{ "_id": "6a1eef75b401979e73412bc6", "Package": "epm", "Type": "Package", "Title": "EcoPhyloMapper", "Version": "1.1.6", "Authors@R": "c(\nperson(\"Pascal\", \"Title\", email = \"pascal.title@stonybrook.edu\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6316-0736\")),\nperson(\"Donald\", \"Swiderski\", role = \"aut\"),\nperson(\"Miriam\", \"Zelditch\", role = \"aut\"))", "Description": "Facilitates the aggregation of species' geographic ranges\nfrom vector or raster spatial data, and that enables the\ncalculation of various morphological and phylogenetic community\nmetrics across geography. Citation: Title, PO, DL Swiderski and\nML Zelditch (2022) .", "License": "GPL (>= 3)", "URL": "https://github.com/ptitle/epm", "BugReports": "https://github.com/ptitle/epm/issues", "NeedsCompilation": "yes", "LazyData": "true", "RoxygenNote": "7.3.2", "ByteCompile": "true", "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://ptitle.r-universe.dev", "Date/Publication": "2025-08-20 18:24:49 UTC", "RemoteUrl": "https://github.com/ptitle/epm", "RemoteRef": "HEAD", "RemoteSha": "cf3944fc03cdaf92bc5ce949dfb9bfb600f6523d", "Packaged": { "Date": "2026-05-19 08:36:33 UTC", "User": "root" }, "Author": "Pascal Title [aut, cre] (ORCID:\n),\nDonald Swiderski [aut],\nMiriam Zelditch [aut]", "Maintainer": "Pascal Title ", "MD5sum": "6a88e37edabe21d8e425c451b3f64b1f", "_user": "ptitle", "_type": "src", "_file": "epm_1.1.6.tar.gz", "_fileid": "03cd65d3fa7c9e11c4f1354df4f4e7eff7468562bcafc4137528a5cd88fbae03", "_filesize": 958538, "_sha256": "03cd65d3fa7c9e11c4f1354df4f4e7eff7468562bcafc4137528a5cd88fbae03", "_created": "2026-05-19T08:36:33.000Z", "_published": "2026-06-02T14:57:57.440Z", "_distro": "noble", "_jobs": [ { "job": 79101209887, "time": 170, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7078729555" }, { "job": 79101209751, "time": 177, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7078732163" }, { "job": 79101210545, "time": 167, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7078728693" }, { "job": 79101211209, "time": 178, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7078732160" }, { "job": 79101209068, "time": 222, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7078736379" }, { "job": 79101208898, "time": 290, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7078764025" }, { "job": 79101208781, "time": 175, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7078725115" }, { "job": 79101209558, "time": 277, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7078759645" }, { "job": 79101208471, "time": 224, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7078671462" }, { "job": 79101208123, "time": 134, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7361409245" }, { "job": 79101208760, "time": 186, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7078735342" }, { "job": 79101209463, "time": 134, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7078718456" }, { "job": 79101208965, "time": 153, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7078724473" } ], "_buildurl": "https://github.com/r-universe/ptitle/actions/runs/26085819836", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/ptitle/epm", "_commit": { "id": "cf3944fc03cdaf92bc5ce949dfb9bfb600f6523d", "author": "Pascal Title ", "committer": "Pascal Title ", "message": "two changes: search for empty geometries, and allow for single-species epmGrid objects\n", "time": 1755714289 }, "_maintainer": { "name": "Pascal Title", "email": "pascal.title@stonybrook.edu", "orcid": "0000-0002-6316-0736" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppProgress", "role": "LinkingTo" }, { "package": "terra", "version": ">= 1.5-21", "role": "Imports" }, { "package": "sf", "role": "Imports" }, { "package": "ape", "role": "Imports" }, { "package": "viridisLite", "role": "Imports" }, { "package": "pbapply", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "Rcpp", "version": ">= 0.12.9", "role": "Imports" }, { "package": "RcppProgress", "role": "Imports" }, { "package": "tmap", "role": "Suggests" }, { "package": "data.table", "role": "Suggests" }, { "package": "spdep", "role": "Suggests" }, { "package": "exactextractr", "role": "Suggests" } ], "_owner": "ptitle", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-23", "n": 1 }, { "week": "2025-34", "n": 1 } ], "_tags": [], "_stars": 16, "_contributors": [ { "user": "ptitle", "count": 141, "uuid": 5825910 } ], "_userbio": { "uuid": 5825910, "type": "user", "name": "ptitle" }, "_downloads": { "count": 292, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/epm" }, "_devurl": "https://github.com/ptitle/epm", "_searchresults": 18, "_topics": [ "cpp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/epm.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/ptitle/epm", "_realowner": "ptitle", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2022-05-17" }, { "version": "1.0.1", "date": "2022-05-19" }, { "version": "1.0.2", "date": "2022-06-22" }, { "version": "1.1.0", "date": "2022-08-08" }, { "version": "1.1.1", "date": "2023-03-03" }, { "version": "1.1.2", "date": "2023-12-19" }, { "version": "1.1.3", "date": "2024-09-13" }, { "version": "1.1.4", "date": "2025-02-14" }, { "version": "1.1.5", "date": "2025-07-03" }, { "version": "1.1.6", "date": "2025-08-20" } ], "_exports": [ "addLegend", "addPhylo", "addTraits", "betadiv_disparity", "betadiv_phylogenetic", "betadiv_taxonomic", "calcMeanShape", "coordsFromEpmGrid", "createEPMgrid", "customBetaDiv", "customGridMetric", "dropSpecies", "DRstat", "epmToPhyloComm", "expandSpeciesCellList", "extractFromEpmGrid", "faithPD", "generateOccurrenceMatrix", "getExtentOfList", "getMultiMapRamp", "getSpPartialDisparities", "gridMetrics", "identify.epmGrid", "interactiveExtent", "plot.epmGrid", "plotDispersionField", "plotSpRange", "rasterToGrid", "read.epmGrid", "reduceToCommonTaxa", "singleSpCellIndex", "spCountIndex", "summarizeEpmGridList", "tableFromEpmGrid", "write.epmGrid", "writeEpmSpatial" ], "_datasets": [ { "name": "tamiasEPM", "title": "Eco Phylo Mapper datasets", "object": "tamiasEPM", "class": [ "epmGrid" ], "fields": [], "table": false, "tojson": false }, { "name": "tamiasPolyList", "title": "Eco Phylo Mapper datasets", "object": "tamiasPolyList", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "tamiasTraits", "title": "Eco Phylo Mapper datasets", "object": "tamiasTraits", "class": [ "data.frame" ], "fields": [ "V2", "V3", "V4", "V5", "V6", "V7", "V8", "V9", "V10", "V11", "V12", "V13", "V14", "V15", "V16", "V17", "V18", "V19", "V20", "V21", "V22", "V23", "V24", "V25", "V26", "V27", "V28", "V29", "V30", "V31", "V32", "V33", "V34", "V35", "V36", "V37", "V38", "V39", "V40", "V41", "V42", "V43", "V44", "V45", "V46", "V47", "V48", "V49", "V50", "V51", "V52", "V53", "V54", "V55", "V56", "V57", "V58", "V59", "V60", "V61", "V62", "V63", "V64", "V65", "V66", "V67", "V68", "V69", "V70", "V71", "V72", "V73", "V74", "V75", "V76", "V77", "V78", "V79", "V80", "V81", "V82", "V83", "V84", "V85", "V86", "V87", "V88", "V89", "V90", "V91", "V92", "V93", "V94", "V95", "V96", "V97", "V98", "V99", "V100", "V101", "V102", "V103", "V104", "V105", "V106", "V107", "V108", "V109", "V110", "V111", "V112", "V113", "V114", "V115", "V116", "V117", "V118", "V119", "V120", "V121", "V122", "V123", "V124", "V125", "V126", "V127", "V128", "V129", "V130", "V131", "V132", "V133", "V134", "V135", "V136", "V137", "V138", "V139", "V140", "V141", "V142", "V143", "V144", "V145", "V146", "V147", "V148", "V149", "V150", "V151", "V152", "V153", "V154", "V155", "V156", "V157", "V158", "V159", "V160", "V161", "V162", "V163", "V164", "V165", "V166", "V167", "V168", "V169", "V170", "V171", "V172", "V173", "V174", "V175", "V176", "V177", "V178", "V179", "V180", "V181", "V182", "V183", "V184", "V185", "V186", "V187", "V188", "V189", "V190", "V191", "V192", "V193", "V194", "V195", "V196", "V197" ], "rows": 28, "table": true, "tojson": true }, { "name": "tamiasTree", "title": "Eco Phylo Mapper datasets", "object": "tamiasTree", "class": [ "phylo" ], "fields": [], "table": false, "tojson": false }, { "name": "tamiasTreeSet", "title": "Eco Phylo Mapper datasets", "object": "tamiasTreeSet", "class": [ "multiPhylo" ], "fields": [], "table": true, "tojson": false } ], "_help": [ { "page": "addLegend", "title": "addLegend", "topics": [ "addLegend" ] }, { "page": "addPhylo", "title": "addPhylo", "topics": [ "addPhylo" ] }, { "page": "addTraits", "title": "addTraits", "topics": [ "addTraits" ] }, { "page": "betadiv_disparity", "title": "Map change in morphological disparity", "topics": [ "betadiv_disparity" ] }, { "page": "betadiv_phylogenetic", "title": "Map phylogenetic turnover in species communities", "topics": [ "betadiv_phylogenetic" ] }, { "page": "betadiv_taxonomic", "title": "Map turnover in species communities", "topics": [ "betadiv_taxonomic" ] }, { "page": "calcMeanShape", "title": "Calculate mean shape per grid cell", "topics": [ "calcMeanShape" ] }, { "page": "coordsFromEpmGrid", "title": "Retrieve coordinates from epmGrid", "topics": [ "coordsFromEpmGrid" ] }, { "page": "createEPMgrid", "title": "Create epmGrid object", "topics": [ "createEPMgrid" ] }, { "page": "customBetaDiv", "title": "Custom beta diversity metrics", "topics": [ "customBetaDiv" ] }, { "page": "customGridMetric", "title": "Custom grid metrics", "topics": [ "customGridMetric" ] }, { "page": "dropSpecies", "title": "Drop species from epmGrid", "topics": [ "dropSpecies" ] }, { "page": "DRstat", "title": "Calculate the DR statistic", "topics": [ "DRstat" ] }, { "page": "epm", "title": "EcoPhyloMapper (epm)", "topics": [ "epm-package", "epm" ] }, { "page": "epm-example", "title": "Eco Phylo Mapper datasets", "topics": [ "epm-example", "tamiasEPM", "tamiasPolyList", "tamiasTraits", "tamiasTree", "tamiasTreeSet" ] }, { "page": "epmToPhyloComm", "title": "Convert epmGrid to community matrix", "topics": [ "epmToPhyloComm" ] }, { "page": "expandSpeciesCellList", "title": "Expand species list", "topics": [ "expandSpeciesCellList" ] }, { "page": "extractFromEpmGrid", "title": "Extract from epmGrid", "topics": [ "extractFromEpmGrid" ] }, { "page": "faithPD", "title": "Calculate Faith's Phylogenetic Diversity", "topics": [ "faithPD" ] }, { "page": "generateOccurrenceMatrix", "title": "Convert epmGrid to community matrix", "topics": [ "generateOccurrenceMatrix" ] }, { "page": "getExtentOfList", "title": "Get extent of list", "topics": [ "getExtentOfList" ] }, { "page": "getMultiMapRamp", "title": "Extract min and max for multiple epmGrids", "topics": [ "getMultiMapRamp" ] }, { "page": "getSpPartialDisparities", "title": "Partial Disparity", "topics": [ "getSpPartialDisparities" ] }, { "page": "gridMetrics", "title": "Grid Metrics", "topics": [ "gridMetrics" ] }, { "page": "identify", "title": "Interactively identify species in epmGrid", "topics": [ "identify.epmGrid" ] }, { "page": "interactiveExtent", "title": "Interactively choose extent", "topics": [ "interactiveExtent" ] }, { "page": "plot", "title": "Plot epmGrid", "topics": [ "plot.epmGrid" ] }, { "page": "plotDispersionField", "title": "Plot dispersion fields", "topics": [ "plotDispersionField" ] }, { "page": "plotSpRange", "title": "plot a single species' range", "topics": [ "plotSpRange" ] }, { "page": "rasterToGrid", "title": "Convert raster to sf grid", "topics": [ "rasterToGrid" ] }, { "page": "read.epmGrid", "title": "Read a epmGrid object", "topics": [ "read.epmGrid" ] }, { "page": "reduceToCommonTaxa", "title": "Subset epmGrid to shared taxa", "topics": [ "reduceToCommonTaxa" ] }, { "page": "singleSpCellIndex", "title": "Identify single-species cells", "topics": [ "singleSpCellIndex" ] }, { "page": "spCountIndex", "title": "Identify cells that have a certain number of taxa", "topics": [ "spCountIndex" ] }, { "page": "summarizeEpmGridList", "title": "Summarize lists of epmGrid objects", "topics": [ "summarizeEpmGridList" ] }, { "page": "summary", "title": "epmGrid summary", "topics": [ "summary.epmGrid" ] }, { "page": "tableFromEpmGrid", "title": "Data table from epmGrid", "topics": [ "tableFromEpmGrid" ] }, { "page": "write.epmGrid", "title": "Save epmGrid object", "topics": [ "write.epmGrid" ] }, { "page": "writeEpmSpatial", "title": "Write epmGrid Spatial Object to Disk", "topics": [ "writeEpmSpatial" ] } ], "_readme": "https://github.com/ptitle/epm/raw/HEAD/README.md", "_rundeps": [ "ape", "class", "classInt", "DBI", "digest", "e1071", "KernSmooth", "lattice", "MASS", "nlme", "pbapply", "proxy", "Rcpp", "RcppProgress", "s2", "sf", "terra", "units", "viridisLite", "wk" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_score": 4.4593924877592315, "_indexed": true, "_nocasepkg": "epm", "_universes": [ "ptitle" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.6", "date": "2026-05-19T08:39:06.000Z", "distro": "noble", "arch": "aarch64", "commit": "cf3944fc03cdaf92bc5ce949dfb9bfb600f6523d", "fileid": "4be01efd504d31d8c9ff268cccdedfe8a3db8630944134861e0771052e00c7d4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ptitle/actions/runs/26085819836" }, { "r": "4.7.0", "os": "linux", "version": "1.1.6", "date": "2026-05-19T08:39:11.000Z", "distro": "noble", "arch": "x86_64", "commit": "cf3944fc03cdaf92bc5ce949dfb9bfb600f6523d", "fileid": "56a4ca8a06d734a283f71f9c25dc8654d5e0417e250be25284be61211c7c4f1c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ptitle/actions/runs/26085819836" }, { "r": "4.6.0", "os": "linux", "version": "1.1.6", "date": "2026-05-19T08:39:05.000Z", "distro": "noble", "arch": "aarch64", "commit": "cf3944fc03cdaf92bc5ce949dfb9bfb600f6523d", "fileid": "5c449958f0f5d33f1a8842dbe997261781331c275e40fc3d5547efc5a30fe8b6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ptitle/actions/runs/26085819836" }, { "r": "4.6.0", "os": "linux", "version": "1.1.6", "date": "2026-05-19T08:39:12.000Z", "distro": "noble", "arch": "x86_64", "commit": "cf3944fc03cdaf92bc5ce949dfb9bfb600f6523d", "fileid": "6766f74b49b0300dba942e2c407d51dd4396c9eb3e3cea3cfdb08423c8919e59", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ptitle/actions/runs/26085819836" }, { "r": "4.5.3", "os": "mac", "version": "1.1.6", "date": "2026-05-19T08:39:24.000Z", "arch": "aarch64", "commit": "cf3944fc03cdaf92bc5ce949dfb9bfb600f6523d", "fileid": "b5a7d592b1e1282a6b237700f6e8bf5b17d7d19c0f03936c834dc9f7dba75620", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ptitle/actions/runs/26085819836" }, { "r": "4.5.3", "os": "mac", "version": "1.1.6", "date": "2026-05-19T08:40:19.000Z", "arch": "x86_64", "commit": "cf3944fc03cdaf92bc5ce949dfb9bfb600f6523d", "fileid": "14fd018dac370f72652dfbeecb6ccc72dbe26f07ff2049d56d40b686d7e0993a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ptitle/actions/runs/26085819836" }, { "r": "4.6.0", "os": "mac", "version": "1.1.6", "date": "2026-05-19T08:38:57.000Z", "arch": "aarch64", "commit": "cf3944fc03cdaf92bc5ce949dfb9bfb600f6523d", "fileid": "2a5cf8ec3d718de69c9c17ab41fc9dd2a9ada7f3f38c14b678716d751c8b6812", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ptitle/actions/runs/26085819836" }, { "r": "4.6.0", "os": "mac", "version": "1.1.6", "date": "2026-05-19T08:40:04.000Z", "arch": "x86_64", "commit": "cf3944fc03cdaf92bc5ce949dfb9bfb600f6523d", "fileid": "5662262f1aaaf18951963cc93d2dcb3faa6251cd8d62f72c99b40948fd1e11f2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ptitle/actions/runs/26085819836" }, { "r": "4.7.0", "os": "win", "version": "1.1.6", "date": "2026-05-19T08:38:24.000Z", "arch": "x86_64", "commit": "cf3944fc03cdaf92bc5ce949dfb9bfb600f6523d", "fileid": "ffab4b4a42e2157979cdba1ac9ef862018a2184eef8db788863df79e74c6a5b3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ptitle/actions/runs/26085819836" }, { "r": "4.5.3", "os": "win", "version": "1.1.6", "date": "2026-05-19T08:38:01.000Z", "arch": "x86_64", "commit": "cf3944fc03cdaf92bc5ce949dfb9bfb600f6523d", "fileid": "837504a88e87e489219582919f14ab565a25907eb2bd727ea53444c2fddf9dda", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ptitle/actions/runs/26085819836" }, { "r": "4.6.0", "os": "win", "version": "1.1.6", "date": "2026-05-19T08:38:17.000Z", "arch": "x86_64", "commit": "cf3944fc03cdaf92bc5ce949dfb9bfb600f6523d", "fileid": "f2a4e539dc9c3b7fc8a5582ba4c949ffc6a2e22b41991ef99bae820656ee0430", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ptitle/actions/runs/26085819836" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.6", "date": "2026-06-02T14:57:24.000Z", "arch": "emscripten", "commit": "cf3944fc03cdaf92bc5ce949dfb9bfb600f6523d", "fileid": "ffd4d6c9be2335e39b8f8632911934b4b76d85c9bdc5a85df32f1a6db4232dec", "status": "success", "buildurl": "https://github.com/r-universe/ptitle/actions/runs/26085819836" } ] }