Models for Data from Unmarked Animals

---

Documentation for package ‘unmarked’ version 1.4.1

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

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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	Class '"unmarkedRanef"'
bup-method	Class '"unmarkedRanef"'

-- 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 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'
coordinates	Class "unmarkedFrame"
coordinates-method	Class "unmarkedFrame"
coords	Class "unmarkedFrame"
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	constructor of unmarkedFitList objects
fitted-method	Methods for Function fitted in Package 'unmarked'
fitted-methods	Methods for Function fitted in Package 'unmarked'
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	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 "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 multi-scale occupancy models
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"
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
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
mapInfo	Class "unmarkedFrame"
masspcru	Massachusetts North American Amphibian Monitoring Program Data
MesoCarnivores	Occupancy data for coyote, red fox, and bobcat
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
multmixOpen	Open population multinomial N-mixture model

-- N --

names-method	Class "unmarkedEstimateList"
names-method	Class "unmarkedFit"
nllFun	Class "unmarkedFit"
nllFun-method	Class "unmarkedFit"
nmixTTD	Fit N-mixture Time-to-detection Models
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
occuCOP	Fit the occupancy model using count dta
occuFP	Fit occupancy models when false positive detections occur (e.g., Royle and Link [2006] and Miller et al. [2011])
occuMS	Fit Single-Season and Dynamic Multi-State Occupancy Models
occuMulti	Fit the Rota et al. (2016) Multi-species Occupancy Model
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 method for fitted models inheriting class.
parboot-method	Class "unmarkedFit"
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 and extensions
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"
plot-method	Create or 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 on an unmarked model
predict	Methods for Function predict in Package 'unmarked'
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 --

randomTerms	Extract estimates of random effect terms
randomTerms-method	Extract estimates of random effect terms
randomTerms-methods	Extract estimates of random effect terms
ranef	Methods for Function 'ranef' in Package 'unmarked'
ranef-method	Methods for Function 'ranef' in Package 'unmarked'
ranef-methods	Methods for Function 'ranef' in Package 'unmarked'
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'
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	Model selection results from an unmarkedFitList
show-method	Parametric bootstrap method for fitted models inheriting class.
show-method	Draw samples from the posterior predictive distribution
show-method	Class "unmarkedEstimate"
show-method	Class "unmarkedEstimateList"
show-method	Class "unmarkedFit"
show-method	Class "unmarkedFrame"
show-method	Methods for unmarkedPower objects
show-method	Create or summarize a series of unmarked power analyses
show-method	Class '"unmarkedRanef"'
sight2perpdist	Convert sight distance and sight angle to perpendicular distance.
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-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.
SSE-method	Compute Sum of Squared Residuals for a Model Fit.
SSE-methods	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"
summary-method	Methods for unmarkedPower objects
summary-method	Create or 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"
unmarkedFitDS-class	Class "unmarkedFit"
unmarkedFitDSO-class	Class "unmarkedFit"
unmarkedFitGMM-class	Class "unmarkedFit"
unmarkedFitList-class	Class "unmarkedFitList"
unmarkedFitMMO-class	Class "unmarkedFit"
unmarkedFitMPois-class	Class "unmarkedFit"
unmarkedFitNmixTTD-class	Class "unmarkedFit"
unmarkedFitOccu-class	Class "unmarkedFit"
unmarkedFitOccuFP-class	Class "unmarkedFit"
unmarkedFitOccuMS-class	Class "unmarkedFit"
unmarkedFitOccuMulti-class	Class "unmarkedFit"
unmarkedFitOccuPEN-class	Class "unmarkedFit"
unmarkedFitOccuPEN_CV-class	Class "unmarkedFit"
unmarkedFitOccuTTD-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"
unmarkedFrameDSO	Create an object of class unmarkedFrameDSO that contains data used by distsampOpen.
unmarkedFrameDSO-class	Class "unmarkedFrame"
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
unmarkedFrameGDS-class	Class "unmarkedFrame"
unmarkedFrameGMM	Create an unmarkedMultFrame, unmarkedFrameGMM, unmarkedFrameGDS, or unmarkedFrameGPC object
unmarkedFrameGMM-class	Class "unmarkedFrame"
unmarkedFrameGOccu	Create an unmarkedMultFrame, unmarkedFrameGMM, unmarkedFrameGDS, or unmarkedFrameGPC object
unmarkedFrameGPC	Create an unmarkedMultFrame, unmarkedFrameGMM, unmarkedFrameGDS, or unmarkedFrameGPC object
unmarkedFrameGPC-class	Class "unmarkedFrame"
unmarkedFrameMMO	Create an object of class unmarkedFrameMMO that contains data used by multmixOpen.
unmarkedFrameMMO-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"
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
unmarkedFrameOccuMS-class	Class "unmarkedFrame"
unmarkedFrameOccuMulti	Organize data for the multispecies occupancy model fit by occuMulti
unmarkedFrameOccuMulti-class	Class "unmarkedFrame"
unmarkedFrameOccuTTD	Create an unmarkedFrameOccuTTD object for the time-to-detection model fit by occuTTD
unmarkedFrameOccuTTD-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, unmarkedFrameGMM, unmarkedFrameGDS, or unmarkedFrameGPC object
unmarkedMultFrame-class	Class "unmarkedFrame"
unmarkedPostSamples-class	Draw samples from the posterior predictive distribution
unmarkedPower-class	Methods for unmarkedPower objects
unmarkedPower-methods	Methods for unmarkedPower objects
unmarkedPowerList	Create or summarize a series of unmarked power analyses
unmarkedPowerList-class	Create or summarize a series of unmarked power analyses
unmarkedPowerList-method	Create or summarize a series of unmarked power analyses
unmarkedPowerList-methods	Create or summarize a series of unmarked power analyses
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
[-method	Class "unmarkedFrame"
[-methods	Methods for bracket extraction [ in Package 'unmarked'