This package is considered a duplicate. The official version of this package is found at:https://biodiverse.r-universe.dev/spOccupancy

Package: spOccupancy 0.8.0

Jeffrey Doser

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

Fits single-species, multi-species, and integrated non-spatial and spatial occupancy models using Markov Chain Monte Carlo (MCMC). Models are fit using Polya-Gamma data augmentation detailed in Polson, Scott, and Windle (2013) <doi:10.1080/01621459.2013.829001>. Spatial models are fit using either Gaussian processes or Nearest Neighbor Gaussian Processes (NNGP) for large spatial datasets. Details on NNGP models are given in Datta, Banerjee, Finley, and Gelfand (2016) <doi:10.1080/01621459.2015.1044091> and Finley, Datta, and Banerjee (2022) <doi:10.18637/jss.v103.i05>. Provides functionality for data integration of multiple single-species occupancy data sets using a joint likelihood framework. Details on data integration are given in Miller, Pacifici, Sanderlin, and Reich (2019) <doi:10.1111/2041-210X.13110>. Details on single-species and multi-species models are found in MacKenzie, Nichols, Lachman, Droege, Royle, and Langtimm (2002) <doi:10.1890/0012-9658(2002)083[2248:ESORWD]2.0.CO;2> and Dorazio and Royle <doi:10.1198/016214505000000015>, respectively.

Authors:Jeffrey Doser [aut, cre], Andrew Finley [aut], Marc Kery [ctb]

spOccupancy_0.8.0.tar.gz
spOccupancy_0.8.0.tar.gz(r-4.5-noble)spOccupancy_0.8.0.tar.gz(r-4.4-noble)
spOccupancy_0.8.0.tgz(r-4.4-emscripten)spOccupancy_0.8.0.tgz(r-4.3-emscripten)
spOccupancy.pdf |spOccupancy.html✨
spOccupancy/json (API)
NEWS

# Install 'spOccupancy' in R:

install.packages('spOccupancy', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/biodiverse/spoccupancy/issues

Pkgdown site:https://www.doserlab.com

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3
openmp– GCC OpenMP (GOMP) support library

Datasets:

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

openblas cpp openmp

2.18 score 199 scripts 971 downloads 38 exports 18 dependencies

Last updated 17 days agofrom:77c83a1c97. Checks:OK: 2. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Dec 14 2024
R-4.5-linux-x86_64	OK	Dec 14 2024

Exports:getSVCSamples intMsPGOcc intPGOcc lfJSDM lfMsPGOcc msPGOcc PGOcc postHocLM ppcOcc sfJSDM sfMsPGOcc simBinom simIntMsOcc simIntOcc simMsOcc simOcc simTBinom simTIntOcc simTMsOcc simTOcc spIntPGOcc spMsPGOcc spPGOcc stIntPGOcc stMsPGOcc stPGOcc svcMsPGOcc svcPGBinom svcPGOcc svcTIntPGOcc svcTMsPGOcc svcTPGBinom svcTPGOcc tIntPGOcc tMsPGOcc tPGOcc updateMCMC waicOcc

Dependencies:abind boot coda codetools doParallel foreach iterators lattice lme4 MASS Matrix minqa nlme nloptr RANN Rcpp RcppEigen spAbundance

Help page	Topics
Single-Species, Multi-Species, and Integrated Spatial Occupancy Models	spOccupancy-package spOccupancy
Extract Model Fitted Values for intPGOcc Object	fitted.intPGOcc
Extract Model Fitted Values for lfJSDM Object	fitted.lfJSDM
Extract Model Fitted Values for lfMsPGOcc Object	fitted.lfMsPGOcc
Extract Model Fitted Values for msPGOcc Object	fitted.msPGOcc
Extract Model Fitted Values for PGOcc Object	fitted.PGOcc
Extract Model Fitted Values for sfJSDM Object	fitted.sfJSDM
Extract Model Fitted Values for sfMsPGOcc Object	fitted.sfMsPGOcc
Extract Model Fitted Values for spIntPGOcc Object	fitted.spIntPGOcc
Extract Model Fitted Values for spMsPGOcc Object	fitted.spMsPGOcc
Extract Model Fitted Values for spPGOcc Object	fitted.spPGOcc
Extract Model Fitted Values for stIntPGOcc Object	fitted.stIntPGOcc
Extract Model Fitted Values for stMsPGOcc Object	fitted.stMsPGOcc
Extract Model Fitted Values for stPGOcc Object	fitted.stPGOcc
Extract Model Fitted Values for svcMsPGOcc Object	fitted.svcMsPGOcc
Extract Model Fitted Values for svcPGBinom Object	fitted.svcPGBinom
Extract Model Fitted Values for svcPGOcc Object	fitted.svcPGOcc
Extract Model Fitted Values for svcTIntPGOcc Object	fitted.svcTIntPGOcc
Extract Model Fitted Values for svcTMsPGOcc Object	fitted.svcTMsPGOcc
Extract Model Fitted Values for svcTPGBinom Object	fitted.svcTPGBinom
Extract Model Fitted Values for svcTPGOcc Object	fitted.svcTPGOcc
Extract Model Fitted Values for tIntPGOcc Object	fitted.tIntPGOcc
Extract Model Fitted Values for tMsPGOcc Object	fitted.tMsPGOcc
Extract Model Fitted Values for tPGOcc Object	fitted.tPGOcc
Extract spatially-varying coefficient MCMC samples	getSVCSamples
Detection-nondetection data of 12 foliage gleaning bird species in 2015 in the Hubbard Brook Experimental Forest	hbef2015
Elevation in meters extracted at a 30m resolution across the Hubbard Brook Experimental Forest	hbefElev
Detection-nondetection data of 12 foliage gleaning bird species from 2010-2018 in the Hubbard Brook Experimental Forest	hbefTrends
Function for Fitting Integrated Multi-Species Occupancy Models Using Polya-Gamma Latent Variables	intMsPGOcc
Function for Fitting Single-Species Integrated Occupancy Models Using Polya-Gamma Latent Variables	intPGOcc
Function for Fitting a Latent Factor Joint Species Distribution Model	lfJSDM
Function for Fitting Latent Factor Multi-Species Occupancy Models	lfMsPGOcc
Function for Fitting Multi-Species Occupancy Models Using Polya-Gamma Latent Variables	msPGOcc
Detection-nondetection data of 12 foliage gleaning bird species in 2015 in Bartlett Experimental Forest in New Hampshire, USA	neon2015
Function for Fitting Single-Species Occupancy Models Using Polya-Gamma Latent Variables	PGOcc
Function for Fitting Linear Mixed Models with Previous Model Estimates	postHocLM
Function for performing posterior predictive checks	ppcOcc
Function for prediction at new locations for integrated multi-species occupancy models	predict.intMsPGOcc
Function for prediction at new locations for single-species integrated occupancy models	predict.intPGOcc
Function for prediction at new locations for latent factor joint species distribution models	predict.lfJSDM
Function for prediction at new locations for latent factor multi-species occupancy models	predict.lfMsPGOcc
Function for prediction at new locations for multi-species occupancy models	predict.msPGOcc
Function for prediction at new locations for single-species occupancy models	predict.PGOcc
Function for prediction at new locations for spatial factor joint species distribution model	predict.sfJSDM
Function for prediction at new locations for spatial factor multi-species occupancy models	predict.sfMsPGOcc
Function for prediction at new locations for single-species integrated spatial occupancy models	predict.spIntPGOcc
Function for prediction at new locations for multi-species spatial occupancy models	predict.spMsPGOcc
Function for prediction at new locations for single-species spatial occupancy models	predict.spPGOcc
Function for prediction at new locations for multi-season single-species spatial integrated occupancy models	predict.stIntPGOcc
Function for prediction at new locations for multi-season multi-species spatial occupancy models	predict.stMsPGOcc
Function for prediction at new locations for multi-season single-species spatial occupancy models	predict.stPGOcc
Function for prediction at new locations for spatially varying coefficient multi-species occupancy models	predict.svcMsPGOcc
Function for prediction at new locations for single-species spatially-varying coefficient Binomial models	predict.svcPGBinom
Function for prediction at new locations for single-species spatially-varying coefficient occupancy models	predict.svcPGOcc
Function for prediction at new locations for multi-season single-species spatially-varying coefficient integrated occupancy models	predict.svcTIntPGOcc
Function for prediction at new locations for multi-season multi-species spatially-varying coefficient occupancy models	predict.svcTMsPGOcc
Function for prediction at new locations for multi-season single-species spatially-varying coefficient binomial models	predict.svcTPGBinom
Function for prediction at new locations for multi-season single-species spatially-varying coefficient occupancy models	predict.svcTPGOcc
Function for prediction at new locations for multi-season single-species integrated occupancy models	predict.tIntPGOcc
Function for prediction at new locations for multi-season multi-species occupancy models	predict.tMsPGOcc
Function for prediction at new locations for multi-season single-species occupancy models	predict.tPGOcc
Occupancy and detection residuals for 'PGOcc' models	residuals.PGOcc
Occupancy and detection residuals for 'spPGOcc' models	residuals.spPGOcc
Occupancy and detection residuals for 'svcPGOcc' models	residuals.svcPGOcc
Function for Fitting a Spatial Factor Joint Species Distribution Model	sfJSDM
Function for Fitting Spatial Factor Multi-Species Occupancy Models	sfMsPGOcc
Simulate Single-Species Binomial Data	simBinom
Simulate Multi-Species Detection-Nondetection Data from Multiple Data Sources	simIntMsOcc
Simulate Single-Species Detection-Nondetection Data from Multiple Data Sources	simIntOcc
Simulate Multi-Species Detection-Nondetection Data	simMsOcc
Simulate Single-Species Detection-Nondetection Data	simOcc
Simulate Multi-Season Single-Species Binomial Data	simTBinom
Simulate Single-Species Multi-Season Detection-Nondetection Data from Multiple Data Sources	simTIntOcc
Simulate Multi-Species Multi-Season Detection-Nondetection Data	simTMsOcc
Simulate Multi-Season Single-Species Detection-Nondetection Data	simTOcc
Function for Fitting Single-Species Integrated Spatial Occupancy Models Using Polya-Gamma Latent Variables	spIntPGOcc
Function for Fitting Multi-Species Spatial Occupancy Models Using Polya-Gamma Latent Variables	spMsPGOcc
Function for Fitting Single-Species Spatial Occupancy Models Using Polya-Gamma Latent Variables	spPGOcc
Function for Fitting Multi-Season Single-Species Spatial Integrated Occupancy Models Using Polya-Gamma Latent Variables	stIntPGOcc
Function for Fitting Multi-Species Multi-Season Spatial Occupancy Models	stMsPGOcc
Function for Fitting Multi-Season Single-Species Spatial Occupancy Models Using Polya-Gamma Latent Variables	stPGOcc
Methods for intMsPGOcc Object	plot.intMsPGOcc print.intMsPGOcc summary.intMsPGOcc
Methods for intPGOcc Object	plot.intPGOcc print.intPGOcc summary.intPGOcc
Methods for lfJSDM Object	plot.lfJSDM print.lfJSDM summary.lfJSDM
Methods for lfMsPGOcc Object	plot.lfMsPGOcc print.lfMsPGOcc summary.lfMsPGOcc
Methods for msPGOcc Object	plot.msPGOcc print.msPGOcc summary.msPGOcc
Methods for PGOcc Object	plot.PGOcc print.PGOcc summary.PGOcc
Methods for postHocLM Object	print.postHocLM summary.postHocLM
Methods for ppcOcc Object	summary.ppcOcc
Methods for sfJSDM Object	plot.sfJSDM print.sfJSDM summary.sfJSDM
Methods for sfMsPGOcc Object	plot.sfMsPGOcc print.sfMsPGOcc summary.sfMsPGOcc
Methods for spIntPGOcc Object	plot.spIntPGOcc print.spIntPGOcc summary.spIntPGOcc
Methods for spMsPGOcc Object	plot.spMsPGOcc print.spMsPGOcc summary.spMsPGOcc
Methods for spPGOcc Object	plot.spPGOcc print.spPGOcc summary.spPGOcc
Methods for stIntPGOcc Object	plot.stIntPGOcc print.stIntPGOcc summary.stIntPGOcc
Methods for stMsPGOcc Object	plot.stMsPGOcc print.stMsPGOcc summary.stMsPGOcc
Methods for stPGOcc Object	plot.stPGOcc print.stPGOcc summary.stPGOcc
Methods for svcMsPGOcc Object	plot.svcMsPGOcc print.svcMsPGOcc summary.svcMsPGOcc
Methods for svcPGBinom Object	plot.svcPGBinom print.svcPGBinom summary.svcPGBinom
Methods for svcPGOcc Object	plot.svcPGOcc print.svcPGOcc summary.svcPGOcc
Methods for svcTIntPGOcc Object	plot.svcTIntPGOcc print.svcTIntPGOcc summary.svcTIntPGOcc
Methods for svcTMsPGOcc Object	plot.svcTMsPGOcc print.svcTMsPGOcc summary.svcTMsPGOcc
Methods for svcTPGBinom Object	plot.svcTPGBinom print.svcTPGBinom summary.svcTPGBinom
Methods for svcTPGOcc Object	plot.svcTPGOcc print.svcTPGOcc summary.svcTPGOcc
Methods for tIntPGOcc Object	plot.tIntPGOcc print.tIntPGOcc summary.tIntPGOcc
Methods for tMsPGOcc Object	plot.tMsPGOcc print.tMsPGOcc summary.tMsPGOcc
Methods for tPGOcc Object	plot.tPGOcc print.tPGOcc summary.tPGOcc
Function for Fitting Multi-Species Spatially-Varying Coefficient Occupancy Models	svcMsPGOcc
Function for Fitting Single-Species Spatially-Varying Coefficient Binomial Models Using Polya-Gamma Latent Variables	svcPGBinom
Function for Fitting Single-Species Spatially-Varying Coefficient Occupancy Models Using Polya-Gamma Latent Variables	svcPGOcc
Function for Fitting Multi-Season Single-Species Spatially-varying Coefficient Integrated Occupancy Models Using Polya-Gamma Latent Variables	svcTIntPGOcc
Function for Fitting Multi-Species Multi-Season Spatially-Varying Coefficient Occupancy Models	svcTMsPGOcc
Function for Fitting Multi-Season Single-Species Spatially-Varying Coefficient Binomial Models Using Polya-Gamma Latent Variables	svcTPGBinom
Function for Fitting Multi-Season Single-Species Spatially-Varying Coefficient Occupancy Models Using Polya-Gamma Latent Variables	svcTPGOcc
Function for Fitting Multi-Season Single-Species Integrated Occupancy Models Using Polya-Gamma Latent Variables	tIntPGOcc
Function for Fitting Multi-Species Multi-Season Occupancy Models	tMsPGOcc
Function for Fitting Multi-Season Single-Species Occupancy Models Using Polya-Gamma Latent Variables	tPGOcc
Update a spOccupancy or spAbundance model run with more MCMC iterations	updateMCMC
Compute Widely Applicable Information Criterion for spOccupancy Model Objects	waicOcc

Package: spOccupancy 0.8.0

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

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