{ "_id": "6a2153f2cd65a98ecbd2dc7a", "Package": "TAF", "Version": "4.4.0", "Date": "2026-02-19", "Title": "Transparent Assessment Framework for Reproducible Research", "Authors@R": "c(person(\"Arni\", \"Magnusson\", role=c(\"aut\",\"cre\"), email=\"thisisarni@gmail.com\"),\nperson(\"Colin\", \"Millar\", role=\"aut\"),\nperson(\"Iago\", \"Mosqueira\", role=\"aut\"),\nperson(\"Alexandros\", \"Kokkalis\", role=\"ctb\"),\nperson(\"Ibrahim\", \"Umar\", role=\"ctb\"),\nperson(\"Hjalte\", \"Parner\", role=\"ctb\"))", "LazyData": "yes", "Description": "General framework to organize data, methods, and results\nused in reproducible scientific analyses. A TAF analysis\nconsists of four scripts (data.R, model.R, output.R, report.R)\nthat are run sequentially. Each script starts by reading files\nfrom a previous step and ends with writing out files for the\nnext step. Convenience functions are provided to version\ncontrol the required data and software, run analyses, clean\nresidues from previous runs, manage files, manipulate tables,\nand produce figures. With a focus on stability and reproducible\nanalyses, the TAF package comes with no dependencies. TAF forms\na base layer for the 'icesTAF' package and other scientific\napplications.", "License": "GPL-3", "URL": "https://github.com/ices-tools-prod/TAF", "Encoding": "UTF-8", "Config/roxygen2/version": "8.0.0", "Roxygen": "list(old_usage=TRUE)", "Repository": "https://ices-tools-prod.r-universe.dev", "Date/Publication": "2026-05-05 05:21:46 UTC", "RemoteUrl": "https://github.com/ices-tools-prod/TAF", "RemoteRef": "HEAD", "RemoteSha": "54ea855fc78db36d37c2d1cf22f443c3efd7748d", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-04 10:28:37 UTC", "User": "root" }, "Author": "Arni Magnusson [aut, cre],\nColin Millar [aut],\nIago Mosqueira [aut],\nAlexandros Kokkalis [ctb],\nIbrahim Umar [ctb],\nHjalte Parner [ctb]", "Maintainer": "Arni Magnusson ", "MD5sum": "e9469f1c35cc79fb9605e16cf38c6f61", "_user": "ices-tools-prod", "_type": "src", "_file": "TAF_4.4.0.tar.gz", "_fileid": "9562fc60208e4fb66d02f9997b6a2fffcbbcd81224f99b3fb7c9732688f5ad1f", "_filesize": 483541, "_sha256": "9562fc60208e4fb66d02f9997b6a2fffcbbcd81224f99b3fb7c9732688f5ad1f", "_created": "2026-06-04T10:28:37.000Z", "_published": "2026-06-04T10:31:14.084Z", "_distro": "noble", "_jobs": [ { "job": 79499648607, "time": 108, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7409147161" }, { "job": 79499648581, "time": 97, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7409143679" }, { "job": 79499648594, "time": 106, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7409146689" }, { "job": 79499648679, "time": 86, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7409139729" }, { "job": 79499310909, "time": 128, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7409111250" }, { "job": 79499648595, "time": 87, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7409140247" }, { "job": 79499648597, "time": 124, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7409152236" }, { "job": 79499648606, "time": 64, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7409132683" }, { "job": 79499648634, "time": 71, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7409134769" } ], "_buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/26946078819", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/ices-tools-prod/TAF", "_commit": { "id": "54ea855fc78db36d37c2d1cf22f443c3efd7748d", "author": "Arni Magnusson ", "committer": "Arni Magnusson ", "message": "Update Roxygen versionst\n", "time": 1777958506 }, "_maintainer": { "name": "Arni Magnusson", "email": "thisisarni@gmail.com", "login": "arni-magnusson", "description": "", "uuid": 3720910 }, "_registered": true, "_dependencies": [ { "package": "grDevices", "role": "Imports" }, { "package": "lattice", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "tools", "role": "Imports" }, { "package": "utils", "role": "Imports" } ], "_owner": "ices-tools-prod", "_selfowned": true, "_usedby": 2, "_updates": [ { "week": "2025-26", "n": 2 }, { "week": "2025-35", "n": 6 }, { "week": "2025-36", "n": 4 }, { "week": "2025-38", "n": 3 }, { "week": "2025-49", "n": 1 }, { "week": "2026-07", "n": 1 }, { "week": "2026-08", "n": 12 }, { "week": "2026-16", "n": 1 }, { "week": "2026-19", "n": 1 } ], "_tags": [ { "name": "4.3.0", "date": "2025-09-01" }, { "name": "4.3.1", "date": "2025-09-18" } ], "_stars": 3, "_contributors": [ { "user": "arni-magnusson", "count": 334, "uuid": 3720910 }, { "user": "colinpmillar", "count": 72, "uuid": 1502848 }, { "user": "iagomosqueira", "count": 5, "uuid": 1029847 }, { "user": "alko989", "count": 2, "uuid": 3840557 }, { "user": "hjalteparner", "count": 1, "uuid": 23259812 } ], "_userbio": { "uuid": 20533792, "type": "organization", "name": "ICES tools (production)", "description": "Tools that are operational and maintained by the ICES Secretariat" }, "_downloads": { "count": 445, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/TAF" }, "_devurl": "https://github.com/ices-tools-prod/taf", "_searchresults": 416, "_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/TAF.html", "manual.pdf" ], "_homeurl": "https://github.com/ices-tools-prod/taf", "_realowner": "ices-tools-prod", "_cranurl": true, "_releases": [ { "version": "4.0.0", "date": "2021-04-07" }, { "version": "4.1.0", "date": "2023-01-23" }, { "version": "4.2.0", "date": "2023-03-21" }, { "version": "4.3.0", "date": "2025-09-02" }, { "version": "4.3.1", "date": "2025-09-18" } ], "_exports": [ "already.in.taf.library", "boot.dir", "boot.dir.inside", "boot.exists", "check.data", "check.software", "clean", "clean.boot", "clean.data", "clean.library", "clean.software", "convert.spaces", "cp", "ddim", "deps", "detach.packages", "dir.tree", "div", "dos2unix", "download", "download.github", "draft.data", "draft.readme", "draft.software", "ds.file", "ds.package", "extract.subdir", "file.encoding", "flr2taf", "get.remote.sha", "git.repo", "install.deps", "is.r.package", "latin1.to.utf8", "lim", "line.endings", "long2taf", "long2xtab", "make", "make.all", "make.taf", "makeAll", "makeTAF", "mkdir", "model.dir", "model.script", "msg", "os", "os.linux", "os.macos", "os.unix", "os.windows", "parse.repo", "pdeps", "period", "plus", "process.bibfile", "process.entry", "read.bib", "read.taf", "rmdir", "rnd", "sam2taf", "source.all", "source.dir", "source.taf", "sourceAll", "sourceDir", "sourceTAF", "stamp.description", "taf.boot", "taf.boot.path", "taf.bootstrap", "taf.data.path", "taf.example", "taf.install", "taf.libPaths", "taf.libraries", "taf.library", "taf.pkg", "taf.png", "taf.session", "taf.skeleton", "taf.sources", "taf.unzip", "taf2html", "taf2long", "taf2xtab", "tafpng", "tt", "unix2dos", "utf8.to.latin1", "wide2long", "write.taf", "xtab2long", "xtab2taf", "zoom", "zoom.trellis" ], "_datasets": [ { "name": "catage.long", "title": "Catch at Age in Long Format", "object": "catage.long", "class": [ "data.frame" ], "fields": [ "Year", "Age", "Catch" ], "rows": 32, "table": true, "tojson": true }, { "name": "catage.taf", "title": "Catch at Age in TAF Format", "object": "catage.taf", "class": [ "data.frame" ], "fields": [ "Year", "1", "2", "3", "4" ], "rows": 8, "table": true, "tojson": true }, { "name": "catage.wide", "title": "Catch at Age in Wide Format", "object": "catage.wide", "class": [ "data.frame" ], "fields": [ "Area", "Year", "1", "2", "3", "4" ], "rows": 8, "table": true, "tojson": true }, { "name": "catage.xtab", "title": "Catch at Age in Crosstab Format", "object": "catage.xtab", "class": [ "data.frame" ], "fields": [ "1", "2", "3", "4" ], "rows": 8, "table": true, "tojson": true }, { "name": "summary.taf", "title": "Summary Results in TAF Format", "object": "summary.taf", "class": [ "data.frame" ], "fields": [ "Year", "Rec", "Rec_lo", "Rec_hi", "TSB", "TSB_lo", "TSB_hi", "SSB", "SSB_lo", "SSB_hi", "Removals", "Removals_lo", "Removals_hi", "Fbar", "Fbar_lo", "Fbar_hi" ], "rows": 3, "table": true, "tojson": true }, { "name": "taf.blue", "title": "TAF Colors", "object": "taf.colors", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "taf.dark", "title": "TAF Colors", "object": "taf.colors", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "taf.green", "title": "TAF Colors", "object": "taf.colors", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "taf.light", "title": "TAF Colors", "object": "taf.colors", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "taf.orange", "title": "TAF Colors", "object": "taf.colors", "class": [ "character" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "TAF-package", "title": "Transparent Assessment Framework for Reproducible Research", "topics": [ "TAF-package", "TAF" ] }, { "page": "catage.long", "title": "Catch at Age in Long Format", "topics": [ "catage.long" ] }, { "page": "catage.taf", "title": "Catch at Age in TAF Format", "topics": [ "catage.taf" ] }, { "page": "catage.wide", "title": "Catch at Age in Wide Format", "topics": [ "catage.wide" ] }, { "page": "catage.xtab", "title": "Catch at Age in Crosstab Format", "topics": [ "catage.xtab" ] }, { "page": "check.data", "title": "Check DATA.bib Entries", "topics": [ "check.data" ] }, { "page": "check.software", "title": "Check SOFTWARE.bib Against Global Packages", "topics": [ "check.software" ] }, { "page": "clean", "title": "Clean TAF Directories", "topics": [ "clean" ] }, { "page": "clean.boot", "title": "Clean Boot Directory", "topics": [ "clean.boot" ] }, { "page": "clean.data", "title": "Clean Data", "topics": [ "clean.data" ] }, { "page": "clean.library", "title": "Clean TAF Library", "topics": [ "clean.library" ] }, { "page": "clean.software", "title": "Clean TAF Software", "topics": [ "clean.software" ] }, { "page": "convert.spaces", "title": "Convert Spaces", "topics": [ "convert.spaces" ] }, { "page": "cp", "title": "Copy Files", "topics": [ "cp" ] }, { "page": "ddim", "title": "Data Dimensions", "topics": [ "ddim" ] }, { "page": "deps", "title": "Dependencies of a Workflow", "topics": [ "deps" ] }, { "page": "detach.packages", "title": "Detach Packages", "topics": [ "detach.packages" ] }, { "page": "dir.tree", "title": "Directory Tree", "topics": [ "dir.tree" ] }, { "page": "div", "title": "Divide Columns", "topics": [ "div" ] }, { "page": "dos2unix", "title": "Convert Line Endings", "topics": [ "dos2unix", "unix2dos" ] }, { "page": "download", "title": "Download File", "topics": [ "download" ] }, { "page": "download.github", "title": "Download GitHub Repository", "topics": [ "download.github" ] }, { "page": "draft.data", "title": "Draft DATA.bib", "topics": [ "draft.data" ] }, { "page": "draft.readme", "title": "Draft Readme", "topics": [ "draft.readme" ] }, { "page": "draft.software", "title": "Draft SOFTWARE.bib", "topics": [ "draft.software" ] }, { "page": "file.encoding", "title": "File Encoding", "topics": [ "file.encoding" ] }, { "page": "flr2taf", "title": "Convert FLR Table to TAF Format", "topics": [ "flr2taf" ] }, { "page": "get.remote.sha", "title": "Get Remote SHA", "topics": [ "get.remote.sha" ] }, { "page": "git.repo", "title": "Git Repo", "topics": [ "git.repo" ] }, { "page": "install.deps", "title": "Install Dependencies", "topics": [ "install.deps" ] }, { "page": "is.r.package", "title": "Is R Package", "topics": [ "is.r.package" ] }, { "page": "latin1.to.utf8", "title": "Convert File Encoding", "topics": [ "latin1.to.utf8", "utf8.to.latin1" ] }, { "page": "lim", "title": "Axis Limits", "topics": [ "lim" ] }, { "page": "line.endings", "title": "Line Endings", "topics": [ "line.endings" ] }, { "page": "linreg", "title": "Linear Regression", "topics": [ "linreg" ] }, { "page": "long2taf", "title": "Convert Long Table to TAF Format", "topics": [ "long2taf" ] }, { "page": "long2xtab", "title": "Convert Long Table to Crosstab Format", "topics": [ "long2xtab" ] }, { "page": "make", "title": "Run R Script if Needed", "topics": [ "make" ] }, { "page": "make.all", "title": "Run All TAF Scripts as Needed", "topics": [ "make.all", "makeAll" ] }, { "page": "make.taf", "title": "Run TAF Script if Needed", "topics": [ "make.taf", "makeTAF" ] }, { "page": "mkdir", "title": "Create Directory", "topics": [ "mkdir" ] }, { "page": "msg", "title": "Show Message", "topics": [ "msg" ] }, { "page": "os", "title": "Operating System", "topics": [ "os", "os.linux", "os.macos", "os.unix", "os.windows" ] }, { "page": "pdeps", "title": "Dependencies of a Package", "topics": [ "pdeps" ] }, { "page": "period", "title": "Period", "topics": [ "period" ] }, { "page": "plus", "title": "Rename Plus Group Column", "topics": [ "plus" ] }, { "page": "read.bib", "title": "Read Metadata Entries", "topics": [ "read.bib" ] }, { "page": "read.taf", "title": "Read TAF Table", "topics": [ "read.taf" ] }, { "page": "rmdir", "title": "Remove Empty Directory", "topics": [ "rmdir" ] }, { "page": "rnd", "title": "Round Columns", "topics": [ "rnd" ] }, { "page": "sam2taf", "title": "Convert SAM Table to TAF Format", "topics": [ "sam2taf" ] }, { "page": "source.all", "title": "Run All TAF Scripts", "topics": [ "source.all", "sourceAll" ] }, { "page": "source.dir", "title": "Source Directory", "topics": [ "source.dir", "sourceDir" ] }, { "page": "source.taf", "title": "Run TAF Script", "topics": [ "source.taf", "sourceTAF" ] }, { "page": "summary.taf", "title": "Summary Results in TAF Format", "topics": [ "summary.taf" ] }, { "page": "taf.boot", "title": "Boot TAF Analysis", "topics": [ "taf.boot", "taf.bootstrap" ] }, { "page": "taf.boot.path", "title": "Construct Boot Path", "topics": [ "taf.boot.path" ] }, { "page": "taf.colors", "title": "TAF Colors", "topics": [ "taf.blue", "taf.colors", "taf.dark", "taf.green", "taf.light", "taf.orange" ] }, { "page": "taf.data.path", "title": "Construct Boot Data Path", "topics": [ "taf.data.path" ] }, { "page": "taf.example", "title": "TAF Example", "topics": [ "taf.example" ] }, { "page": "taf.install", "title": "TAF Install", "topics": [ "taf.install" ] }, { "page": "taf.libPaths", "title": "Add TAF Library Path", "topics": [ "taf.libPaths" ] }, { "page": "taf.libraries", "title": "TAF Libraries", "topics": [ "taf.libraries" ] }, { "page": "taf.library", "title": "TAF Library", "topics": [ "taf.library" ] }, { "page": "taf.png", "title": "PNG Device", "topics": [ "taf.png", "tafpng" ] }, { "page": "taf.session", "title": "TAF Session", "topics": [ "taf.session" ] }, { "page": "taf.skeleton", "title": "TAF Skeleton", "topics": [ "taf.skeleton" ] }, { "page": "taf.sources", "title": "List Sources", "topics": [ "taf.sources" ] }, { "page": "taf.unzip", "title": "Unzip File", "topics": [ "taf.unzip" ] }, { "page": "taf2html", "title": "Convert TAF Table to HTML", "topics": [ "taf2html" ] }, { "page": "taf2long", "title": "Convert TAF Table to Long Format", "topics": [ "taf2long" ] }, { "page": "taf2xtab", "title": "Convert TAF Table to Crosstab Format", "topics": [ "taf2xtab" ] }, { "page": "tt", "title": "TAF Transpose", "topics": [ "tt" ] }, { "page": "wide2long", "title": "Convert Wide Table to Long Format", "topics": [ "wide2long" ] }, { "page": "write.taf", "title": "Write TAF Table", "topics": [ "write.taf" ] }, { "page": "xtab2long", "title": "Convert Crosstab Table to Long Format", "topics": [ "xtab2long" ] }, { "page": "xtab2taf", "title": "Convert Crosstab Table to TAF Format", "topics": [ "xtab2taf" ] }, { "page": "zoom", "title": "Zoom", "topics": [ "zoom", "zoom.trellis" ] } ], "_readme": "https://github.com/ices-tools-prod/TAF/raw/HEAD/README.md", "_rundeps": [ "lattice" ], "_score": 7.129638340833355, "_indexed": true, "_nocasepkg": "taf", "_universes": [ "ices-tools-prod", "arni-magnusson" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "4.4.0", "date": "2026-06-04T10:30:26.000Z", "distro": "noble", "commit": "54ea855fc78db36d37c2d1cf22f443c3efd7748d", "fileid": "5ff8fbc844c7f3c7c16c9bcaa3da1942a297713b96ff929c776813188da0d9b0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/26946078819" }, { "r": "4.6.0", "os": "linux", "version": "4.4.0", "date": "2026-06-04T10:30:18.000Z", "distro": "noble", "commit": "54ea855fc78db36d37c2d1cf22f443c3efd7748d", "fileid": "07d56b86051850b5233a2e48a32e6cf3e571cd693802e57eab3b6afa797a8054", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/26946078819" }, { "r": "4.5.3", "os": "mac", "version": "4.4.0", "date": "2026-06-04T10:30:31.000Z", "commit": "54ea855fc78db36d37c2d1cf22f443c3efd7748d", "fileid": "28f160166dbf0fdf0df924fc17d2620dd2a21807ea158f76e43b5758550758f8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/26946078819" }, { "r": "4.6.0", "os": "mac", "version": "4.4.0", "date": "2026-06-04T10:30:09.000Z", "commit": "54ea855fc78db36d37c2d1cf22f443c3efd7748d", "fileid": "0107a23bc43fb5b59547f8ee286a0ec581165cc1f9c6ebf861f289f4fec58045", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/26946078819" }, { "r": "4.6.0", "os": "wasm", "version": "4.4.0", "date": "2026-06-04T10:30:21.000Z", "commit": "54ea855fc78db36d37c2d1cf22f443c3efd7748d", "fileid": "8c229f77480560e7631a460c88f358af22b107ad10daa4d856c3745fd7b7fde3", "status": "success", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/26946078819" }, { "r": "4.7.0", "os": "win", "version": "4.4.0", "date": "2026-06-04T10:30:23.000Z", "commit": "54ea855fc78db36d37c2d1cf22f443c3efd7748d", "fileid": "b6e32810b725f5ad75a7fb03909ffa692a453fe77027e4d8b2fa84a0a73703ac", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/26946078819" }, { "r": "4.5.3", "os": "win", "version": "4.4.0", "date": "2026-06-04T10:29:37.000Z", "commit": "54ea855fc78db36d37c2d1cf22f443c3efd7748d", "fileid": "3236d4de241caf3044b2dd8feec14f6d2f59ea818a4f1c0edea8054d31bb4f86", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/26946078819" }, { "r": "4.6.0", "os": "win", "version": "4.4.0", "date": "2026-06-04T10:29:43.000Z", "commit": "54ea855fc78db36d37c2d1cf22f443c3efd7748d", "fileid": "1fd1127f65f39d557ff155567cbdf45b3348e5cb1a615bd18eeb928dd015403c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/26946078819" } ] }