{ "_id": "6a169542acfb0bcc41d7aeb3", "Type": "Package", "Package": "itsdm", "Title": "Isolation Forest-Based Presence-Only Species Distribution\nModeling", "Version": "0.2.2", "Authors@R": "c(\nperson(\"Lei\", \"Song\", , \"lsong@clarku.edu\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-4371-1473\")),\nperson(\"Lyndon\", \"Estes\", , \"lestes@clarku.edu\", role = \"ths\")\n)", "Description": "Collection of R functions to do purely presence-only\nspecies distribution modeling with isolation forest (iForest)\nand its variations such as Extended isolation forest and\nSCiForest. See the details of these methods in references: Liu,\nF.T., Ting, K.M. and Zhou, Z.H. (2008)\n, Hariri, S., Kind, M.C. and Brunner,\nR.J. (2019) , Liu, F.T., Ting,\nK.M. and Zhou, Z.H. (2010) ,\nGuha, S., Mishra, N., Roy, G. and Schrijvers, O. (2016)\n, Cortes, D.\n(2021) . Additionally, Shapley\nvalues are used to explain model inputs and outputs. See\ndetails in references: Shapley, L.S. (1953)\n, Lundberg, S.M. and Lee, S.I.\n(2017)\n,\nMolnar, C. (2020) , Štrumbelj, E. and\nKononenko, I. (2014) . itsdm\nalso provides functions to diagnose variable response, analyze\nvariable importance, draw spatial dependence of variables and\nexamine variable contribution. As utilities, the package\nincludes a few functions to download bioclimatic variables\nincluding 'WorldClim' version 2.0 (see Fick, S.E. and Hijmans,\nR.J. (2017) ) and 'CMCC-BioClimInd' (see\nNoce, S., Caporaso, L. and Santini, M. (2020)\n.", "License": "MIT + file LICENSE", "URL": "https://github.com/LLeiSong/itsdm,\nhttps://lleisong.github.io/itsdm/", "BugReports": "https://github.com/LLeiSong/itsdm/issues", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "Language": "en-US", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "Config/pak/sysreqs": "libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev\nlibicu-dev libnetcdf-dev libssl-dev libproj-dev libsqlite3-dev\nlibudunits2-dev", "Repository": "https://lleisong.r-universe.dev", "Date/Publication": "2025-07-01 22:51:54 UTC", "RemoteUrl": "https://github.com/lleisong/itsdm", "RemoteRef": "HEAD", "RemoteSha": "cb8625f1d4ed466c0a99743b6e0651697a403a38", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-27 06:47:19 UTC", "User": "root" }, "Author": "Lei Song [aut, cre] (ORCID: ),\nLyndon Estes [ths]", "Maintainer": "Lei Song ", "MD5sum": "cd5cbe541ea277662e5cb64beca3c329", "_user": "lleisong", "_type": "src", "_file": 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"_updates": [ { "week": "2025-27", "n": 3 } ], "_tags": [], "_topics": [ "isolation-forest", "outlier-detection", "presence-onlymodel", "shapley-value", "species-distribution-modelling" ], "_stars": 5, "_contributors": [ { "user": "lleisong", "count": 6, "uuid": 10140848 }, { "user": "david-cortes", "count": 1, "uuid": 11860098 } ], "_userbio": { "uuid": 10140848, "type": "user", "name": "Lei Song", "description": "Assistant professor of Geography" }, "_downloads": { "count": 175, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/itsdm" }, "_devurl": "https://github.com/lleisong/itsdm", "_pkgdown": "https://lleisong.github.io/itsdm/", "_searchresults": 65, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/itsdm.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/lleisong/itsdm", "_realowner": "lleisong", "_cranurl": true, "_releases": [ { "version": "0.1.0", "date": "2022-01-07" }, { "version": "0.1.1", "date": "2022-01-12" }, { "version": "0.1.2", "date": "2022-06-20" }, { "version": "0.1.3", "date": "2022-09-11" }, { "version": "0.2.0", "date": "2023-01-15" }, { "version": "0.2.1", "date": "2023-06-11" }, { "version": "0.2.2", "date": "2025-07-01" } ], "_exports": [ "cmcc_bioclim", "convert_to_pa", "detect_envi_change", "dim_reduce", "evaluate_po", "format_observation", "future_cmcc_bioclim", "future_worldclim2", "independent_response", "isotree_po", "marginal_response", "probability", "shap_dependence", "shap_spatial_response", "spatial_response", "suspicious_env_outliers", "variable_analysis", "variable_contrib", "worldclim2" ], "_datasets": [ { "name": "mainland_africa", "title": "Boundary of mainland Africa", "object": "mainland_africa", "class": [ "sf", "data.frame" ], "fields": [ "name", "area", "geometry" ], "rows": 1, "table": false, "tojson": false }, { "name": "occ_virtual_species", "title": "Occurrence dataset of a virtual species", "object": "occ_virtual_species", "class": [ "data.frame" ], "fields": [ "x", "y", "observation", "usage" ], "rows": 500, "table": true, "tojson": true } ], "_help": [ { "page": "itsdm-package", "title": "Isolation forest-based presence-only species distribution modeling", "topics": [ "itsdm-package", "itsdm" ] }, { "page": "cmcc_bioclim", "title": "Download historic Bioclimatic indicators (BIOs) named CMCC-BioClimInd.", "topics": [ "cmcc_bioclim" ] }, { "page": "convert_to_pa", "title": "Convert predicted suitability to presence-absence map.", "topics": [ "convert_to_pa" ] }, { "page": "detect_envi_change", "title": "Detect areas influenced by a changing environment variable.", "topics": [ "detect_envi_change" ] }, { "page": "dim_reduce", "title": "Remove environmental variables that have high correlation with others.", "topics": [ "dim_reduce" ] }, { "page": "evaluate_po", "title": "Evaluate the model based on presence-only data.", "topics": [ "evaluate_po" ] }, { "page": "format_observation", "title": "Format the occurrence dataset for usage in 'itsdm'", "topics": [ "format_observation" ] }, { "page": "future_cmcc_bioclim", "title": "Download future Bioclimatic indicators (BIOs) named CMCC-BioClimInd.", "topics": [ "future_cmcc_bioclim" ] }, { "page": "future_worldclim2", "title": "A function to parse the future climate from worldclim version 2.1.", "topics": [ "future_worldclim2" ] }, { "page": "independent_response", "title": "Calculate independent responses of each variables.", "topics": [ "independent_response" ] }, { "page": "isotree_po", "title": "Build Isolation forest species distribution model and explain the the model and outputs.", "topics": [ "isotree_po" ] }, { "page": "mainland_africa", "title": "Boundary of mainland Africa", "topics": [ "mainland_africa" ] }, { "page": "marginal_response", "title": "Calculate marginal responses of each variables.", "topics": [ "marginal_response" ] }, { "page": "occ_virtual_species", "title": "Occurrence dataset of a virtual species", "topics": [ "occ_virtual_species" ] }, { "page": "plot.EnviChange", "title": "Display the figure and map of the 'EnviChange' object.", "topics": [ "plot.EnviChange" ] }, { "page": "plot.EnvironmentalOutlier", "title": "Exhibit suspicious outliers in an observation dataset.", "topics": [ "plot.EnvironmentalOutlier" ] }, { "page": "plot.IndependentResponse", "title": "Show independent response curves.", "topics": [ "plot.IndependentResponse" ] }, { "page": "plot.MarginalResponse", "title": "Show marginal response curves.", "topics": [ "plot.MarginalResponse" ] }, { "page": "plot.PAConversion", "title": "Display results of conversion to presence-absence (PA).", "topics": [ "plot.PAConversion" ] }, { "page": "plot.POEvaluation", "title": "Show model evaluation.", "topics": [ "plot.POEvaluation" ] }, { "page": "plot.ShapDependence", "title": "Show variable dependence plots and variable interaction plots obtained from Shapley values.", "topics": [ "plot.ShapDependence" ] }, { "page": "plot.SHAPSpatial", "title": "Display Shapley values-based spatial variable dependence maps.", "topics": [ "plot.SHAPSpatial" ] }, { "page": "plot.SpatialResponse", "title": "Display spatial variable dependence maps.", "topics": [ "plot.SpatialResponse" ] }, { "page": "plot.VariableAnalysis", "title": "Display variable importance.", "topics": [ "plot.VariableAnalysis" ] }, { "page": "plot.VariableContribution", "title": "Exhibit variable contribution for target observations.", "topics": [ "plot.VariableContribution" ] }, { "page": "print.EnviChange", "title": "Print summary information from 'EnviChange' object.", "topics": [ "print.EnviChange" ] }, { "page": "print.EnvironmentalOutlier", "title": "Print summary information from 'EnvironmentalOutlier' object.", "topics": [ "print.EnvironmentalOutlier" ] }, { "page": "print.FormatOccurrence", "title": "Print summary information from 'FormatOccurrence' object.", "topics": [ "print.FormatOccurrence" ] }, { "page": "print.PAConversion", "title": "Print summary information from 'PAConversion' object.", "topics": [ "print.PAConversion" ] }, { "page": "print.POEvaluation", "title": "Print summary information from model evaluation object ('POEvaluation').", "topics": [ "print.POEvaluation" ] }, { "page": "print.POIsotree", "title": "Print summary information from 'POIsotree' object.", "topics": [ "print.POIsotree" ] }, { "page": "print.ReducedImageStack", "title": "Print summary information from 'ReducedImageStack' object.", "topics": [ "print.ReducedImageStack" ] }, { "page": "print.VariableAnalysis", "title": "Print summary information from variable importance object ('VariableAnalysis').", "topics": [ "print.VariableAnalysis" ] }, { "page": "probability", "title": "Estimate suitability on 'stars' object using trained 'isolation.forest' model.", "topics": [ "probability" ] }, { "page": "shap_dependence", "title": "Calculate Shapley value-based variable dependence.", "topics": [ "shap_dependence" ] }, { "page": "shap_spatial_response", "title": "Calculate shapley values-based spatial response.", "topics": [ "shap_spatial_response" ] }, { "page": "spatial_response", "title": "Calculate spatial response or dependence figures.", "topics": [ "spatial_response" ] }, { "page": "suspicious_env_outliers", "title": "Function to detect suspicious outliers based on environmental variables.", "topics": [ "suspicious_env_outliers" ] }, { "page": "variable_analysis", "title": "Function to evaluate relative importance of each variable.", "topics": [ "variable_analysis" ] }, { "page": "variable_contrib", "title": "Evaluate variable contributions for targeted observations.", "topics": [ "variable_contrib" ] }, { "page": "worldclim2", "title": "Download environmental variables made by worldclim version 2.1.", "topics": [ "worldclim2" ] } ], "_readme": "https://github.com/lleisong/itsdm/raw/HEAD/README.md", 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