# Models for Data from Unmarked Animals

## Documentation for package ‘unmarked’ version 0.9-3

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## Help Pages

B C D F G H I L M N O P R S U V W Y misc

unmarked-package | Models for Data from Unmarked Animals

## -- B --

backTransform | Methods for Function backTransform in Package 'unmarked'
backTransform-method | Methods for Function backTransform in Package 'unmarked'
backTransform-methods | Methods for Function backTransform in Package 'unmarked'
birds | BBS Point Count and Occurrence Data from 2 Bird Species

## -- C --

catbird | BBS Point Count and Occurrence Data from 2 Bird Species
catbird.bin | BBS Point Count and Occurrence Data from 2 Bird Species
coef-method | Methods for Function coef in Package 'unmarked'
coef-method | Model selection results from an unmarkedFitList
coef-method | Class "unmarkedFitList"
coef-methods | Methods for Function coef in Package 'unmarked'
colext | Fit the colonization-extinction model.
confint-method | Methods for Function confint in Package 'unmarked'
confint-methods | Methods for Function confint in Package 'unmarked'
coordinates | Class "unmarkedFrame"
coordinates-method | Class "unmarkedFrame"
coords | Class "unmarkedFrame"
csvToUMF | Convert .CSV File to an unmarkedFrame

## -- D --

detFuns | Distance-sampling detection functions and associated density functions
distsamp | Fit the hierarchical distance sampling model of Royle et al. (2004)
doublePiFun | Compute multinomial cell probabilities
drexp | Distance-sampling detection functions and associated density functions
drhaz | Distance-sampling detection functions and associated density functions
drhn | Distance-sampling detection functions and associated density functions
dxexp | Distance-sampling detection functions and associated density functions
dxhaz | Distance-sampling detection functions and associated density functions
dxhn | Distance-sampling detection functions and associated density functions

## -- F --

fitList | constructor of unmarkedFitList objects
fitted-method | Methods for Function fitted in Package 'unmarked'
fitted-methods | Methods for Function fitted in Package 'unmarked'
formatDistData | Convert individual-level distance data to the transect-level format required by distsamp
formatLong | Convert between wide and long data formats.
formatMult | Create unmarkedMultFrame from Long Format Data Frame
formatWide | Convert between wide and long data formats.
frog2001pcru | 2001 Delaware North American Amphibian Monitoring Program Data
frog2001pfer | 2001 Delaware North American Amphibian Monitoring Program Data
frogs | 2001 Delaware North American Amphibian Monitoring Program Data

## -- G --

gdistsamp | Fit the generalized distance sampling model of Chandler et al. (2011).
getData | Class "unmarkedFit"
getData-method | Class "unmarkedFit"
getP | Methods for Function getP in Package 'unmarked'
getP-method | Methods for Function getP in Package 'unmarked'
getP-methods | Methods for Function getP in Package 'unmarked'
getY | Class "unmarkedFrame"
getY-method | Class "unmarkedFrame"
gf | Green frog count index data
gf.data | Green frog count index data
gf.obs | Green frog count index data
gmultmix | Generalized multinomial-mixture model
grexp | Distance-sampling detection functions and associated density functions
grhaz | Distance-sampling detection functions and associated density functions
grhn | Distance-sampling detection functions and associated density functions
gxexp | Distance-sampling detection functions and associated density functions
gxhaz | Distance-sampling detection functions and associated density functions
gxhn | Distance-sampling detection functions and associated density functions

## -- H --

head-method | Class "unmarkedFrame"
hessian | Class "unmarkedFit"
hessian-method | Class "unmarkedFit"
hist-method | Class "unmarkedFit"
hist-method | Class "unmarkedFrame"

## -- I --

imputeMissing | A function to impute missing entries in continuous obsCovs

## -- L --

lambda2psi | Convert Poisson mean (lambda) to probability of occurrence (psi).
linearComb | Methods for Function linearComb in Package 'unmarked'
linearComb-method | Methods for Function linearComb in Package 'unmarked'
linearComb-methods | Methods for Function linearComb in Package 'unmarked'
linetran | Simulated line transect data
logLik | Class "unmarkedFit"
logLik-method | Class "unmarkedFit"
LRT | Class "unmarkedFit"
LRT-method | Class "unmarkedFit"

## -- M --

mallard | Mallard count data
mallard.obs | Mallard count data
mallard.site | Mallard count data
mallard.y | Mallard count data
mapInfo | Class "unmarkedFrame"
masspcru | Massachusetts North American Amphibian Monitoring Program Data
mle | Class "unmarkedFit"
mle-method | Class "unmarkedFit"
modSel | Model selection results from an unmarkedFitList
modSel-method | Class "unmarkedFitList"
modSel-methods | Model selection results from an unmarkedFitList
multinomPois | Multinomial-Poisson Mixtures Model

## -- N --

names-method | Class "unmarkedEstimateList"
names-method | Class "unmarkedFit"
nllFun | Class "unmarkedFit"
nllFun-method | Class "unmarkedFit"
nonparboot | Nonparametric bootstrapping in unmarked
nonparboot-method | Nonparametric bootstrapping in unmarked
nonparboot-methods | Nonparametric bootstrapping in unmarked
numSites | Class "unmarkedFrame"
numSites-method | Class "unmarkedFrame"
numY | Class "unmarkedFrame"
numY-method | Class "unmarkedFrame"

## -- O --

obsCovs | Class "unmarkedFrame"
obsCovs-method | Class "unmarkedFrame"
obsCovs<- | Class "unmarkedFrame"
obsCovs<--method | Class "unmarkedFrame"
obsNum | Class "unmarkedFrame"
obsNum-method | Class "unmarkedFrame"
obsToY | Class "unmarkedFrame"
obsToY-method | Class "unmarkedFrame"
obsToY<- | Class "unmarkedFrame"
obsToY<--method | Class "unmarkedFrame"
occu | Fit the MacKenzie et al. (2002) Occupancy Model
occuRN | Fit the occupancy model of Royle and Nichols (2003)
ovendata | Removal data for the Ovenbird
ovendata.list | Removal data for the Ovenbird

## -- P --

parboot | Parametric bootstrap method for fitted models inheriting class.
parboot-method | Class "unmarkedFit"
pcount | Fit the N-mixture model of Royle (2004)
pcountOpen | Fit the open N-mixture model of Dail and Madsen
pcru.bin | 2001 Delaware North American Amphibian Monitoring Program Data
pcru.data | 2001 Delaware North American Amphibian Monitoring Program Data
pcru.y | 2001 Delaware North American Amphibian Monitoring Program Data
pfer.bin | 2001 Delaware North American Amphibian Monitoring Program Data
pfer.data | 2001 Delaware North American Amphibian Monitoring Program Data
pfer.y | 2001 Delaware North American Amphibian Monitoring Program Data
piFuns | Compute multinomial cell probabilities
plot-method | Parametric bootstrap method for fitted models inheriting class.
plot-method | Class "unmarkedFit"
plot-method | Class "unmarkedFrame"
pointtran | Simulated point-transect data
powerAnalysis | Class "unmarkedFrame"
powerAnalysis-method | Class "unmarkedFrame"
predict-method | Methods for Function predict in Package 'unmarked'
predict-methods | Methods for Function predict in Package 'unmarked'
profile-method | Class "unmarkedFit"
projected | Class "unmarkedFit"
projected-method | Class "unmarkedFit"
projection | Class "unmarkedFrame"
projection-method | Class "unmarkedFrame"

## -- R --

removalPiFun | Compute multinomial cell probabilities
residuals-method | Class "unmarkedFit"

## -- S --

sampleSize | Class "unmarkedFit"
sampleSize-method | Class "unmarkedFit"
SE | Methods for Function SE in Package 'unmarked'
SE-method | Methods for Function SE in Package 'unmarked'
SE-method | Model selection results from an unmarkedFitList
SE-method | Class "unmarkedFitList"
SE-methods | Methods for Function SE in Package 'unmarked'
show-method | Methods for Function backTransform in Package 'unmarked'
show-method | Methods for Function linearComb in Package 'unmarked'
show-method | Model selection results from an unmarkedFitList
show-method | Parametric bootstrap method for fitted models inheriting class.
show-method | Class "unmarkedEstimate"
show-method | Class "unmarkedEstimateList"
show-method | Class "unmarkedFit"
show-method | Class "unmarkedFrame"
sight2perpdist | Convert sight distance and sight angle to perpendicular distance.
simulate-method | Methods for Function simulate in Package 'unmarked'
simulate-methods | Methods for Function simulate in Package 'unmarked'
siteCovs | Class "unmarkedFrame"
siteCovs-method | Class "unmarkedFrame"
siteCovs<- | Class "unmarkedFrame"
siteCovs<--method | Class "unmarkedFrame"
smoothed | Class "unmarkedFit"
smoothed-method | Class "unmarkedFit"
SSE | Compute Sum of Squared Residuals for a Model Fit.
summary-method | Model selection results from an unmarkedFitList
summary-method | Class "unmarkedEstimate"
summary-method | Class "unmarkedEstimateList"
summary-method | Class "unmarkedFit"
summary-method | Class "unmarkedFitList"
summary-method | Class "unmarkedFrame"

## -- U --

unmarked | Models for Data from Unmarked Animals
unmarkedEstimate | Class "unmarkedEstimate"
unmarkedEstimate-class | Class "unmarkedEstimate"
unmarkedEstimateList-class | Class "unmarkedEstimateList"
unmarkedFit | Class "unmarkedFit"
unmarkedFit-class | Class "unmarkedFit"
unmarkedFitDS-class | Class "unmarkedFit"
unmarkedFitGMM-class | Class "unmarkedFit"
unmarkedFitList-class | Class "unmarkedFitList"
unmarkedFitMPois-class | Class "unmarkedFit"
unmarkedFitOccu-class | Class "unmarkedFit"
unmarkedFitPCO-class | Class "unmarkedFit"
unmarkedFitPCount-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. (2004) fit by distsamp
unmarkedFrameDS-class | Class "unmarkedFrame"
unmarkedFrameGDS | Create an unmarkedMultFrame or an unmarkedFrameGMM.
unmarkedFrameGDS-class | Class "unmarkedFrame"
unmarkedFrameGMM | Create an unmarkedMultFrame or an unmarkedFrameGMM.
unmarkedFrameGMM-class | Class "unmarkedFrame"
unmarkedFrameMPois | Organize data for the multinomial-Poisson mixture model of Royle (2004) fit by multinomPois
unmarkedFrameMPois-class | Class "unmarkedFrame"
unmarkedFrameOccu | Organize data for the single season occupancy models fit by occu and occuRN
unmarkedFrameOccu-class | Class "unmarkedFrame"
unmarkedFramePCO | Create an object of class unmarkedFramePCO that contains data used by pcountOpen.
unmarkedFramePCO-class | Class "unmarkedFrame"
unmarkedFramePCount | Organize data for the N-mixture model fit by pcount
unmarkedFramePCount-class | Class "unmarkedFrame"
unmarkedModSel-class | Model selection results from an unmarkedFitList
unmarkedMultFrame | Create an unmarkedMultFrame or an unmarkedFrameGMM.
unmarkedMultFrame-class | Class "unmarkedFrame"
update-method | Class "unmarkedFit"

## -- V --

vcov-method | Methods for Function vcov in Package 'unmarked'
vcov-methods | Methods for Function vcov in Package 'unmarked'

## -- W --

woodthrush | BBS Point Count and Occurrence Data from 2 Bird Species
woodthrush.bin | BBS Point Count and Occurrence Data from 2 Bird Species

## -- Y --

yearlySiteCovs | Create an unmarkedMultFrame or an unmarkedFrameGMM.
yearlySiteCovs-method | Create an unmarkedMultFrame or an unmarkedFrameGMM.
yearlySiteCovs<- | Create an unmarkedMultFrame or an unmarkedFrameGMM.
yearlySiteCovs<--method | Create an unmarkedMultFrame or an unmarkedFrameGMM.

## -- misc --

[-method | Methods for bracket extraction [ in Package 'unmarked'
[-methods | Methods for bracket extraction [ in Package 'unmarked'