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: | 1.0.2 |
| 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: | 2022-06-23 |
| Author: | Maximilian Pichler
 [aut, cre],
Florian Hartig
[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_1.0.2.tar.gz |
| Windows binaries: | r-devel: sjSDM_1.0.2.zip, r-release: sjSDM_1.0.2.zip, r-oldrel: sjSDM_1.0.2.zip |
| macOS binaries: | r-release (arm64): sjSDM_1.0.2.tgz, r-oldrel (arm64): sjSDM_1.0.2.tgz, r-release (x86_64): sjSDM_1.0.2.tgz, r-oldrel (x86_64): sjSDM_1.0.2.tgz |
| Old sources: | sjSDM archive |
Linking:
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