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

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Documentation for package ‘spOccupancy’ version 0.3.0

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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
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
intPGOcc Function for Fitting Single-Species Integrated Occupancy Models Using Polya-Gamma Latent Variables
lfJSDM Function for Fitting a Latent Factor Joint Species Distribution Model
lfMsPGOcc Function for Fitting Latent Factor Multi-Species Occupancy Models
msPGOcc Function for Fitting Multi-Species Occupancy Models Using Polya-Gamma Latent Variables
neon2015 Detection-nondetection data of 12 foliage gleaning bird species in 2015 in Bartlett Experimental Forest in New Hampshire, USA
PGOcc Function for Fitting Single-Species Occupancy Models Using Polya-Gamma Latent Variables
ppcOcc Function for performing posterior predictive checks
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
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.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
sfJSDM Function for Fitting a Spatial Factor Joint Species Distribution Model
sfMsPGOcc Function for Fitting Spatial Factor Multi-Species Occupancy Models
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
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
spPGOcc Function for Fitting Single-Species Spatial Occupancy Models Using Polya-Gamma Latent Variables
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.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
waicOcc Compute Widely Applicable Information Criterion for spOccupancy Model Objects