Models for Data from Unmarked Animals


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Documentation for package ‘unmarked’ version 0.8-6

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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-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 --

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
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

-- 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

-- 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 Occupancy Model
occuRN Fit the Occupancy model of Royle and Nichols...
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 point count model...
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 Class "unmarkedFit"
predict-method Class "unmarkedFitList"
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-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 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"
unmarkedFitList-class Class "unmarkedFitList"
unmarkedFitMPois-class Class "unmarkedFit"
unmarkedFitOccu-class Class "unmarkedFit"
unmarkedFitPCount-class Class "unmarkedFit"
unmarkedFrame Create an unmarkedFrame, or one of its child classes.
unmarkedFrame-class Class "unmarkedFrame"
unmarkedFrameDS Create an unmarkedFrame, or one of its child classes.
unmarkedFrameDS-class Class "unmarkedFrame"
unmarkedFrameMPois Create an unmarkedFrame, or one of its child classes.
unmarkedFrameMPois-class Class "unmarkedFrame"
unmarkedFrameOccu Create an unmarkedFrame, or one of its child classes.
unmarkedFrameOccu-class Class "unmarkedFrame"
unmarkedFramePCount Create an unmarkedFrame, or one of its child classes.
unmarkedFramePCount-class Class "unmarkedFrame"
unmarkedModSel-class Model selection results from an unmarkedFitList
unmarkedMultFrame Create an unmarkedMultFrame.
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.
yearlySiteCovs-method Create an unmarkedMultFrame.
yearlySiteCovs<- Create an unmarkedMultFrame.
yearlySiteCovs<--method Create an unmarkedMultFrame.

-- misc --

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