{ "_id": "6a103b63acfb0bcc41c9b791", "Package": "S4DM", "Title": "Small Sample Size Species Distribution Modeling", "Version": "0.0.3", "Authors@R": "c(\nperson(given = \"Brian S.\",\nfamily = \"Maitner\",\nrole = c(\"aut\", \"cre\"),\nemail = \"bmaitner@usf.edu\",\ncomment = c(ORCID = \"https://orcid.org/0000-0002-2118-9880\")),\nperson(given = \"Robert L.\",\nfamily = \"Richards\",\nrole = c(\"aut\"),\nemail = \"r.richards@gatech.edu\"),\nperson(given = \"Ben S.\",\nfamily = \"Carlson\",\nrole = c(\"aut\"),\nemail = \"ben.s.carlson@gmail.com\"),\nperson(given = \"John M.\",\nfamily = \"Drake\",\nrole = c(\"aut\"),\nemail = \"john@drakeresearchlab.com\"),\nperson(given = \"Cory\",\nfamily = \"Merow\",\nrole = c(\"aut\"),\nemail = \"cory.merow@gmail.com\")\n)", "Description": "Implements a set of distribution modeling methods that are\nsuited to species with small sample sizes (e.g., poorly sampled\nspecies or rare species). While these methods can also be used\non well-sampled taxa, they are united by the fact that they can\nbe utilized with relatively few data points. More details on\nthe currently implemented methodologies can be found in Maitner\net al. (2026) , Drake and Richards\n(2018) , Drake (2015)\n, and Drake (2014)\n.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "VignetteBuilder": "knitr", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "RdMacros": "Rdpack", "Config/pak/sysreqs": "libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev\nmake libssl-dev libproj-dev libsqlite3-dev libudunits2-dev", "Repository": "https://bmaitner.r-universe.dev", "Date/Publication": "2026-05-11 13:41:37 UTC", "RemoteUrl": "https://github.com/bmaitner/s4dm", "RemoteRef": "HEAD", "RemoteSha": "0522870c53d59c4ff1522ded29a053f7ce26c502", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-11 13:55:03 UTC", "User": "root" }, "Author": "Brian S. Maitner [aut, cre] (ORCID:\n),\nRobert L. Richards [aut],\nBen S. Carlson [aut],\nJohn M. Drake [aut],\nCory Merow [aut]", "Maintainer": "Brian S. Maitner ", "MD5sum": "1170de31324fa0319622b83c5ad89c87", "_user": "bmaitner", "_type": "src", "_file": "S4DM_0.0.3.tar.gz", "_fileid": "c098bedad2a4419e326471b8212eae6b9bde9ff0c976e26587b7a709e71a4b33", "_filesize": 599575, "_sha256": "c098bedad2a4419e326471b8212eae6b9bde9ff0c976e26587b7a709e71a4b33", "_created": "2026-05-11T13:55:03.000Z", "_published": "2026-05-22T11:17:55.494Z", "_distro": "noble", "_jobs": [ { "job": 77368805555, "time": 397, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "6920540566" }, { "job": 77368805578, "time": 357, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6920524002" }, { "job": 77368805488, "time": 239, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "6920482944" }, { "job": 77368805467, "time": 212, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "6920466433" }, { "job": 77368805307, "time": 297, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6920368017" }, { "job": 77368805013, "time": 171, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7159212237" }, { "job": 77368805386, "time": 895, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "6920719425" }, { "job": 77368806098, "time": 785, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "6920679884" }, { "job": 77368805705, "time": 393, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "6920535838" } ], "_buildurl": "https://github.com/r-universe/bmaitner/actions/runs/25674331688", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bmaitner/s4dm", "_commit": { "id": "0522870c53d59c4ff1522ded29a053f7ce26c502", "author": "Brian Maitner ", "committer": "Brian Maitner ", "message": "incremented version in anticipation of future development\n", "time": 1778506897 }, "_maintainer": { "name": "Brian S. Maitner", "email": "bmaitner@usf.edu", "login": "bmaitner", "orcid": "0000-0002-2118-9880", "uuid": 11130881 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "corpcor", "role": "Imports" }, { "package": "densratio", "version": ">= 0.3.1", "role": "Imports" }, { "package": "flexclust", "role": "Imports" }, { "package": "geometry", "role": "Imports" }, { "package": "kernlab", "role": "Imports" }, { "package": "maxnet", "role": "Imports" }, { "package": "mvtnorm", "role": "Imports" }, { "package": "np", "role": "Imports" }, { "package": "pROC", "role": "Imports" }, { "package": "robust", "role": "Imports" }, { "package": "rvinecopulib", "role": "Imports" }, { "package": "sf", "role": "Imports" }, { "package": "terra", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "Rdpack", "role": "Imports" }, { "package": "geodata", "role": "Suggests" }, { "package": "BIEN", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "tidyterra", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bmaitner", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-19", "n": 17 }, { "week": "2026-20", "n": 1 } ], "_tags": [ { "name": "v0.0.2", "date": "2026-05-09" } ], "_topics": [ "open-science", "range-modelling", "rare-species", "species-distribution-modeling", "species-distribution-modelling" ], "_stars": 4, "_contributors": [ { "user": "bmaitner", "count": 128, "uuid": 11130881 } ], "_userbio": { "uuid": 11130881, "type": "user", "name": "Brian Maitner" }, "_downloads": { "count": 183, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/S4DM" }, "_devurl": "https://github.com/bmaitner/s4dm", "_searchresults": 44, "_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/readme.html", "extra/readme.md", "extra/S4DM.html", "manual.pdf" ], "_homeurl": "https://github.com/bmaitner/s4dm", "_realowner": "bmaitner", "_cranurl": true, "_releases": [ { "version": "0.0.1", "date": "2025-01-10" }, { "version": "0.0.2", "date": "2026-05-11" } ], "_exports": [ "ensemble_range_map", "evaluate_range_map", "fit_density_ratio", "fit_plug_and_play", "get_env_bg", "get_env_pres", "make_range_map", "project_density_ratio", "project_plug_and_play", "sdm_threshold", "stratify_random", "stratify_spatial" ], "_datasets": [ { "name": "sample_points", "title": "Example S4DM occurrence data", "object": "sample_points", "class": [ "data.frame" ], "fields": [ "longitude", "latitude" ], "rows": 65, "table": true, "tojson": true } ], "_help": [ { "page": "ensemble_range_map", "title": "Generate ensemble predictions from S4DM range maps", "topics": [ "ensemble_range_map" ] }, { "page": "evaluate_range_map", "title": "Evaluate S4DM range map quality", "topics": [ "evaluate_range_map" ] }, { "page": "fit_density_ratio", "title": "Fit density-ratio distribution models in a plug-and-play framework.", "topics": [ "fit_density_ratio" ] }, { "page": "fit_plug_and_play", "title": "Fit presence-background distribution models in a plug-and-play framework.", "topics": [ "fit_plug_and_play" ] }, { "page": "get_env_bg", "title": "Extract background data for SDM fitting.", "topics": [ "get_env_bg" ] }, { "page": "get_env_pres", "title": "Extract presence data for SDM fitting.", "topics": [ "get_env_pres" ] }, { "page": "get_response_curves", "title": "Generate Response Curves", "topics": [ "get_response_curves" ] }, { "page": "make_range_map", "title": "Make a range map using plug-and-play modeling.", "topics": [ "make_range_map" ] }, { "page": "project_density_ratio", "title": "Projects fitted density-ratio distribution models onto new covariates.", "topics": [ "project_density_ratio" ] }, { "page": "project_plug_and_play", "title": "Projects fitted plug-and-play distribution models onto new covariates.", "topics": [ "project_plug_and_play" ] }, { "page": "sample_points", "title": "Example S4DM occurrence data", "topics": [ "sample_points" ] }, { "page": "sdm_threshold", "title": "Thresholds a continuous relative occurrence rate raster to create a binary raster.", "topics": [ "sdm_threshold" ] }, { "page": "stratify_random", "title": "Split data for k-fold spatially stratified cross validation", "topics": [ "stratify_random" ] }, { "page": "stratify_spatial", "title": "Split data for k-fold spatially stratified cross validation", "topics": [ "stratify_spatial" ] } ], "_readme": "https://github.com/bmaitner/s4dm/raw/HEAD/README.md", "_rundeps": [ "abind", "assertthat", "BH", "boot", "class", "classInt", "cli", "codetools", "corpcor", "cubature", "DBI", "densratio", "DEoptimR", "dplyr", "e1071", "fit.models", "flexclust", "foreach", "generics", "geometry", "glmnet", "glue", "iterators", "kde1d", "kernlab", "KernSmooth", "lattice", "lifecycle", "linprog", "lpSolve", "magic", "magrittr", "MASS", "Matrix", "MatrixModels", "maxnet", "modeltools", "mvtnorm", "np", "pcaPP", "pillar", "pkgconfig", "pROC", "proxy", "quadprog", "quantreg", "R6", "randtoolbox", "rbibutils", "Rcpp", "RcppEigen", "RcppProgress", "RcppThread", "Rdpack", "rlang", "rngWELL", "robust", "robustbase", "rrcov", "rvinecopulib", "s2", "sf", "shape", "SparseM", "survival", "terra", "tibble", "tidyselect", "units", "utf8", "vctrs", "wdm", "withr", "wk" ], "_vignettes": [ { "source": "S4DM.Rmd", "filename": "S4DM.html", "title": "S4DM R package", "author": "Brian Maitner", "engine": "knitr::rmarkdown", "headings": [ "Plug-and-play models", "Density-ratio models", "Environmental-range models", "The S4DM package", "Obtaining Occurrence and Climate data", "Simplest case", "Working with model objects", "Flexibility", "ulsif", "Model Quality", "References" ], "created": "2024-12-16 16:12:49", "modified": "2024-12-26 19:42:41", "commits": 2 } ], "_score": 5.24551266781415, "_indexed": true, "_nocasepkg": "s4dm", "_universes": [ "bmaitner" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.0.3", "date": "2026-05-11T13:58:30.000Z", "distro": "noble", "commit": "0522870c53d59c4ff1522ded29a053f7ce26c502", "fileid": "0e2d6d764e0428cf7c3e04df0a6430679245d511d2558b6da06eceebf6440deb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bmaitner/actions/runs/25674331688" }, { "r": "4.6.0", "os": "linux", "version": "0.0.3", "date": "2026-05-11T13:58:16.000Z", "distro": "noble", "commit": "0522870c53d59c4ff1522ded29a053f7ce26c502", "fileid": "24c2f3bb3bb0f09968610283688b48938b1bc3bbb0c1fa22f24ccae9ff1dc0d6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bmaitner/actions/runs/25674331688" }, { "r": "4.5.3", "os": "mac", "version": "0.0.3", "date": "2026-05-11T13:57:36.000Z", "commit": "0522870c53d59c4ff1522ded29a053f7ce26c502", "fileid": "4702eaaded14ac782590a71bb07eff7f3d1a9e6aa683c162ecbe6af09bb92f7b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bmaitner/actions/runs/25674331688" }, { "r": "4.6.0", "os": "mac", "version": "0.0.3", "date": "2026-05-11T13:57:07.000Z", "commit": "0522870c53d59c4ff1522ded29a053f7ce26c502", "fileid": "53f7f825449c0ab0703f9b600b963174ca2b19eb2db76d039e2ce98b5a9d12d1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bmaitner/actions/runs/25674331688" }, { "r": "4.7.0", "os": "win", "version": "0.0.3", "date": "2026-05-11T14:05:28.000Z", "commit": "0522870c53d59c4ff1522ded29a053f7ce26c502", "fileid": "1f2e81735d074703d95a31b69b5760e079d95313708d22fce35aa586e85b2b2c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bmaitner/actions/runs/25674331688" }, { "r": "4.5.3", "os": "win", "version": "0.0.3", "date": "2026-05-11T14:04:31.000Z", "commit": "0522870c53d59c4ff1522ded29a053f7ce26c502", "fileid": "d43e11a124e162e4f54231ac0b5400c1d0517d49775a1026f9718ac33d3c3c2d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bmaitner/actions/runs/25674331688" }, { "r": "4.6.0", "os": "win", "version": "0.0.3", "date": "2026-05-11T13:57:47.000Z", "commit": "0522870c53d59c4ff1522ded29a053f7ce26c502", "fileid": "b86155957a917694bcb0e09dbbd515240bbac8dacdc39769dafbbd57d4707897", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bmaitner/actions/runs/25674331688" }, { "r": "4.6.0", "os": "wasm", "version": "0.0.3", "date": "2026-05-22T11:17:33.000Z", "commit": "0522870c53d59c4ff1522ded29a053f7ce26c502", "fileid": "27ad43546df9e7842cd1ec0ad93c3c6bd146b5e5481a1ed5f629b5a5a65dab71", "status": "success", "buildurl": "https://github.com/r-universe/bmaitner/actions/runs/25674331688" } ] }