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Package overview

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

Fitting Models

PGOcc()
Function for Fitting Single-Species Occupancy Models Using Polya-Gamma Latent Variables
spPGOcc()
Function for Fitting Single-Species Spatial Occupancy Models Using Polya-Gamma Latent Variables
msPGOcc()
Function for Fitting Multi-Species Occupancy Models Using Polya-Gamma Latent Variables
spMsPGOcc()
Function for Fitting Multi-Species Spatial Occupancy Models Using Polya-Gamma Latent Variables
intPGOcc()
Function for Fitting Single-Species Integrated Occupancy Models Using Polya-Gamma Latent Variables
spIntPGOcc()
Function for Fitting Single-Species Integrated Spatial Occupancy Models Using Polya-Gamma Latent Variables
lfJSDM()
Function for Fitting a Latent Factor Joint Species Distribution Model
sfJSDM()
Function for Fitting a Spatial Factor Joint Species Distribution Model
lfMsPGOcc()
Function for Fitting Latent Factor Multi-Species Occupancy Models
sfMsPGOcc()
Function for Fitting Spatial Factor Multi-Species Occupancy Models
tPGOcc()
Function for Fitting Multi-Season Single-Species Occupancy Models Using Polya-Gamma Latent Variables
stPGOcc()
Function for Fitting Multi-Season Single-Species Spatial Occupancy Models Using Polya-Gamma Latent Variables
svcPGOcc()
Function for Fitting Single-Species Spatially-Varying Coefficient Occupancy Models Using Polya-Gamma Latent Variables
svcPGBinom()
Function for Fitting 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
svcTPGBinom()
Function for Fitting Multi-Season Single-Species Spatially-Varying Coefficient Binomial Models Using Polya-Gamma Latent Variables

Goodness of Fit and Model Assessment

ppcOcc()
Function for performing posterior predictive checks
waicOcc()
Compute Widely Applicable Information Criterion for spOccupancy Model Objects

Data Simulation

simOcc()
Simulate Single-Species Detection-Nondetection Data
simMsOcc()
Simulate Multi-Species Detection-Nondetection Data
simIntOcc()
Simulate Single-Species Detection-Nondetection Data from Multiple Data Sources
simTOcc()
Simulate Multi-Season Single-Species Detection-Nondetection Data
simBinom()
Simulate Single-Species Binomial Data
simTBinom()
Simulate Multi-Season Single-Species Binomial Data

Summary

summary(<PGOcc>) print(<PGOcc>)
Methods for PGOcc Object
summary(<spPGOcc>) print(<spPGOcc>)
Methods for spPGOcc Object
summary(<msPGOcc>) print(<msPGOcc>)
Methods for msPGOcc Object
summary(<spMsPGOcc>) print(<spMsPGOcc>)
Methods for spMsPGOcc Object
summary(<intPGOcc>) print(<intPGOcc>)
Methods for intPGOcc Object
summary(<spIntPGOcc>) print(<spIntPGOcc>)
Methods for spIntPGOcc Object
summary(<lfJSDM>) print(<lfJSDM>)
Methods for lfJSDM Object
summary(<sfJSDM>) print(<sfJSDM>)
Methods for sfJSDM Object
summary(<lfMsPGOcc>) print(<lfMsPGOcc>)
Methods for lfMsPGOcc Object
summary(<sfMsPGOcc>) print(<sfMsPGOcc>)
Methods for sfMsPGOcc Object
summary(<tPGOcc>) print(<tPGOcc>)
Methods for tPGOcc Object
summary(<stPGOcc>) print(<stPGOcc>)
Methods for stPGOcc Object
summary(<ppcOcc>)
Methods for ppcOcc Object
summary(<svcPGOcc>) print(<svcPGOcc>)
Methods for svcPGOcc Object
summary(<svcPGBinom>) print(<svcPGBinom>)
Methods for svcPGBinom Object
summary(<svcTPGOcc>) print(<svcTPGOcc>)
Methods for svcTPGOcc Object
summary(<svcTPGBinom>) print(<svcTPGBinom>)
Methods for svcTPGBinom Object

Prediction

predict(<PGOcc>)
Function for prediction at new locations for single-species occupancy models
predict(<spPGOcc>)
Function for prediction at new locations for single-species spatial occupancy models
predict(<msPGOcc>)
Function for prediction at new locations for multi-species occupancy models
predict(<spMsPGOcc>)
Function for prediction at new locations for multi-species spatial occupancy models
predict(<intPGOcc>)
Function for prediction at new locations for single-species integrated occupancy models
predict(<spIntPGOcc>)
Function for prediction at new locations for single-species integrated spatial occupancy models
predict(<lfJSDM>)
Function for prediction at new locations for latent factor joint species distribution models
predict(<sfJSDM>)
Function for prediction at new locations for spatial factor joint species distribution model
predict(<lfMsPGOcc>)
Function for prediction at new locations for latent factor multi-species occupancy models
predict(<sfMsPGOcc>)
Function for prediction at new locations for spatial factor multi-species occupancy models
predict(<tPGOcc>)
Function for prediction at new locations for multi-season single-species occupancy models
predict(<stPGOcc>)
Function for prediction at new locations for multi-season single-species spatial occupancy models
predict(<svcPGOcc>)
Function for prediction at new locations for single-species spatially-varying coefficient occupancy models
predict(<svcPGBinom>)
Function for prediction at new locations for 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(<svcTPGBinom>)
Function for prediction at new locations for multi-season single-species spatially-varying coefficient binomial models

Fitted values

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

Other

getSVCSamples()
Extract spatially-varying coefficient MCMC samples

Data

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
neon2015
Detection-nondetection data of 12 foliage gleaning bird species in 2015 in Bartlett Experimental Forest in New Hampshire, USA
hbefTrends
Detection-nondetection data of 12 foliage gleaning bird species from 2010-2018 in the Hubbard Brook Experimental Forest