Models for Data from Unmarked Animals


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Documentation for package ‘unmarked’ version 0.12-3

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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_)
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)
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 --

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'
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 N-mixture model
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 --

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
occuFP Fit occupancy models when false positive detections occur (e.g., Royle and Link [2006] and Miller et al. [2011])
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)
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 Class '"unmarkedRanef"'
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 --

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'
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"
show-method Class '"unmarkedRanef"'
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"
Switzerland Swiss landscape data

-- 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"
unmarkedFitOccuFP-class Class "unmarkedFit"
unmarkedFitOccuMulti-class Class "unmarkedFit"
unmarkedFitOccuPEN-class Class "unmarkedFit"
unmarkedFitOccuPEN_CV-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, unmarkedFrameGMM, unmarkedFrameGDS, or unmarkedFrameGPC object
unmarkedFrameGDS-class Class "unmarkedFrame"
unmarkedFrameGMM Create an unmarkedMultFrame, unmarkedFrameGMM, unmarkedFrameGDS, or unmarkedFrameGPC object
unmarkedFrameGMM-class Class "unmarkedFrame"
unmarkedFrameGPC Create an unmarkedMultFrame, unmarkedFrameGMM, unmarkedFrameGDS, or unmarkedFrameGPC object
unmarkedFrameGPC-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"
unmarkedFrameOccuFP Organize data for the single season occupancy models fit by occuFP
unmarkedFrameOccuMulti Organize data for the multispecies occupancy model fit by occuMulti
unmarkedFrameOccuMulti-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"
unmarkedRanef-class Class '"unmarkedRanef"'
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, 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 Class "unmarkedFrame"
[-methods Methods for bracket extraction [ in Package 'unmarked'