sjSDM: Scalable Joint Species Distribution Modeling

A scalable and fast method for estimating joint Species Distribution Models (jSDMs) for big community data, including eDNA data. The package estimates a full (i.e. non-latent) jSDM with different response distributions (including the traditional multivariate probit model). The package allows to perform variation partitioning (VP) / ANOVA on the fitted models to separate the contribution of environmental, spatial, and biotic associations. In addition, the total R-squared can be further partitioned per species and site to reveal the internal metacommunity structure, see Leibold et al., <doi:10.1111/oik.08618>. The internal structure can then be regressed against environmental and spatial distinctiveness, richness, and traits to analyze metacommunity assembly processes. The package includes support for accounting for spatial autocorrelation and the option to fit responses using deep neural networks instead of a standard linear predictor. As described in Pichler & Hartig (2021) <doi:10.1111/2041-210X.13687>, scalability is achieved by using a Monte Carlo approximation of the joint likelihood implemented via 'PyTorch' and 'reticulate', which can be run on CPUs or GPUs.

Version:	1.0.6
Depends:	R (≥ 3.0)
Imports:	reticulate, stats, mvtnorm, utils, rstudioapi, abind, graphics, grDevices, Metrics, parallel, mgcv, cli, crayon, ggplot2, checkmate, mathjaxr, ggtern, beeswarm, qgam, scales
Suggests:	testthat, knitr, rmarkdown, iml, fields
Published:	2024-08-19
DOI:	10.32614/CRAN.package.sjSDM
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://github.com/TheoreticalEcology/s-jSDM/
NeedsCompilation:	no
Citation:	sjSDM citation info
Materials:	README NEWS
In views:	Environmetrics
CRAN checks:	sjSDM results

Documentation:

Reference manual:	sjSDM.pdf
Vignettes:	sjSDM: Getting started with sjSDM - a scalable joint Species Distribution Model (source)

Downloads:

Package source:	sjSDM_1.0.6.tar.gz
Windows binaries:	r-devel: sjSDM_1.0.6.zip, r-release: sjSDM_1.0.6.zip, r-oldrel: sjSDM_1.0.6.zip
macOS binaries:	r-release (arm64): sjSDM_1.0.6.tgz, r-oldrel (arm64): sjSDM_1.0.6.tgz, r-release (x86_64): sjSDM_1.0.6.tgz, r-oldrel (x86_64): sjSDM_1.0.6.tgz
Old sources:	sjSDM archive

Linking:

Please use the canonical form https://CRAN.R-project.org/package=sjSDM to link to this page.