The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.

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>, Å 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: 0.2.1
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
DOI: 10.32614/CRAN.package.itsdm
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
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:

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

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.