R: Models for Data from Unmarked Animals

# Models for Data from Unmarked Animals

## Documentation for package ‘unmarked’ version 1.5.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS

## Help Pages

B C D F G H I J 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
bup | Extract Best Unbiased Predictors (BUPs) of latent variables from 'ranef' output
bup-method | Extract Best Unbiased Predictors (BUPs) of latent variables from 'ranef' output

## -- 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 | Class "unmarkedFitList"
coef-method | unmarkedModSel class and methods
coef-methods | Methods for Function coef in Package 'unmarked'
colext | Fit the dynamic occupancy model of MacKenzie et. al (2003)
computeMPLElambda | Compute the penalty weight for the MPLE penalized likelihood method
confint-method | Methods for Function confint in Package 'unmarked'
confint-method | Class '"unmarkedRanef"'
confint-methods | Methods for Function confint in Package 'unmarked'
crossbill | Detection/non-detection data on the European crossbill (_Loxia curvirostra_)
crossVal | Cross-validation methods for fitted 'unmarked' models and fit lists
crossVal-method | Cross-validation methods for fitted 'unmarked' models and fit lists
crossVal-methods | Cross-validation methods for fitted 'unmarked' models and fit lists
cruz | Landscape data for Santa Cruz Island
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)
distsampOpen | Open population model for distance sampling data
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 | Create a list of fitted 'unmarked' models
fitted | Calculate fitted (expected) values from a model
fitted-method | Calculate fitted (expected) values from a model
formatDistData | Bin distance data
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 --

gdistremoval | Fit the combined distance and removal model of Amundson et al. (2014).
gdistsamp | Fit the generalized distance sampling model of Chandler et al. (2011).
getB | Methods for Function getB in Package 'unmarked'
getB-method | Methods for Function getB in Package 'unmarked'
getB-methods | Methods for Function getB in Package 'unmarked'
getData | Class "unmarkedFit"
getData-method | Class "unmarkedFit"
getFP | Methods for Function getFP in Package 'unmarked'
getFP-method | Methods for Function getFP in Package 'unmarked'
getFP-methods | Methods for Function getFP in Package 'unmarked'
getL | Organize data for the occupancy model using count data fit by 'occuCOP'
getL-method | Organize data for the occupancy model using count data fit by 'occuCOP'
getP | Get detection probability matrix from a fitted model
getP-method | Get detection probability matrix from a fitted model
getY | Class "unmarkedFrame"
getY-method | Class "unmarkedFit"
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 N-mixture model
goccu | Fit the multi-scale occupancy model of Nichols et al. (2008)
gpcount | Generalized binomial N-mixture model for repeated count data
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"
hist-method | Fit the integrated distance sampling model of Kery et al. (2022).
hist-method | Class "unmarkedFit"
hist-method | Class "unmarkedFrame"

## -- I --

IDS | Fit the integrated distance sampling model of Kery et al. (2022).
issj | Distance-sampling data for the Island Scrub Jay (_Aphelocoma insularis_)

## -- J --

jay | European Jay data from the Swiss Breeding Bird Survey 2002

## -- 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 --

makeCrPiFun | Create functions to compute multinomial cell probabilities
makeCrPiFunMb | Create functions to compute multinomial cell probabilities
makeCrPiFunMh | Create functions to compute multinomial cell probabilities
makePiFuns | Create functions to compute multinomial cell probabilities
makeRemPiFun | Create functions to compute multinomial cell probabilities
mallard | Mallard count data
mallard.obs | Mallard count data
mallard.site | Mallard count data
mallard.y | Mallard count data
masspcru | Massachusetts North American Amphibian Monitoring Program Data
MesoCarnivores | Occupancy data for coyote, red fox, and bobcat
modSel | Model selection on a list of 'unmarked' model fits
modSel-method | Class "unmarkedFitList"
multinomPois | Multinomial-Poisson Mixtures Model
multmixOpen | Open population multinomial N-mixture model

## -- N --

names-method | Fit the integrated distance sampling model of Kery et al. (2022).
names-method | Class "unmarkedEstimateList"
names-method | Class "unmarkedFit"
nmixTTD | Fit the N-mixture Time-to-detection Model of Strebel et al. (2021)
nonparboot | Get non-parametric bootstrap samples from an 'unmarked' model
nonparboot-method | Get non-parametric bootstrap samples from an 'unmarked' model
nonparboot-methods | Get non-parametric bootstrap samples from an 'unmarked' model
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
occuComm | Fit a community occupancy model with species-level random effects
occuCOP | Fit the occupancy model using count data
occuFP | Fit occupancy models when false positive detections occur (e.g., Royle and Link [2006] and Miller et al. [2011])
occuMS | Fit Multi-State Occupancy Models (Nichols et al. 2007, MacKenzie et al. 2009)
occuMulti | Fit the multi-species occupancy model of Rota et al. (2016)
occuPEN | Fit the MacKenzie et al. (2002) Occupancy Model with the penalized likelihood methods of Hutchinson et al. (2015)
occuPEN_CV | Fit the MacKenzie et al. (2002) Occupancy Model with the penalized likelihood methods of Hutchinson et al. (2015) using cross-validation
occuRN | Fit the occupancy model of Royle and Nichols (2003)
occuTTD | Fit Single-Season and Dynamic Time-to-detection Occupancy Models
optimizePenalty | Identify Optimal Penalty Parameter Value
optimizePenalty-method | Identify Optimal Penalty Parameter Value
optimizePenalty-methods | Identify Optimal Penalty Parameter Value
ovendata | Removal data for the Ovenbird
ovendata.list | Removal data for the Ovenbird

## -- P --

parboot | Parametric bootstrap for 'unmarked' models
parboot-method | Parametric bootstrap for 'unmarked' models
pcount | Fit the N-mixture model of Royle (2004)
pcount.spHDS | Fit spatial hierarchical distance sampling model.
pcountOpen | Fit the open N-mixture models of Dail and Madsen (2011) and Hostetler and Chandler (2015)
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 for 'unmarked' models
plot-method | Class "unmarkedFit"
plot-method | Class "unmarkedFrame"
plot-method | Methods for unmarkedPower objects
plot-method | Summarize a series of unmarked power analyses
plot-method | Class '"unmarkedRanef"'
plotEffects | Plot marginal effects of covariates in unmarked models
plotEffects-method | Plot marginal effects of covariates in unmarked models
plotEffects-methods | Plot marginal effects of covariates in unmarked models
plotEffectsData | Plot marginal effects of covariates in unmarked models
plotEffectsData-method | Plot marginal effects of covariates in unmarked models
plotEffectsData-methods | Plot marginal effects of covariates in unmarked models
pointtran | Simulated point-transect data
posteriorSamples | Draw samples from the posterior predictive distribution
posteriorSamples-method | Draw samples from the posterior predictive distribution
posteriorSamples-methods | Draw samples from the posterior predictive distribution
powerAnalysis | Conduct a power analysis for an 'unmarked' model
powerAnalysis-method | Conduct a power analysis for an 'unmarked' model
predict | Predict from fitted models and other unmarked objects
predict-method | Predict from fitted models and other unmarked objects
profile-method | Class "unmarkedFit"
projected | Class "unmarkedFit"
projected-method | Class "unmarkedFit"

## -- R --

randomTerms | Extract estimates of random effect terms
randomTerms-method | Extract estimates of random effect terms
randomTerms-methods | Extract estimates of random effect terms
ranef | Estimate posterior distributions of latent occupancy or abundance
ranef-method | Estimate posterior distributions of latent occupancy or abundance
removalPiFun | Compute multinomial cell probabilities
residuals | Calculate residuals from a model
residuals-method | Calculate residuals from a model
richness | Estimate posterior distributions of site richness
richness-method | Estimate posterior distributions of site richness

## -- 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 | Class "unmarkedFitList"
SE-method | unmarkedModSel class and methods
SE-methods | Methods for Function SE in Package 'unmarked'
shinyPower | Launch a Shiny app to help with power analysis
show-method | Methods for Function backTransform in Package 'unmarked'
show-method | Cross-validation methods for fitted 'unmarked' models and fit lists
show-method | Methods for Function linearComb in Package 'unmarked'
show-method | Parametric bootstrap for 'unmarked' models
show-method | Draw samples from the posterior predictive distribution
show-method | Class "unmarkedEstimate"
show-method | Class "unmarkedEstimateList"
show-method | Class "unmarkedFrame"
show-method | unmarkedModSel class and methods
show-method | Methods for unmarkedPower objects
show-method | Summarize a series of unmarked power analyses
show-method | Class '"unmarkedRanef"'
sigma | Extract estimates of random effect standard deviations
sigma-method | Extract estimates of random effect standard deviations
sigma-methods | Extract estimates of random effect standard deviations
simulate | Simulate datasets from any 'unmarked' model type
simulate-method | Simulate datasets from any 'unmarked' model type
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.
SSE-method | Compute Sum of Squared Residuals for a Model Fit.
SSE-methods | Compute Sum of Squared Residuals for a Model Fit.
summary-method | Class "unmarkedEstimate"
summary-method | Class "unmarkedEstimateList"
summary-method | Class "unmarkedFit"
summary-method | Class "unmarkedFitList"
summary-method | Class "unmarkedFrame"
summary-method | Methods for unmarkedPower objects
summary-method | Summarize a series of unmarked power analyses
Switzerland | Swiss landscape data

## -- U --

unmarked | Models for Data from Unmarked Animals
unmarkedCrossVal-class | Cross-validation methods for fitted 'unmarked' models and fit lists
unmarkedCrossValList-class | Cross-validation methods for fitted 'unmarked' models and fit lists
unmarkedEstimate | Class "unmarkedEstimate"
unmarkedEstimate-class | Class "unmarkedEstimate"
unmarkedEstimateList-class | Class "unmarkedEstimateList"
unmarkedFit | Class "unmarkedFit"
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. (2004) fit by distsamp
unmarkedFrameDSO | Create an object of class unmarkedFrameDSO that contains data used by distsampOpen.
unmarkedFrameGDR | Organize data for the combined distance and removal point-count model of Amundson et al. (2014) fit by 'gdistremoval'
unmarkedFrameGDR-class | Organize data for the combined distance and removal point-count model of Amundson et al. (2014) fit by 'gdistremoval'
unmarkedFrameGDS | Create an unmarkedMultFrame, unmarkedFrameGMM, unmarkedFrameGDS, or unmarkedFrameGPC object
unmarkedFrameGMM | Create an unmarkedMultFrame, unmarkedFrameGMM, unmarkedFrameGDS, or unmarkedFrameGPC object
unmarkedFrameGOccu | Create an unmarkedMultFrame, unmarkedFrameGMM, unmarkedFrameGDS, or unmarkedFrameGPC object
unmarkedFrameGPC | Create an unmarkedMultFrame, unmarkedFrameGMM, unmarkedFrameGDS, or unmarkedFrameGPC object
unmarkedFrameMMO | Create an object of class unmarkedFrameMMO that contains data used by multmixOpen.
unmarkedFrameMPois | Organize data for the multinomial-Poisson mixture model of Royle (2004) fit by multinomPois
unmarkedFrameOccu | Organize data for the single season occupancy models fit by occu and occuRN
unmarkedFrameOccuComm | Organize data for the community occupancy model fit by occuComm
unmarkedFrameOccuCOP | Organize data for the occupancy model using count data fit by 'occuCOP'
unmarkedFrameOccuFP | Organize data for the single season occupancy models fit by occuFP
unmarkedFrameOccuMS | Organize data for the multi-state occupancy model fit by occuMS
unmarkedFrameOccuMulti | Organize data for the multispecies occupancy model fit by occuMulti
unmarkedFrameOccuTTD | Create an unmarkedFrameOccuTTD object for the time-to-detection model fit by occuTTD
unmarkedFramePCO | Create an object of class unmarkedFramePCO that contains data used by pcountOpen.
unmarkedFramePCount | Organize data for the N-mixture model fit by pcount
unmarkedModSel-class | unmarkedModSel class and methods
unmarkedMultFrame | Create an unmarkedMultFrame, unmarkedFrameGMM, unmarkedFrameGDS, or unmarkedFrameGPC object
unmarkedPostSamples-class | Draw samples from the posterior predictive distribution
unmarkedPower-class | Methods for unmarkedPower objects
unmarkedPower-methods | Methods for unmarkedPower objects
unmarkedPowerList | Summarize a series of unmarked power analyses
unmarkedPowerList-method | Summarize a series of unmarked power analyses
unmarkedPowerList-methods | Summarize a series of unmarked power analyses
unmarkedPowerList_old-class | Summarize a series of unmarked power analyses
unmarkedPower_old-class | Methods for unmarkedPower objects
unmarkedRanef-class | Class '"unmarkedRanef"'
update-method | Class "unmarkedFit"
update-method | Methods for unmarkedPower objects

## -- V --

vcov-method | Methods for Function vcov in Package 'unmarked'
vcov-methods | Methods for Function vcov in Package 'unmarked'
vif | Compute Variance Inflation Factors for an unmarkedFit Object.

## -- 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, unmarkedFrameGMM, unmarkedFrameGDS, or unmarkedFrameGPC object
yearlySiteCovs-method | Create an unmarkedMultFrame, unmarkedFrameGMM, unmarkedFrameGDS, or unmarkedFrameGPC object
yearlySiteCovs<- | Create an unmarkedMultFrame, unmarkedFrameGMM, unmarkedFrameGDS, or unmarkedFrameGPC object
yearlySiteCovs<--method | Create an unmarkedMultFrame, unmarkedFrameGMM, unmarkedFrameGDS, or unmarkedFrameGPC object

## -- misc --

[-method | Methods for bracket extraction [ in Package 'unmarked'
[-method | Draw samples from the posterior predictive distribution
[-methods | Methods for bracket extraction [ in Package 'unmarked'