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) <doi:10.48550/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>, Štrumbelj, 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: | 0.2.1 |
| Depends: | R (≥ 3.5.0) |
| Imports: | checkmate, dplyr, fastshap, ggplot2, isotree, methods, mgcv, ncdf4, outliertree, patchwork, raster, rlang, ROCit, sf, stars (≥ 0.6-0), stats, stringr, tidyselect, utils |
| Suggests: | knitr, rmarkdown |
| Published: | 2023-06-11 |
| Author: | Lei Song  [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 Applications of Shapley values on SDM explanation |
Downloads:
| Package source: | itsdm_0.2.1.tar.gz |
| Windows binaries: | r-devel: itsdm_0.2.1.zip, r-release: itsdm_0.2.1.zip, r-oldrel: itsdm_0.2.1.zip |
| macOS binaries: | r-release (arm64): itsdm_0.2.1.tgz, r-oldrel (arm64): itsdm_0.2.1.tgz, r-release (x86_64): itsdm_0.2.1.tgz, r-oldrel (x86_64): itsdm_0.2.1.tgz |
| Old sources: | itsdm archive |
Linking:
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