Single-Species, Multi-Species, and Integrated Spatial Occupancy Models

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Documentation for package ‘spOccupancy’ version 0.6.1

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F G H I L M N P S T W

spOccupancy-package Single-Species, Multi-Species, and Integrated Spatial Occupancy Models

-- F --

fitted.intPGOcc Extract Model Fitted Values for intPGOcc Object
fitted.lfJSDM Extract Model Fitted Values for lfJSDM Object
fitted.lfMsPGOcc Extract Model Fitted Values for lfMsPGOcc Object
fitted.msPGOcc Extract Model Fitted Values for msPGOcc Object
fitted.PGOcc Extract Model Fitted Values for PGOcc Object
fitted.sfJSDM Extract Model Fitted Values for sfJSDM Object
fitted.sfMsPGOcc Extract Model Fitted Values for sfMsPGOcc Object
fitted.spIntPGOcc Extract Model Fitted Values for spIntPGOcc Object
fitted.spMsPGOcc Extract Model Fitted Values for spMsPGOcc Object
fitted.spPGOcc Extract Model Fitted Values for spPGOcc Object
fitted.stPGOcc Extract Model Fitted Values for stPGOcc Object
fitted.svcPGBinom Extract Model Fitted Values for svcPGBinom Object
fitted.svcPGOcc Extract Model Fitted Values for svcPGOcc Object
fitted.svcTPGBinom Extract Model Fitted Values for svcTPGBinom Object
fitted.svcTPGOcc Extract Model Fitted Values for svcTPGOcc Object
fitted.tPGOcc Extract Model Fitted Values for tPGOcc Object

-- G --

getSVCSamples Extract spatially-varying coefficient MCMC samples

-- H --

hbef2015 Detection-nondetection data of 12 foliage gleaning bird species in 2015 in the Hubbard Brook Experimental Forest
hbefElev Elevation in meters extracted at a 30m resolution across the Hubbard Brook Experimental Forest
hbefTrends Detection-nondetection data of 12 foliage gleaning bird species from 2010-2018 in the Hubbard Brook Experimental Forest

-- I --

intMsPGOcc Function for Fitting Integrated Multi-Species Occupancy Models Using Polya-Gamma Latent Variables
intPGOcc Function for Fitting Single-Species Integrated Occupancy Models Using Polya-Gamma Latent Variables

-- L --

lfJSDM Function for Fitting a Latent Factor Joint Species Distribution Model
lfMsPGOcc Function for Fitting Latent Factor Multi-Species Occupancy Models

-- M --

msPGOcc Function for Fitting Multi-Species Occupancy Models Using Polya-Gamma Latent Variables

-- N --

neon2015 Detection-nondetection data of 12 foliage gleaning bird species in 2015 in Bartlett Experimental Forest in New Hampshire, USA

-- P --

PGOcc Function for Fitting Single-Species Occupancy Models Using Polya-Gamma Latent Variables
postHocLM Function for Fitting Linear Mixed Models Previous Model Estimates
ppcOcc Function for performing posterior predictive checks
predict.intMsPGOcc Function for prediction at new locations for integrated multi-species occupancy models
predict.intPGOcc Function for prediction at new locations for single-species integrated occupancy models
predict.lfJSDM Function for prediction at new locations for latent factor joint species distribution models
predict.lfMsPGOcc Function for prediction at new locations for latent factor multi-species occupancy models
predict.msPGOcc Function for prediction at new locations for multi-species occupancy models
predict.PGOcc Function for prediction at new locations for single-species occupancy models
predict.sfJSDM Function for prediction at new locations for spatial factor joint species distribution model
predict.sfMsPGOcc Function for prediction at new locations for spatial factor multi-species occupancy models
predict.spIntPGOcc Function for prediction at new locations for single-species integrated spatial occupancy models
predict.spMsPGOcc Function for prediction at new locations for multi-species spatial occupancy models
predict.spPGOcc Function for prediction at new locations for single-species spatial occupancy models
predict.stPGOcc Function for prediction at new locations for multi-season single-species spatial occupancy models
predict.svcPGBinom Function for prediction at new locations for single-species spatially-varying coefficient Binomial models
predict.svcPGOcc Function for prediction at new locations for single-species spatially-varying coefficient occupancy models
predict.svcTPGBinom Function for prediction at new locations for multi-season single-species spatially-varying coefficient binomial models
predict.svcTPGOcc Function for prediction at new locations for multi-season single-species spatially-varying coefficient occupancy models
predict.tPGOcc Function for prediction at new locations for multi-season single-species occupancy models
print.intMsPGOcc Methods for intMsPGOcc Object
print.intPGOcc Methods for intPGOcc Object
print.lfJSDM Methods for lfJSDM Object
print.lfMsPGOcc Methods for lfMsPGOcc Object
print.msPGOcc Methods for msPGOcc Object
print.PGOcc Methods for PGOcc Object
print.postHocLM Methods for postHocLM Object
print.sfJSDM Methods for sfJSDM Object
print.sfMsPGOcc Methods for sfMsPGOcc Object
print.spIntPGOcc Methods for spIntPGOcc Object
print.spMsPGOcc Methods for spMsPGOcc Object
print.spPGOcc Methods for spPGOcc Object
print.stPGOcc Methods for stPGOcc Object
print.svcPGBinom Methods for svcPGBinom Object
print.svcPGOcc Methods for svcPGOcc Object
print.svcTPGBinom Methods for svcTPGBinom Object
print.svcTPGOcc Methods for svcTPGOcc Object
print.tPGOcc Methods for tPGOcc Object

-- S --

sfJSDM Function for Fitting a Spatial Factor Joint Species Distribution Model
sfMsPGOcc Function for Fitting Spatial Factor Multi-Species Occupancy Models
simBinom Simulate Single-Species Binomial Data
simIntMsOcc Simulate Multi-Species Detection-Nondetection Data from Multiple Data Sources
simIntOcc Simulate Single-Species Detection-Nondetection Data from Multiple Data Sources
simMsOcc Simulate Multi-Species Detection-Nondetection Data
simOcc Simulate Single-Species Detection-Nondetection Data
simTBinom Simulate Multi-Season Single-Species Binomial Data
simTOcc Simulate Multi-Season Single-Species Detection-Nondetection Data
spIntPGOcc Function for Fitting Single-Species Integrated Spatial Occupancy Models Using Polya-Gamma Latent Variables
spMsPGOcc Function for Fitting Multi-Species Spatial Occupancy Models Using Polya-Gamma Latent Variables
spOccupancy Single-Species, Multi-Species, and Integrated Spatial Occupancy Models
spPGOcc Function for Fitting Single-Species Spatial Occupancy Models Using Polya-Gamma Latent Variables
stPGOcc Function for Fitting Multi-Season Single-Species Spatial Occupancy Models Using Polya-Gamma Latent Variables
summary.intMsPGOcc Methods for intMsPGOcc Object
summary.intPGOcc Methods for intPGOcc Object
summary.lfJSDM Methods for lfJSDM Object
summary.lfMsPGOcc Methods for lfMsPGOcc Object
summary.msPGOcc Methods for msPGOcc Object
summary.PGOcc Methods for PGOcc Object
summary.postHocLM Methods for postHocLM Object
summary.ppcOcc Methods for ppcOcc Object
summary.sfJSDM Methods for sfJSDM Object
summary.sfMsPGOcc Methods for sfMsPGOcc Object
summary.spIntPGOcc Methods for spIntPGOcc Object
summary.spMsPGOcc Methods for spMsPGOcc Object
summary.spPGOcc Methods for spPGOcc Object
summary.stPGOcc Methods for stPGOcc Object
summary.svcPGBinom Methods for svcPGBinom Object
summary.svcPGOcc Methods for svcPGOcc Object
summary.svcTPGBinom Methods for svcTPGBinom Object
summary.svcTPGOcc Methods for svcTPGOcc Object
summary.tPGOcc Methods for tPGOcc Object
svcPGBinom Function for Fitting Single-Species Spatially-Varying Coefficient Binomial Models Using Polya-Gamma Latent Variables
svcPGOcc Function for Fitting Single-Species Spatially-Varying Coefficient Occupancy Models Using Polya-Gamma Latent Variables
svcTPGBinom Function for Fitting Multi-Season Single-Species Spatially-Varying Coefficient Binomial Models Using Polya-Gamma Latent Variables
svcTPGOcc Function for Fitting Multi-Season Single-Species Spatially-Varying Coefficient Occupancy Models Using Polya-Gamma Latent Variables

-- T --

tPGOcc Function for Fitting Multi-Season Single-Species Occupancy Models Using Polya-Gamma Latent Variables

-- W --

waicOcc Compute Widely Applicable Information Criterion for spOccupancy Model Objects