{ "_id": "6a154da3acfb0bcc41d596b2", "Package": "intSDM", "Title": "Reproducible Integrated Species Distribution Models Across\nNorway using 'INLA'", "Description": "Integration of disparate datasets is needed in order to\nmake efficient use of all available data and thereby address\nthe issues currently threatening biodiversity. Data integration\nis a powerful modeling framework which allows us to combine\nthese datasets together into a single model, yet retain the\nstrengths of each individual dataset. We therefore introduce\nthe package, 'intSDM': an R package designed to help ecologists\ndevelop a reproducible workflow of integrated species\ndistribution models, using data both provided from the user as\nwell as data obtained freely online. An introduction to data\nintegration methods is discussed in Issac, Jarzyna, Keil,\nDambly, Boersch-Supan, Browning, Freeman, Golding,\nGuillera-Arroita, Henrys, Jarvis, Lahoz-Monfort, Pagel,\nPescott, Schmucki, Simmonds and O’Hara (2020)\n.", "Version": "2.1.1", "Authors@R": "c(person(given = \"Philip\",\nfamily = \"Mostert\",\nrole = c(\"aut\", \"cre\"),\nemail = \"philip.s.mostert@ntnu.no\"),\nperson(given = \"Angeline\",\nfamily = \"Bruls\",\nrole = c(\"aut\"),\nemail = \"angeline.bruls@ntnu.no\"),\nperson(given = \"Ragnhild\",\nfamily = \"{Bjørkås}\",\nrole = c(\"aut\"),\nemail = \"ragnhild.bjorkas@ntnu.no\"),\nperson(given = \"Wouter\",\nfamily = \"Koch\",\nrole = c(\"aut\"),\nemail = \"wouter.koch@artsdatabanken.no\"),\nperson(given = \"Ellen\",\nfamily = \"Martin\",\nrole = c(\"aut\"),\nemail = \"ellen.c.martin@ntnu.no\"))", "Additional_repositories": "https://inla.r-inla-download.org/R/testing/", "License": "GPL (>= 3)", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev\nmake libicu-dev libuv1-dev libxml2-dev libssl-dev libproj-dev\nlibsqlite3-dev libudunits2-dev", "Repository": "https://philipmostert.r-universe.dev", "Date/Publication": "2025-08-28 12:03:46 UTC", "RemoteUrl": "https://github.com/philipmostert/intsdm", "RemoteRef": "HEAD", "RemoteSha": "ee6bed0f22ef72be8b692b27b9b3e6b5011b1e86", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-26 07:30:33 UTC", "User": "root" }, "Author": "Philip Mostert [aut, cre],\nAngeline Bruls [aut],\nRagnhild {Bjørkås} [aut],\nWouter Koch [aut],\nEllen Martin [aut]", "Maintainer": "Philip Mostert ", "MD5sum": "b499997be85df6e4b9c82851413134c8", "_user": "philipmostert", "_type": "src", "_file": "intSDM_2.1.1.tar.gz", "_fileid": "5f2080156a27d5a0640d1f7f830f228aa4ca34412f3aca82799641d8fc2122bc", "_filesize": 224557, "_sha256": "5f2080156a27d5a0640d1f7f830f228aa4ca34412f3aca82799641d8fc2122bc", "_created": "2026-05-26T07:30:33.000Z", "_published": "2026-05-26T07:37:07.160Z", "_distro": "noble", "_jobs": [ { "job": 77827634942, "time": 333, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7211380127" }, { "job": 77827634902, "time": 289, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7211366999" }, { "job": 77827634889, "time": 277, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7211357053" }, { "job": 77827634852, "time": 221, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7211341034" }, { "job": 77826995330, "time": 259, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7211278421" }, { "job": 77827634909, "time": 168, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7211330963" }, { "job": 77827634890, "time": 242, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7211352978" }, { "job": 77827634971, "time": 256, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7211357257" }, { "job": 77827634928, "time": 236, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7211351006" } ], "_buildurl": "https://github.com/r-universe/philipmostert/actions/runs/26438528727", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/philipmostert/intsdm", "_commit": { "id": "ee6bed0f22ef72be8b692b27b9b3e6b5011b1e86", "author": "PhilipMostert ", "committer": "PhilipMostert ", "message": "Test updates related to PointedSDMs changes\n", "time": 1756382626 }, "_maintainer": { "name": "Philip Mostert", "email": "philip.s.mostert@ntnu.no", "login": "philipmostert", "description": "", "uuid": 81858712 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1", "role": "Depends" }, { "package": "ggplot2", "role": "Depends" }, { "package": "terra", "role": "Depends" }, { "package": "sf", "role": "Depends" }, { "package": "stats", "role": "Depends" }, { "package": "PointedSDMs", "version": ">= 2.1.0", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "R6", "role": "Imports" }, { "package": "geodata", "role": "Imports" }, { "package": "fmesher", "role": "Imports" }, { "package": "inlabru", "version": ">= 2.3.1", "role": "Imports" }, { "package": "giscoR", "role": "Imports" }, { "package": "blockCV", "role": "Imports" }, { "package": "rgbif", "role": "Imports" }, { "package": "tidyterra", "role": "Imports" }, { "package": "units", "role": "Imports" }, { "package": "viridis", "role": "Suggests" }, { "package": "INLA", "version": ">= 21.08.31", "role": "Suggests" }, { "package": "sn", "role": "Suggests" }, { "package": "R.utils", "role": "Suggests" }, { "package": "lwgeom", "role": "Suggests" }, { "package": "spatstat", "role": "Suggests" }, { "package": "RColorBrewer", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "philipmostert", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-35", "n": 4 } ], "_tags": [], "_stars": 7, "_contributors": [ { "user": "philipmostert", "count": 367, "uuid": 81858712 }, { "user": "finnlindgren", "count": 2, "uuid": 7162803 } ], "_userbio": { "uuid": 81858712, "type": "user", "name": "Philip Mostert" }, "_downloads": { "count": 511, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/intSDM" }, "_devurl": "https://github.com/philipmostert/intsdm", "_searchresults": 25, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/intSDM.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/philipmostert/intsdm", "_realowner": "philipmostert", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2022-08-30" }, { "version": "1.0.5", "date": "2023-02-17" }, { "version": "2.0.0", "date": "2023-08-17" }, { "version": "2.0.1", "date": "2023-10-11" }, { "version": "2.0.2", "date": "2023-10-20" }, { "version": "2.1.0", "date": "2024-08-21" }, { "version": "2.1.1", "date": "2025-01-13" }, { "version": "2.1.2", "date": "2025-09-04" } ], "_exports": [ "obtainRichness", "sdmWorkflow", "species_model", "startWorkflow" ], "_help": [ { "page": "formatStructured", "title": "formatStructured: Function to add structured data into the workflow.", "topics": [ "formatStructured" ] }, { "page": "generateAbsences", "title": "Function to generate absences for data that comes from checklist data.", "topics": [ "generateAbsences" ] }, { "page": "initValues", "title": "'initValues': Function to obtain initial values from a 'intModel' object.", "topics": [ "initValues" ] }, { "page": "obtainArea", "title": "obtainArea: Function to obtain a boundry for a specified country.", "topics": [ "obtainArea" ] }, { "page": "obtainCovariate", "title": "obtainCovariate: Function to obtain a covariate later for a specified country.", "topics": [ "obtainCovariate" ] }, { "page": "obtainGBIF", "title": "obtainGBIF: Function to obtain occurrence data from GBIF.", "topics": [ "obtainGBIF" ] }, { "page": "obtainRichness", "title": "'obtainRichness': Function to obtain richness estimates from a 'fitISDM' object.", "topics": [ "obtainRichness" ] }, { "page": "sdmWorkflow", "title": "'sdmWorkflow': Function to compile the reproducible workflow.", "topics": [ "sdmWorkflow" ] }, { "page": "species_model", "title": "R6 class for creating a 'species_model' object.", "topics": [ "species_model" ] }, { "page": "startWorkflow", "title": "'startWorkflow': function to commence the integrated species distribution model workflow.", "topics": [ "startWorkflow" ] } ], "_readme": "https://github.com/philipmostert/intsdm/raw/HEAD/README.md", "_rundeps": [ "abind", "askpass", "automap", "base64enc", "blockCV", "brio", "callr", "class", "classInt", "cli", "countrycode", "cowplot", "cpp11", "crayon", "crul", "curl", "data.table", "DBI", "desc", "diffobj", "dplyr", "e1071", "evaluate", "farver", "fmesher", "FNN", "fs", "generics", "geodata", "ggplot2", "giscoR", "glue", "gstat", "gtable", "httpcode", "httr", "httr2", "inlabru", "intervals", "isoband", "jsonlite", "KernSmooth", "labeling", "lattice", "lazyeval", "lifecycle", "magrittr", "MASS", "Matrix", "MatrixModels", "mime", "oai", "openssl", "pillar", "pkgbuild", "pkgconfig", "pkgload", "plyr", "PointedSDMs", "praise", "processx", "proxy", "ps", "purrr", "R.devices", "R.methodsS3", "R.oo", "R.utils", "R6", "rappdirs", "raster", "RColorBrewer", "Rcpp", "reshape", "rgbif", "rlang", "rprojroot", "s2", "S7", "scales", "sf", "sftime", "sp", "spacetime", "splancs", "stars", "stringi", "stringr", "sys", "terra", "testthat", "tibble", "tidyr", "tidyselect", "tidyterra", "triebeard", "units", "urltools", "utf8", "vctrs", "viridisLite", "waldo", "whisker", "withr", "wk", "xml2", "xts", "zoo" ], "_vignettes": [ { "source": "RedList.Rmd", "filename": "RedList.html", "title": "intSDM: R package to produce species distribution models in a reproducible framework", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Workflow setup", "Select area", "Adding occurrence data", "Adding covariate data", "Metadata", "Creating an fm_mesh_2d object", "Specify priors", "Bias field", "Model options", "Running workflow", "Maps" ], "created": "2023-06-06 08:57:03", "modified": "2025-01-13 14:00:26", "commits": 20 }, { "source": "PennsylvaniaWarbler.Rmd", "filename": "PennsylvaniaWarbler.html", "title": "Building a worklfow for Warblers acorss Pennsylvania state", "engine": "knitr::rmarkdown", "headings": [], "created": "2023-09-15 10:31:47", "modified": "2025-01-03 10:33:26", "commits": 7 }, { "source": "Richness.Rmd", "filename": "Richness.html", "title": "Species richness example", "engine": "knitr::rmarkdown", "headings": [], "created": "2024-06-21 14:39:24", "modified": "2024-08-20 13:20:34", "commits": 2 } ], "_score": 5.419129307741976, "_indexed": true, "_nocasepkg": "intsdm", "_universes": [ "philipmostert" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.1.1", "date": "2026-05-26T07:34:01.000Z", "distro": "noble", "commit": "ee6bed0f22ef72be8b692b27b9b3e6b5011b1e86", "fileid": "68378d658e28f1e3fe9bf1b62344dcbc13a12eee78b6a253cdd66cc1ad0765d0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/philipmostert/actions/runs/26438528727" }, { "r": "4.6.0", "os": "linux", "version": "2.1.1", "date": "2026-05-26T07:33:42.000Z", "distro": "noble", "commit": "ee6bed0f22ef72be8b692b27b9b3e6b5011b1e86", "fileid": "96461e11e55e986f973cb2407fe77ff6cef17e9e2ee08528d5263f6bce40393f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/philipmostert/actions/runs/26438528727" }, { "r": "4.5.3", "os": "mac", "version": "2.1.1", "date": "2026-05-26T07:33:38.000Z", "commit": "ee6bed0f22ef72be8b692b27b9b3e6b5011b1e86", "fileid": "4b2b69b888d6b73a75e5a7e78c933be12def7461343c0387618a14702e77ed6e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/philipmostert/actions/runs/26438528727" }, { "r": "4.6.0", "os": "mac", "version": "2.1.1", "date": "2026-05-26T07:32:59.000Z", "commit": "ee6bed0f22ef72be8b692b27b9b3e6b5011b1e86", "fileid": "2d09b536cc093a0f40972d16cfc92baf0a35c11f62a6735a7cefad678b41f6ff", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/philipmostert/actions/runs/26438528727" }, { "r": "4.6.0", "os": "wasm", "version": "2.1.1", "date": "2026-05-26T07:33:55.000Z", "commit": "ee6bed0f22ef72be8b692b27b9b3e6b5011b1e86", "fileid": "a6abc8983a04039234e137a084ecea62e58f641268de3c4a3e29325ab6d05cda", "status": "success", "buildurl": "https://github.com/r-universe/philipmostert/actions/runs/26438528727" }, { "r": "4.7.0", "os": "win", "version": "2.1.1", "date": "2026-05-26T07:32:18.000Z", "commit": "ee6bed0f22ef72be8b692b27b9b3e6b5011b1e86", "fileid": "041966142a5b8a6cc8e97da7c52211e10b5a766ac77c96dfe2836f79fb9f7c63", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/philipmostert/actions/runs/26438528727" }, { "r": "4.5.3", "os": "win", "version": "2.1.1", "date": "2026-05-26T07:32:33.000Z", "commit": "ee6bed0f22ef72be8b692b27b9b3e6b5011b1e86", "fileid": "907e35d82d59469adcd7505fdf5f28032f353b7771df7f0b7b9a54c01a7d74c7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/philipmostert/actions/runs/26438528727" }, { "r": "4.6.0", "os": "win", "version": "2.1.1", "date": "2026-05-26T07:32:24.000Z", "commit": "ee6bed0f22ef72be8b692b27b9b3e6b5011b1e86", "fileid": "7062a4a194a9678043ca49bd8204ef55d0ee1fb8d00a0c1caa950f62f27d9255", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/philipmostert/actions/runs/26438528727" } ] }