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spOccupancy  

Single-Species, Multi-Species, and Integrated Spatial Occupancy Models
View on CRAN: Click here


Download and install spOccupancy package within the R console
Install from CRAN:
install.packages("spOccupancy")

Install from Github:
library("remotes")
install_github("cran/spOccupancy")

Install by package version:
library("remotes")
install_version("spOccupancy", "0.8.0")



Attach the package and use:
library("spOccupancy")
Maintained by
Jeffrey Doser
[Scholar Profile | Author Map]
First Published: 2021-11-11
Latest Update: 2023-08-31
Description:
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.
How to cite:
Jeffrey Doser (2021). spOccupancy: Single-Species, Multi-Species, and Integrated Spatial Occupancy Models. R package version 0.8.0, https://cran.r-project.org/web/packages/spOccupancy. Accessed 29 Mar. 2025.
Previous versions and publish date:
0.1.2 (2021-11-11 10:00), 0.1.3 (2021-11-25 07:30), 0.2.0 (2021-12-19 18:50), 0.2.1 (2022-01-07 14:50), 0.3.0 (2022-03-29 23:50), 0.3.1 (2022-04-13 10:10), 0.3.2 (2022-05-22 01:10), 0.4.0 (2022-07-13 15:20), 0.5.0 (2022-11-16 19:30), 0.5.1 (2022-12-08 22:50), 0.5.2 (2022-12-21 17:10), 0.6.0 (2023-03-03 23:50), 0.6.1 (2023-03-11 10:40), 0.7.0 (2023-08-16 17:22), 0.7.1 (2023-09-01 00:10), 0.7.2 (2023-11-01 06:00), 0.7.3 (2024-03-28 22:10), 0.7.6 (2024-04-19 14:22)
Other packages that cited spOccupancy R package
View spOccupancy citation profile
Other R packages that spOccupancy depends, imports, suggests or enhances
Complete documentation for spOccupancy
Functions, R codes and Examples using the spOccupancy R package
Some associated functions: PGOcc . fitted.PGOcc . fitted.intPGOcc . fitted.lfJSDM . fitted.lfMsPGOcc . fitted.msPGOcc . fitted.sfJSDM . fitted.sfMsPGOcc . fitted.spIntPGOcc . fitted.spMsPGOcc . fitted.spPGOcc . fitted.stMsPGOcc . fitted.stPGOcc . fitted.svcMsPGOcc . fitted.svcPGBinom . fitted.svcPGOcc . fitted.svcTMsPGOcc . fitted.svcTPGBinom . fitted.svcTPGOcc . fitted.tMsPGOcc . fitted.tPGOcc . getSVCSamples . hbef2015.rda . hbefElev.rda . hbefTrends.rda . intMsPGOcc . intPGOcc . lfJSDM . lfMsPGOcc . msPGOcc . neon2015.rda . postHocLM . ppcOcc . predict.PGOcc . predict.intMsPGOcc . predict.intPGOcc . predict.lfJSDM . predict.lfMsPGOcc . predict.msPGOcc . predict.sfJSDM . predict.sfMsPGOcc . predict.spIntPGOcc . predict.spMsPGOcc . predict.spPGOcc . predict.stMsPGOcc . predict.stPGOcc . predict.svcMsPGOcc . predict.svcPGBinom . predict.svcPGOcc . predict.svcTMsPGOcc . predict.svcTPGBinom . predict.svcTPGOcc . predict.tMsPGOcc . predict.tPGOcc . sfJSDM . sfMsPGOcc . simBinom . simIntMsOcc . simIntOcc . simMsOcc . simOcc . simTBinom . simTMsOcc . simTOcc . spIntPGOcc . spMsPGOcc . spOccupancy-package . spPGOcc . stMsPGOcc . stPGOcc . summary.PGOcc . summary.intMsPGOcc . summary.intPGOcc . summary.lfJSDM . summary.lfMsPGOcc . summary.msPGOcc . summary.postHocLM . summary.ppcOcc . summary.sfJSDM . summary.sfMsPGOcc . summary.spIntPGOcc . summary.spMsPGOcc . summary.spPGOcc . summary.stMsPGOcc . summary.stPGOcc . summary.svcMsPGOcc . summary.svcPGBinom . summary.svcPGOcc . summary.svcTMsPGOcc . summary.svcTPGBinom . summary.svcTPGOcc . summary.tMsPGOcc . summary.tPGOcc . svcMsPGOcc . svcPGBinom . svcPGOcc . svcTMsPGOcc . svcTPGBinom . svcTPGOcc . tMsPGOcc . tPGOcc . waicOcc . 
Some associated R codes: PGOcc.R . generics.R . getSVCSamples.R . idist.R . intMsPGOcc.R . intPGOcc.R . lfJSDM.R . lfMsPGOcc.R . mkMatUtil.R . mkSpCov.R . msPGOcc.R . nn.R . plot-generics.R . postHocLM.R . ppcOcc.R . sfJSDM.R . sfMsPGOcc.R . simBinom.R . simIntMsOcc.R . simIntOcc.R . simMsOcc.R . simOcc.R . simTBinom.R . simTMsOcc.R . simTOcc.R . spIntPGOcc.R . spMsPGOcc.R . spPGOcc.R . stMsPGOcc.R . stPGOcc.R . svcMsPGOcc.R . svcPGBinom.R . svcPGOcc.R . svcTMsPGOcc.R . svcTPGBinom.R . svcTPGOcc.R . tMsPGOcc.R . tPGOcc.R . updateMCMC.R . waicOcc.R .  Full spOccupancy package functions and examples
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