Package: itsdm 0.2.1
Lei Song
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>, 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>.
Authors:
itsdm_0.2.1.tar.gz
itsdm_0.2.1.zip(r-4.5)itsdm_0.2.1.zip(r-4.4)itsdm_0.2.1.zip(r-4.3)
itsdm_0.2.1.tgz(r-4.4-any)itsdm_0.2.1.tgz(r-4.3-any)
itsdm_0.2.1.tar.gz(r-4.5-noble)itsdm_0.2.1.tar.gz(r-4.4-noble)
itsdm_0.2.1.tgz(r-4.4-emscripten)itsdm_0.2.1.tgz(r-4.3-emscripten)
itsdm.pdf |itsdm.html✨
itsdm/json (API)
NEWS
# Install 'itsdm' in R: |
install.packages('itsdm', repos = c('https://lleisong.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/lleisong/itsdm/issues
- mainland_africa - Boundary of mainland Africa
- occ_virtual_species - Occurrence dataset of a virtual species
isolation-forestoutlier-detectionpresence-onlymodelshapley-valuespecies-distribution-modelling
Last updated 1 years agofrom:14fb9c83b4. Checks:OK: 1 NOTE: 6. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 02 2024 |
R-4.5-win | NOTE | Nov 02 2024 |
R-4.5-linux | NOTE | Nov 02 2024 |
R-4.4-win | NOTE | Nov 02 2024 |
R-4.4-mac | NOTE | Nov 02 2024 |
R-4.3-win | NOTE | Nov 02 2024 |
R-4.3-mac | NOTE | Nov 02 2024 |
Exports:cmcc_bioclimconvert_to_padetect_envi_changedim_reduceevaluate_poformat_observationfuture_cmcc_bioclimfuture_worldclim2independent_responseisotree_pomarginal_responseprobabilityshap_dependenceshap_spatial_responsespatial_responsesuspicious_env_outliersvariable_analysisvariable_contribworldclim2
Dependencies:abindbackportscheckmateclassclassIntclicodetoolscolorspaceDBIdplyre1071fansifarverfastshapforeachgenericsggplot2gluegtableisobandisotreeiteratorsjsonliteKernSmoothlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellncdf4nlmeoutliertreepatchworkpillarpkgconfigproxyR6rasterRcerealRColorBrewerRcppRcppArmadillorlangROCits2scalessfspstarsstringistringrterratibbletidyselectunitsutf8vctrsviridisLitewithrwk
Applications of Shapley values on SDM explanation
Rendered fromshap_application.Rmd
usingknitr::rmarkdown_notangle
on Nov 02 2024.Last update: 2022-12-01
Started: 2022-12-01
Introduction of itsdm with a virtual species
Rendered fromintroduction_of_itsdm.Rmd
usingknitr::rmarkdown_notangle
on Nov 02 2024.Last update: 2022-11-16
Started: 2021-11-11
Using itsdm to a real species: Africa savanna elephant
Rendered fromitsdm_example.Rmd
usingknitr::rmarkdown_notangle
on Nov 02 2024.Last update: 2022-11-16
Started: 2022-01-03