sjSDM: Scalable Joint Species Distribution Modeling

A scalable method to estimate joint Species Distribution Models (jSDMs) for big community datasets based on a Monte Carlo approximation of the joint likelihood. The numerical approximation is based on 'PyTorch' and 'reticulate', and can be run on CPUs and GPUs alike. The method is described in Pichler & Hartig (2021) <doi:10.1111/2041-210X.13687>. The package contains various extensions, including support for different response families, ability to account for spatial autocorrelation, and deep neural networks instead of the linear predictor in jSDMs.

Version: 1.0.1
Depends: R (≥ 3.0)
Imports: reticulate, stats, mvtnorm, utils, rstudioapi, abind, graphics, grDevices, Metrics, parallel, mgcv, Ternary, cli, crayon, ggplot2, checkmate, mathjaxr, ggtern
Suggests: testthat, knitr, rmarkdown
Published: 2022-03-11
Author: Maximilian Pichler ORCID iD [aut, cre], Florian Hartig ORCID iD [aut], Wang Cai [ctb]
Maintainer: Maximilian Pichler <maximilian.pichler at biologie.uni-regensburg.de>
BugReports: https://github.com/TheoreticalEcology/s-jSDM/issues
License: GPL-3
URL: https://theoreticalecology.github.io/s-jSDM/
NeedsCompilation: no
Citation: sjSDM citation info
Materials: README NEWS
CRAN checks: sjSDM results

Documentation:

Reference manual: sjSDM.pdf
Vignettes: sjSDM: Help with the installation of dependencies
Getting started with sjSDM: a scalable joint Species Distribution Model

Downloads:

Package source: sjSDM_1.0.1.tar.gz
Windows binaries: r-devel: sjSDM_1.0.1.zip, r-release: sjSDM_1.0.1.zip, r-oldrel: sjSDM_1.0.1.zip
macOS binaries: r-release (arm64): sjSDM_1.0.1.tgz, r-oldrel (arm64): sjSDM_1.0.1.tgz, r-release (x86_64): sjSDM_1.0.1.tgz, r-oldrel (x86_64): sjSDM_1.0.1.tgz
Old sources: sjSDM archive

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