bamm: Species Distribution Models as a Function of Biotic, Abiotic and Movement Factors (BAM)

Species Distribution Modeling (SDM) is a practical methodology that aims to estimate the area of distribution of a species. However, most of the work has focused on estimating static expressions of the correlation between environmental variables. The outputs of correlative species distribution models can be interpreted as maps of the suitable environment for a species but not generally as maps of its actual distribution. Soberón and Peterson (2005) <doi:10.17161/bi.v2i0.4> presented the BAM scheme, a heuristic framework that states that the occupied area of a species occurs on sites that have been accessible through dispersal (M) and have both favorable biotic (B) and abiotic conditions (A). The 'bamm' package implements classes and functions to operate on each element of the BAM and by using a cellular automata model where the occupied area of a species at time t is estimated by the multiplication of three binary matrices: one matrix represents movements (M), another abiotic -niche- tolerances (A), and a third, biotic interactions (B). The theoretical background of the package can be found in Soberón and Osorio-Olvera (2022) <doi:10.48550/arXiv.2212.06308>.

Version: 0.4.3
Depends: R (≥ 3.5.0)
Imports: raster (≥ 3.4-13), Matrix (≥ 1.2.14), RSpectra (≥ 0.13.1), methods (≥ 3.3), magrittr (≥ 1.2), dplyr (≥ 0.8.0), purrr (≥ 0.2), igraph (≥ 1.2), leaflet (≥ 2.0), Rdpack (≥ 0.11.0), animation (≥ 2.3), future (≥ 1.18.0), furrr (≥ 0.1.0), Rcpp (≥ 0.12.18), sp (≥ 1.3.0)
LinkingTo: Rcpp, RcppArmadillo
Suggests: knitr, crosstalk, plotly, rmarkdown, testthat (≥ 3.0.0), covr
Published: 2022-12-20
Author: Luis Osorio-Olvera ORCID iD [aut, cre], Jorge Soberón ORCID iD [aut]
Maintainer: Luis Osorio-Olvera <luismurao at gmail.com>
BugReports: https://github.com/luismurao/bamm/issues
License: GPL (≥ 3)
URL: https://luismurao.github.io/bamm/
NeedsCompilation: yes
SystemRequirements: C++11, GDAL (>= 2.2.3): gdal-bin (deb), libgdal-dev (deb) or gdal-devel (rmp), GEOS (>= 3.4.0), PROJ (>= 4.9.3): libproj-dev (deb), sqlite3, ImageMagick++: imagemagick (deb), libmagic-dev (deb), libmagick++-dev (deb) or ImageMagick-c++-devel (rpm) ImageMagick (http://imagemagick.org) or GraphicsMagick (http://www.graphicsmagick.org) or LyX (http://www.lyx.org) for saveGIF(); (PDF)LaTeX for saveLatex(); SWF Tools (http://swftools.org) for saveSWF(); FFmpeg (http://ffmpeg.org) or avconv (https://libav.org/avconv.html) for saveVideo()
Materials: README NEWS
CRAN checks: bamm results

Documentation:

Reference manual: bamm.pdf
Vignettes: bamm

Downloads:

Package source: bamm_0.4.3.tar.gz
Windows binaries: r-prerel: bamm_0.4.3.zip, r-release: bamm_0.4.3.zip, r-oldrel: bamm_0.4.3.zip
macOS binaries: r-prerel (arm64): bamm_0.4.3.tgz, r-release (arm64): bamm_0.4.3.tgz, r-oldrel (arm64): bamm_0.4.3.tgz, r-prerel (x86_64): bamm_0.4.3.tgz, r-release (x86_64): bamm_0.4.3.tgz

Linking:

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