
csvToUMF Man page
delaware_bfow_2001-2006 Man page
detFuns Man page
distsamp Man page
doublePiFun Man page
drexp Man page
drhaz Man page
drhn Man page
dxexp Man page
dxhaz Man page
dxhn Man page
fitList Man page
fitted-methods Man page
fitted,unmarkedFitColExt-method Man page
fitted,unmarkedFitDS-method Man page
fitted,unmarkedFitGMM-method Man page
fitted,unmarkedFit-method Man page
fitted,unmarkedFitOccuFP-method Man page
fitted,unmarkedFitOccu-method Man page
fitted,unmarkedFitOccuRN-method Man page
fitted,unmarkedFitPCO-method Man page
fitted,unmarkedFitPCount-method Man page
formatDistData Man page
formatLong Man page
formatMult Man page
formatWide Man page
frog2001pcru Man page
frog2001pfer Man page
frogs Man page
gdistsamp Man page
getB Man page
getB-methods Man page
getB,unmarkedFitOccuFP-method Man page
getData Man page
getData,unmarkedFit-method Man page
getFP Man page
getFP-methods Man page
getFP,unmarkedFitOccuFP-method Man page
getP Man page
getP-methods Man page
getP,unmarkedFitColExt-method Man page
getP,unmarkedFitDS-method Man page
getP,unmarkedFitGDS-method Man page
getP,unmarkedFitGMM-method Man page
getP,unmarkedFitGPC-method Man page
getP,unmarkedFit-method Man page
getP,unmarkedFitMPois-method Man page
getP,unmarkedFitOccuFP-method Man page
getP,unmarkedFitPCO-method Man page
getY Man page
getY,unmarkedFrame-method Man page
gf Man page
gf.data Man page
gf.obs Man page
gmultmix Man page
gpcount Man page
grexp Man page
grhaz Man page
grhn Man page
gxexp Man page
gxhaz Man page
gxhn Man page
head,unmarkedFrame-method Man page
hessian Man page
hessian,unmarkedFit-method Man page
hist,unmarkedFitDS-method Man page
hist,unmarkedFrameDS-method Man page
imputeMissing Man page
issj Man page
jay Man page
lambda2psi Man page
linearComb Man page
linearComb-methods Man page
linearComb,unmarkedEstimate,matrixOrVector-method Man page
linearComb,unmarkedFit,matrixOrVector-method Man page
linetran Man page
logLik Man page
logLik,unmarkedFit-method Man page
LRT Man page
LRT,unmarkedFit,unmarkedFit-method Man page
mallard Man page
mallard.obs Man page
mallard.site Man page
mallard.y Man page
mapInfo Man page
masspcru Man page
[-methods Man page
mle Man page
mle,unmarkedFit-method Man page
modSel Man page
modSel-methods Man page
multinomPois Man page
names,unmarkedEstimateList-method Man page
names,unmarkedFit-method Man page
nllFun Man page
nllFun,unmarkedFit-method Man page
nonparboot Man page
nonparboot-methods Man page
nonparboot,unmarkedFitColExt-method Man page
nonparboot,unmarkedFitDS-method Man page
nonparboot,unmarkedFitGDS-method Man page
nonparboot,unmarkedFitGMM-method Man page
nonparboot,unmarkedFit-method Man page
nonparboot,unmarkedFitMPois-method Man page
nonparboot,unmarkedFitOccu-method Man page
nonparboot,unmarkedFitOccuPEN_CV-method Man page
nonparboot,unmarkedFitOccuPEN-method Man page
nonparboot,unmarkedFitOccuRN-method Man page
nonparboot,unmarkedFitPCO-method Man page
nonparboot,unmarkedFitPCount-method Man page
numSites Man page
numSites,unmarkedFrame-method Man page
numY Man page
numY,unmarkedFrame-method Man page
obsCovs Man page
obsCovs<- Man page
obsCovs<-,unmarkedFrame-method Man page
obsCovs,unmarkedFrame-method Man page
obsNum Man page
obsNum,unmarkedFrame-method Man page
obsToY Man page
obsToY<- Man page
obsToY<-,unmarkedFrame-method Man page
obsToY,unmarkedFrame-method Man page
occu Man page
occuFP Man page
occuPEN Man page
occuPEN_CV Man page
occuRN Man page
ovendata Man page
ovendata.list Man page
parboot Man page
parboot,unmarkedFit-method Man page
pcount Man page
pcountOpen Man page
pcount.spHDS Man page
pcru.bin Man page
pcru.data Man page
pcru.y Man page
pfer.bin Man page
pfer.data Man page
pfer.y Man page
piFuns Man page
plot,parboot,missing-method Man page
plot,profile,missing-method Man page
plot,unmarkedFit,missing-method Man page
plot,unmarkedFrame,missing-method Man page
plot,unmarkedRanef,missing-method Man page
pointtran Man page
powerAnalysis Man page
powerAnalysis,formula,unmarkedFramePCount,numeric-method Man page
predict,ANY-method Man page
predict-methods Man page
predict,unmarkedFitColExt-method Man page
predict,unmarkedFitGDS-method Man page
predict,unmarkedFitGMM-method Man page
predict,unmarkedFitList-method Man page
predict,unmarkedFit-method Man page
predict,unmarkedFitOccuFP-method Man page
predict,unmarkedFitPCO-method Man page
predict,unmarkedFitPCount-method Man page
profile,unmarkedFit-method Man page
projected Man page
projected,unmarkedFitColExt-method Man page
projection Man page
projection,unmarkedFrame-method Man page
ranef Man page
ranef-methods Man page
ranef,unmarkedFitColExt-method Man page
ranef,unmarkedFitDS-method Man page
ranef,unmarkedFitGDS-method Man page
ranef,unmarkedFitGMM-method Man page
ranef,unmarkedFitGMMorGDS-method Man page
ranef,unmarkedFitGPC-method Man page
ranef,unmarkedFitMPois-method Man page
ranef,unmarkedFitOccuFP-method Man page
ranef,unmarkedFitOccu-method Man page
ranef,unmarkedFitOccuRN-method Man page
ranef,unmarkedFitPCO-method Man page
ranef,unmarkedFitPCount-method Man page
removalPiFun Man page
residuals,unmarkedFit-method Man page
residuals,unmarkedFitOccuFP-method Man page
residuals,unmarkedFitOccu-method Man page
residuals,unmarkedFitOccuRN-method Man page
sampleSize Man page
sampleSize,unmarkedFit-method Man page
SE Man page
SE,linCombOrBackTrans-method Man page
SE-methods Man page
SE,unmarkedEstimate-method Man page
SE,unmarkedFit-method Man page
SE,unmarkedModSel-method Man page
show,parboot-method Man page
show,unmarkedEstimateList-method Man page
show,unmarkedEstimate-method Man page
show,unmarkedFit-method Man page
show,unmarkedFrame-method Man page
show,unmarkedLinComb-method Man page
show,unmarkedModSel-method Man page
show,unmarkedMultFrame-method Man page
show,unmarkedRanef-method Man page
sight2perpdist Man page
simulate-methods Man page
simulate,unmarkedFitColExt-method Man page
simulate,unmarkedFitDS-method Man page
simulate,unmarkedFitGDS-method Man page
simulate,unmarkedFitGMM-method Man page
simulate,unmarkedFitGPC-method Man page
simulate,unmarkedFitMPois-method Man page
simulate,unmarkedFitOccuFP-method Man page
simulate,unmarkedFitOccu-method Man page
simulate,unmarkedFitOccuRN-method Man page
simulate,unmarkedFitPCO-method Man page
simulate,unmarkedFitPCount-method Man page
siteCovs Man page
siteCovs<- Man page
siteCovs<-,unmarkedFrame-method Man page
siteCovs,unmarkedFrame-method Man page
smoothed Man page
smoothed,unmarkedFitColExt-method Man page
SSE Man page
summary,unmarkedEstimateList-method Man page
summary,unmarkedEstimate-method Man page
summary,unmarkedFitDS-method Man page
summary,unmarkedFit-method Man page
summary,unmarkedFrameDS-method Man page
summary,unmarkedFrame-method Man page
summary,unmarkedModSel-method Man page
summary,unmarkedMultFrame-method Man page
Switzerland Man page
unmarked Man page
unmarkedEstimate Man page
unmarkedEstimate-class Man page
[,unmarkedEstimateList,ANY,ANY,ANY-method Man page
unmarkedEstimateList-class Man page
unmarkedFit Man page
[,unmarkedFit,ANY,ANY,ANY-method Man page
unmarkedFit-class Man page
unmarkedFitDS-class Man page
unmarkedFitGMM-class Man page
unmarkedFitMPois-class Man page
unmarkedFitOccu-class Man page
unmarkedFitOccuFP-class Man page
unmarkedFitOccuPEN-class Man page
unmarkedFitOccuPEN_CV-class Man page
unmarkedFitPCO-class Man page
unmarkedFitPCount-class Man page
unmarkedFrame Man page
unmarkedFrame-class Man page
unmarkedFrameDS Man page
unmarkedFrameDS-class Man page
unmarkedFrameGDS Man page
unmarkedFrameGDS-class Man page
[,unmarkedFrameGDS,numeric,missing,missing-method Man page
unmarkedFrameGMM Man page
unmarkedFrameGMM-class Man page
[,unmarkedFrameGMM,numeric,missing,missing-method Man page
unmarkedFrameGPC Man page
unmarkedFrameGPC-class Man page
[,unmarkedFrameGPC,missing,numeric,missing-method Man page
[,unmarkedFrameGPC,numeric,missing,missing-method Man page
[,unmarkedFrame,list,missing,missing-method Man page
[,unmarkedFrame,missing,numeric,missing-method Man page
unmarkedFrameMPois Man page
unmarkedFrameMPois-class Man page
[,unmarkedFrame,numeric,missing,missing-method Man page
[,unmarkedFrame,numeric,numeric,missing-method Man page
unmarkedFrameOccu Man page
unmarkedFrameOccu-class Man page
unmarkedFrameOccuFP Man page
unmarkedFramePCO Man page
unmarkedFramePCO-class Man page
[,unmarkedFramePCO,missing,numeric,missing-method Man page
[,unmarkedFramePCO,numeric,missing,missing-method Man page
unmarkedFramePCount Man page
unmarkedFramePCount-class Man page
unmarkedModSel-class Man page
unmarkedMultFrame Man page
unmarkedMultFrame-class Man page
[,unmarkedMultFrame,missing,numeric,missing-method Man page
[,unmarkedMultFrame,numeric,missing,missing-method Man page
unmarked-package Man page
unmarkedRanef-class Man page
update,unmarkedFitColExt-method Man page
update,unmarkedFitGMM-method Man page
update,unmarkedFit-method Man page
update,unmarkedFitPCO-method Man page
vcov,linCombOrBackTrans-method Man page
vcov-methods Man page
vcov,unmarkedEstimate-method Man page
vcov,unmarkedFit-method Man page
woodthrush Man page
woodthrush.bin Man page
yearlySiteCovs Man page
yearlySiteCovs<- Man page
yearlySiteCovs<-,unmarkedMultFrame-method Man page
yearlySiteCovs,unmarkedMultFrame-method Man page


inst/bench/bench.pcountOpen.R inst/bench/bench.occu.R inst/bench/bench.pcount.R
inst/doc/unmarked.R inst/doc/colext.R inst/doc/spp-dist.R
inst/unitTests/sim.distsamp.R inst/unitTests/runit.gpcount.R inst/unitTests/runit.unmarkedMultFrame.R inst/unitTests/runit.format.R inst/unitTests/sim.pcount.R inst/unitTests/runit.unmarkedFrame.R inst/unitTests/runit.occu.R inst/unitTests/runit.gmultmix.R inst/unitTests/sim.pcountOpen.r inst/unitTests/runit.ranef.R inst/unitTests/runit.parboot.R inst/unitTests/runit.pcount.spHDS.R inst/unitTests/sim.colext.R inst/unitTests/runit.gdistsamp.R inst/unitTests/runit.utils.R inst/unitTests/sim.gdistsamp.R inst/unitTests/sim.gmultmix.R inst/unitTests/sim.gpcount.R inst/unitTests/runit.pcountOpen.R inst/unitTests/runit.colext.R inst/unitTests/sim.ranef.R inst/unitTests/runit.pcount.R inst/unitTests/runit.modSel.R inst/unitTests/runit.multinomPois.R inst/unitTests/runit.distsamp.r inst/unitTests/runTests.R inst/unitTests/runit.occuPEN.R inst/unitTests/runit.predict.R inst/unitTests/runit.nonparboot.R
R/gmultmix.R R/classes.R R/multinomPois.R R/utils.R R/pcount.R R/unmarkedLinComb.R R/unmarkedFit.R R/mapInfo.R R/occuRN.R R/boot.R R/colext.R R/gpcount.R R/pcountOpen.R R/ranef.R R/distsamp.R R/unmarkedFitList.R R/pcount.spHDS.R R/unmarkedEstimate.R R/unmarkedFrame.R R/getDesign.R R/occuPEN.R R/occu.R R/occuFP.R R/gdistsamp.R
man/getB-methods.Rd man/piFuns.Rd man/gf.Rd
man/unmarkedMultFrame.Rd man/distsamp.Rd man/SSE.Rd man/occuPEN.Rd man/simulate-methods.Rd
man/vcov-methods.Rd man/unmarked-package.Rd man/modSel.Rd man/occuPEN_CV.Rd man/unmarkedFrameMPois.Rd man/SE-methods.Rd man/gpcount.Rd man/detFuns.Rd man/lambda2psi.Rd man/linearComb-methods.Rd man/Switzerland.Rd man/ranef-methods.Rd man/frogs.Rd man/mallard.Rd man/fitted-methods.Rd man/unmarkedRanef-class.Rd man/pointtran.Rd man/unmarkedFramePCO.Rd man/multinomPois.Rd man/imputeMissing.Rd man/unmarkedFrameOccu.Rd man/computeMPLElambdas.Rd man/coef-methods.Rd man/extract-methods.Rd man/formatDistData.Rd man/unmarkedFrame-class.Rd man/gmultmix.Rd man/formatWideLong.Rd man/pcount.Rd man/birds.Rd man/unmarkedEstimate-class.Rd man/confint-methods.Rd man/linetran.Rd man/crossbill.Rd man/formatMult.Rd man/unmarkedFramePCount.Rd man/ovendata.Rd man/unmarkedFit-class.Rd man/csvToUMF.Rd man/sight2perpdist.Rd man/jay.Rd man/colext.Rd man/getP-methods.Rd man/nonparboot-methods.Rd man/unmarkedFrameDS.Rd man/issj.Rd man/pcountOpen.Rd man/occu.Rd man/occuFP.Rd man/predict-methods.Rd man/unmarkedFrame.Rd man/cruz.Rd man/unmarkedEstimateList-class.Rd man/fitList.Rd man/getFP-methods.Rd man/masspcru.Rd man/occuRN.Rd man/gdistsamp.Rd man/parboot.Rd man/unmarkedFrameOccuFP.Rd man/pcount.spHDS.Rd

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

Please suggest features or report bugs with the GitHub issue tracker.

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