{ "_id": "6a1f0b79b401979e7341c789", "Package": "PointedSDMs", "Type": "Package", "Title": "Fit Models Derived from Point Processes to Species Distributions\nusing 'inlabru'", "Version": "2.1.4", "Authors@R": "c(\nperson(given = \"Philip\", family = \"Mostert\", email = \"philip.s.mostert@ntnu.no\",\nrole = c(\"aut\", \"cre\")),\nperson(given = \"Bob\", family = \"O'hara\", email = \"bob.ohara@ntnu.no\",\nrole = c(\"aut\")))", "Maintainer": "Philip Mostert ", "URL": "https://github.com/PhilipMostert/PointedSDMs", "BugReports": "https://github.com/PhilipMostert/PointedSDMs/issues", "Description": "Integrated species distribution modeling is a rising field\nin quantitative ecology thanks to significant rises in the\nquantity of data available, increases in computational speed\nand the proven benefits of using such models. Despite this, the\ngeneral software to help ecologists construct such models in an\neasy-to-use framework is lacking. We therefore introduce the R\npackage 'PointedSDMs': which provides the tools to help\necologists set up integrated models and perform inference on\nthem. There are also functions within the package to help run\nspatial cross-validation for model selection, as well as\ngeneric plotting and predicting functions. An introduction to\nthese methods is discussed in Issac, Jarzyna, Keil, Dambly,\nBoersch-Supan, Browning, Freeman, Golding, Guillera-Arroita,\nHenrys, Jarvis, Lahoz-Monfort, Pagel, Pescott, Schmucki,\nSimmonds and O’Hara (2020) .", "Additional_repositories": "https://inla.r-inla-download.org/R/testing", "RoxygenNote": "7.3.2", "License": "GPL (>= 3)", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "LazyData": "false", "Encoding": "UTF-8", "Config/pak/sysreqs": "libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev\nlibssl-dev libproj-dev libsqlite3-dev libudunits2-dev", "Repository": "https://philipmostert.r-universe.dev", "Date/Publication": "2026-01-30 11:39:34 UTC", "RemoteUrl": "https://github.com/philipmostert/pointedsdms", "RemoteRef": "HEAD", "RemoteSha": "9a15462f20626bad93bfa79bc136305d5f01581f", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-17 09:47:35 UTC", "User": "root" }, "Author": "Philip Mostert [aut, cre],\nBob O'hara [aut]", "MD5sum": 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"uuid": 81858712, "type": "user", "name": "Philip Mostert" }, "_downloads": { "count": 240, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/PointedSDMs" }, "_devurl": "https://github.com/philipmostert/pointedsdms", "_searchresults": 61, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/PointedSDMs.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/philipmostert/pointedsdms", "_realowner": "philipmostert", "_cranurl": true, "_releases": [ { "version": "1.0.5", "date": "2022-06-14" }, { "version": "1.0.6", "date": "2022-06-15" }, { "version": "1.1.0", "date": "2022-08-31" }, { "version": "1.1.1", "date": "2022-09-05" }, { "version": "1.2.0", "date": "2023-01-16" }, { "version": "1.2.1", "date": "2023-02-07" }, { "version": "1.3", "date": "2023-08-09" }, { "version": "1.3.1", "date": "2023-10-10" }, { "version": "1.3.2", "date": "2024-02-02" }, { "version": "2.1.0", "date": "2024-07-08" }, { "version": "2.1.2", "date": "2024-08-21" }, { "version": "2.1.3", "date": "2025-01-13" }, { "version": "2.1.4", "date": "2025-08-29" }, { "version": "2.1.5", "date": "2026-02-18" } ], "_exports": [ "blockedCV", "dataOrganize", "dataSet", "datasetOut", "fitISDM", "intModel", "nearestValue", "runModel", "specifyISDM", "specifyMarks", "specifySpecies", "startISDM", "startMarks", "startSpecies" ], "_datasets": [ { "name": "BBSColinusVirginianus", "title": "Dataset of Colinus Virginianus obtained from the North American Breeding Bird survey across Alabama state.", "object": "BBSColinusVirginianus", "file": "BBSColinusVirginianus.rda", "class": [ "sf", "tbl_df", "tbl", "data.frame" ], "fields": [ "Year", "Ntrials", "NPres", "geometry" ], "rows": 140, "table": true, "tojson": true }, { "name": "Koala", "title": "Dataset of Eucalyptus globulus (common name: blue gum) sightings collected across the Koala conservation reserve on Phillip island (Australia) between 1993 and 2004. Two marks are considered from this dataset: \"koala\" which describes the number of koala visits to each tree, and \"food\" which is some index of the palatability of the leaves.", "object": "Koala", "file": "Koala.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "SetophagaData", "title": "List of all data objects used for the Setophaga vignette.", "object": "SetophagaData", "file": "SetophagaData.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "SolitaryTinamou", "title": "List of all data objects used for the solitary tinamou vignette.", "object": "SolitaryTinamou", "file": "SolitaryTinamou.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "BBA", "title": "Dataset of setophaga caerulescens obtained from the Pennsylvania Atlas of Breeding Birds.", "topics": [ "BBA" ] }, { "page": "BBS", "title": "Dataset of setophaga caerulescens obtained from the North American Breeding Bird survey across Pennsylvania state.", "topics": [ "BBS" ] }, { "page": "BBSColinusVirginianus", "title": "Dataset of Colinus Virginianus obtained from the North American Breeding Bird survey across Alabama state.", "topics": [ "BBSColinusVirginianus" ] }, { "page": "blockedCV", "title": "_blockedCV_: run spatial blocked cross-validation on the integrated model.", "topics": [ "blockedCV" ] }, { "page": "blockedCV-class", "title": "Export class blockedCV", "topics": [ "blockedCV-class" ] }, { "page": "blockedCVpred-class", "title": "Export class blockedCVpred", "topics": [ "blockedCVpred-class" ] }, { "page": "bruSDM_predict-class", "title": "Export class predict_bru_sdm", "topics": [ "bruSDM_predict-class" ] }, { "page": "bruSDM-class", "title": "Export bru_sdm class", "topics": [ "bruSDM-class" ] }, { "page": "changeCoords", "title": "_changeCoords_: function used to change coordinate names.", "topics": [ "changeCoords" ] }, { "page": "checkCoords", "title": "_checkCoords_: function used to check coordinate names.", "topics": [ "checkCoords" ] }, { "page": "checkVar", "title": "_checkVar_: Function used to check variable names.", "topics": [ "checkVar" ] }, { "page": "data2ENV", "title": "_data2ENV_: function used to move objects from one environment to another.", "topics": [ "data2ENV" ] }, { "page": "dataOrganize", "title": "R6 class to assist in reformatting the data to be used in dataSDM.", "topics": [ "dataOrganize" ] }, { "page": "dataSet", "title": "Internal function used to standardize datasets, as well as assign metadata.", "topics": [ "dataSet" ] }, { "page": "datasetOut", "title": "_datasetOut_: function that removes a dataset out of the main model, and calculates some cross-validation score.", "topics": [ "datasetOut" ] }, { "page": "datasetOut-class", "title": "Export class bru_sdm_leave_one_out", "topics": [ "datasetOut-class" ] }, { "page": "eBird", "title": "data.frame object containing solitary tinamou observations from eBird", "topics": [ "eBird" ] }, { "page": "elev_raster", "title": "Raster object containing the elevation across Pennsylvania state.", "topics": [ "elev_raster" ] }, { "page": "fitISDM", "title": "_fitISDM_: function used to run the integrated model.", "topics": [ "fitISDM" ] }, { "page": "Gbif", "title": "data.frame object containing solitary tinamou observations from Gbif", "topics": [ "Gbif" ] }, { "page": "intModel", "title": "_intModel_: Function used to initialize the integrated species distribution model.", "topics": [ "intModel" ] }, { "page": "Koala", "title": "Dataset of Eucalyptus globulus (common name: blue gum) sightings collected across the Koala conservation reserve on Phillip island (Australia) between 1993 and 2004. Two marks are considered from this dataset: \"koala\" which describes the number of koala visits to each tree, and \"food\" which is some index of the palatability of the leaves.", "topics": [ "Koala" ] }, { "page": "makeFormulaComps", "title": "_makeFormulaComps_: function to make components for the covariate and bias Formulas.", "topics": [ "makeFormulaComps" ] }, { "page": "makeLhoods", "title": "_makeLhoods_: function to make likelihoods.", "topics": [ "makeLhoods" ] }, { "page": "modISDM_predict-class", "title": "Export class predict.modISDM", "topics": [ "modISDM_predict-class" ] }, { "page": "modISDM-class", "title": "Export modISDM class", "topics": [ "modISDM-class" ] }, { "page": "modMarks_predict-class", "title": "Export class predict_modMarks", "topics": [ "modMarks_predict-class" ] }, { "page": "modMarks-class", "title": "Export modMarks class", "topics": [ "modMarks-class" ] }, { "page": "modSpecies_predict-class", "title": "Export class predict_modSpecies", "topics": [ "modSpecies_predict-class" ] }, { "page": "modSpecies-class", "title": "Export modSpecies class", "topics": [ "modSpecies-class" ] }, { "page": "nameChanger", "title": "_nameChanger_: function to change a variable name.", "topics": [ "nameChanger" ] }, { "page": "nearestValue", "title": "nearestValue: Match species location data to environmental raster layers", "topics": [ "nearestValue" ] }, { "page": "NLCD_canopy_raster", "title": "Raster object containing the canopy cover across Pennsylvania state.", "topics": [ "NLCD_canopy_raster" ] }, { "page": "Parks", "title": "data.frame object containing solitary tinamou observations from Parks", "topics": [ "Parks" ] }, { "page": "plot", "title": "Generic plot function for 'predict_bru_sdm'.", "topics": [ "plot.bruSDM_predict", "plot.modISDM_predict", "plot.modMarks_predict", "plot.modSpecies_predict" ] }, { "page": "predict", "title": "Generic predict function for 'bru_SDM' objects.", "topics": [ "predict.bruSDM", "predict.modISDM", "predict.modMarks", "predict.modSpecies" ] }, { "page": "print.blockedCV", "title": "Print function for 'blockedCV'.", "topics": [ "print.blockedCV" ] }, { "page": "print.blockedCVpred", "title": "Print function for 'blockedCV'.", "topics": [ "print.blockedCVpred" ] }, { "page": "print.bruSDM", "title": "Generic print function for 'bruSDM'.", "topics": [ "print.bruSDM" ] }, { "page": "print.bruSDM_predict", "title": "Generic print function for 'bru_sdm_predict'.", "topics": [ "print.bruSDM_predict" ] }, { "page": "print.datasetOut", "title": "Generic print function for 'datasetOut'.", "topics": [ "print.datasetOut" ] }, { "page": "print.modISDM", "title": "Generic print function for 'modISDM'.", "topics": [ "print.modISDM" ] }, { "page": "print.modMarks", "title": "Generic print function for 'modMarks'.", "topics": [ "print.modMarks" ] }, { "page": "print.modSpecies", "title": "Generic print function for 'modSpecies'.", "topics": [ "print.modSpecies" ] }, { "page": "reduceComps", "title": "reduceComps: Reduce the components of the model.", "topics": [ "reduceComps" ] }, { "page": "region", "title": "sf object containing the boundary region for solitary tinamouc", "topics": [ "region" ] }, { "page": "removeFormula", "title": "removeFormula: Function to remove term from a formula.", "topics": [ "removeFormula" ] }, { "page": "runModel", "title": "_runModel_: function used to run the integrated model. Note that this function is depreciated, and will be removed in a later version of the package.", "topics": [ "runModel" ] }, { "page": "SetophagaData", "title": "List of all data objects used for the Setophaga vignette.", "topics": [ "SetophagaData" ] }, { "page": "SolitaryTinamou", "title": "List of all data objects used for the solitary tinamou vignette.", "topics": [ "SolitaryTinamou" ] }, { "page": "SolTinCovariates", "title": "spatRaster object containing covariate values", "topics": [ "SolTinCovariates" ] }, { "page": "specifyISDM", "title": "R6 class for creating a 'startISDM' object.", "topics": [ "specifyISDM" ] }, { "page": "specifyMarks", "title": "R6 class for creating a 'specifyMarks' object.", "topics": [ "specifyMarks" ] }, { "page": "specifySpecies", "title": "R6 class for creating a 'startSpecies' object.", "topics": [ "specifySpecies" ] }, { "page": "startISDM", "title": "_startISDM_: Function used to initialize the integrated species distribution model.", "topics": [ "startISDM" ] }, { "page": "startMarks", "title": "_startMarks_: Function used to initialize a marked-point process model.", "topics": [ "startMarks" ] }, { "page": "startSpecies", "title": "_startSpecies_: Function used to initialize a multi-species integrated species distribution model.", "topics": [ "startSpecies" ] }, { "page": "summary", "title": "Generic summary function for 'bruSDM'.", "topics": [ "summary.bruSDM", "summary.modISDM", "summary.modMarks", "summary.modSpecies" ] } ], "_readme": "https://github.com/philipmostert/pointedsdms/raw/HEAD/README.md", "_rundeps": [ "abind", "automap", "base64enc", "blockCV", "class", "classInt", "cli", "cowplot", "cpp11", "DBI", "dplyr", "e1071", "farver", "fmesher", "FNN", "generics", "ggplot2", "glue", "gstat", "gtable", "inlabru", "intervals", "isoband", "KernSmooth", "labeling", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "MatrixModels", "pillar", "pkgconfig", "plyr", "proxy", "R.devices", "R.methodsS3", "R.oo", "R.utils", 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