itsdm: Isolation Forest-Based Presence-Only Species Distribution Modeling

Collection of R functions to do purely presence-only species distribution modeling with isolation forest (iForest) and its variations such as Extended isolation forest and SCiForest. See the details of these methods in references: Liu, F.T., Ting, K.M. and Zhou, Z.H. (2008) <doi:10.1109/ICDM.2008.17>, Hariri, S., Kind, M.C. and Brunner, R.J. (2019) <doi:10.1109/TKDE.2019.2947676>, Liu, F.T., Ting, K.M. and Zhou, Z.H. (2010) <doi:10.1007/978-3-642-15883-4_18>, Guha, S., Mishra, N., Roy, G. and Schrijvers, O. (2016) <https://proceedings.mlr.press/v48/guha16.html>, Cortes, D. (2021) <arXiv:2110.13402>. Additionally, Shapley values are used to explain model inputs and outputs. See details in references: Shapley, L.S. (1953) <doi:10.1515/9781400881970-018>, Lundberg, S.M. and Lee, S.I. (2017) <https://dl.acm.org/doi/abs/10.5555/3295222.3295230>, Molnar, C. (2020) <ISBN:978-0-244-76852-2>, Ċ trumbelj, E. and Kononenko, I. (2014) <doi:10.1007/s10115-013-0679-x>. itsdm also provides functions to diagnose variable response, analyze variable importance, draw spatial dependence of variables and examine variable contribution. As utilities, the package includes a few functions to download bioclimatic variables including 'WorldClim' version 2.0 (see Fick, S.E. and Hijmans, R.J. (2017) <doi:10.1002/joc.5086>) and 'CMCC-BioClimInd' (see Noce, S., Caporaso, L. and Santini, M. (2020) <doi:10.1038/s41597-020-00726-5>.

Version: 0.1.3
Depends: R (≥ 3.5.0)
Imports: checkmate, dplyr, fastshap, ggplot2, isotree, methods, ncdf4, outliertree, patchwork, raster, rlang, ROCit, sf, stars, stats, stringr, tidyselect, utils
Suggests: knitr, rmarkdown
Published: 2022-09-11
Author: Lei Song ORCID iD [aut, cre], Lyndon Estes [ths]
Maintainer: Lei Song <lsong at clarku.edu>
BugReports: https://github.com/LLeiSong/itsdm/issues
License: MIT + file LICENSE
URL: https://github.com/LLeiSong/itsdm, https://lleisong.github.io/itsdm/
NeedsCompilation: no
Language: en-US
Materials: README NEWS
CRAN checks: itsdm results

Documentation:

Reference manual: itsdm.pdf
Vignettes: Introduction of itsdm with a virtual species
Using itsdm to a real species: Africa savanna elephant

Downloads:

Package source: itsdm_0.1.3.tar.gz
Windows binaries: r-devel: itsdm_0.1.3.zip, r-release: itsdm_0.1.3.zip, r-oldrel: itsdm_0.1.3.zip
macOS binaries: r-release (arm64): itsdm_0.1.3.tgz, r-oldrel (arm64): itsdm_0.1.3.tgz, r-release (x86_64): itsdm_0.1.3.tgz, r-oldrel (x86_64): itsdm_0.1.3.tgz
Old sources: itsdm archive

Linking:

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