{ "_id": "6a31ec5b3efcd9bda4375c70", "Package": "ss3diags", "Title": "Stock Synthesis Model Diagnostics for Intergated Stock\nAssessments", "Version": "2.2.2", "Date": "2025-02-25", "Authors@R": "c(\nperson(\"Henning\", \"Winker\", , \"henning.winker@ec.europa.eu\", role = \"aut\"),\nperson(\"Felipe\", \"Carvalho\", , \"felipe.carvalho@noaa.gov\", role = \"aut\"),\nperson(\"Massimiliano\", \"Cardinale\", , \"massimiliano.cardinale@slu.se\", role = \"aut\"),\nperson(\"Laurence\", \"Kell\", , \"laurie@seaplusplus.co.uk\", role = \"aut\"),\nperson(\"Megumi\", \"Oshima\", , \"megumi.oshima@noaa.gov\", role = c(\"aut\", \"cre\")),\nperson(\"Eric\", \"Fletcher\", , \"eric.fletcher@noaa\", role = \"aut\")\n)", "Description": "Compilation of diagnostic functions for Stock Synthesis\nmodels, which developed for the manuscript \"Using Model\nDiagnostics in Integrated Stock Assessments\".", "License": "EUPL", "URL": "https://nmfs-ost.github.io/ss3diags", "BugReports": "https://github.com/nmfs-ost/ss3diags/issues", "Remotes": [ "r4ss/r4ss" ], "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "cmake libfontconfig1-dev libfreetype6-dev\nlibfribidi-dev git make libharfbuzz-dev libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev", "Repository": "https://ices-tools-prod.r-universe.dev", "Date/Publication": "2026-04-29 00:03:47 UTC", "RemoteUrl": "https://github.com/PIFSCstockassessments/ss3diags", "RemoteRef": "HEAD", "RemoteSha": "d8773e0ac9040e9f8771596a1db54945760f923f", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-17 00:33:04 UTC", "User": "root" }, "Author": "Henning Winker [aut],\nFelipe Carvalho [aut],\nMassimiliano Cardinale [aut],\nLaurence Kell [aut],\nMegumi Oshima [aut, cre],\nEric Fletcher [aut]", "Maintainer": "Megumi Oshima ", "MD5sum": "97c56c1e3697962251e6098d9cba3e4a", "_user": "ices-tools-prod", "_type": "src", "_file": "ss3diags_2.2.2.tar.gz", "_fileid": "a71620abdf0deceacdcddc806df66afaf6d2ac30b831f459decdf8df44f872b2", "_filesize": 345049, "_sha256": "a71620abdf0deceacdcddc806df66afaf6d2ac30b831f459decdf8df44f872b2", "_created": "2026-06-17T00:33:04.000Z", "_published": "2026-06-17T00:37:46.990Z", "_distro": "noble", "_jobs": [ { "job": 81794889949, "time": 191, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7683181312" }, { "job": 81794889950, "time": 242, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7683191052" }, { "job": 81794889951, "time": 115, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7683162171" }, { "job": 81794889966, "time": 159, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7683172561" }, { "job": 81794460294, "time": 221, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7683135983" }, { "job": 81794889947, "time": 146, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7683169409" }, { "job": 81794889961, "time": 158, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7683172591" }, { "job": 81794889962, "time": 178, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7683177302" }, { "job": 81794889955, "time": 189, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7683179249" } ], "_buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/27657411280", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/PIFSCstockassessments/ss3diags", "_commit": { "id": "d8773e0ac9040e9f8771596a1db54945760f923f", "author": "Eric Fletcher <37851243+efletcherPIFSC@users.noreply.github.com>", "committer": "GitHub ", "message": "Merge pull request #139 from iantaylor-NOAA/sizefreq\n\nattempt to support runs test for size frequency data", "time": 1777421027 }, "_maintainer": { "name": "Megumi Oshima", "email": "megumi.oshima@noaa.gov", "login": "moshima-pifsc", "description": "", "uuid": 78562167 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1", "role": "Depends" }, { "package": "dplyr", "role": "Imports" }, { "package": "gplots", "role": "Imports" }, { "package": "lifecycle", "role": "Imports" }, { "package": "mvtnorm", "role": "Imports" }, { "package": "r4ss", "version": ">= 1.50.0", "role": "Imports" }, { "package": "randtests", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "markdown", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "pifscstockassessments", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-25", "n": 1 }, { "week": "2025-32", "n": 4 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_topics": [ "stock-synthesis" ], "_stars": 5, "_contributors": [ { "user": "moshima-pifsc", "count": 379, "uuid": 78562167 }, { "user": "efletcherpifsc", "count": 337, "uuid": 37851243 }, { "user": "henning-winker", "count": 64, "uuid": 15005753 }, { "user": "n-ducharmebarth-noaa", "count": 9, "uuid": 97110196 }, { "user": "jabbamodel", "count": 6, "uuid": 35276887 }, { "user": "arni-magnusson", "count": 3, "uuid": 3720910 }, { "user": "iantaylor-noaa", "count": 2, "uuid": 4992918 }, { "user": "pdimens", "count": 1, "uuid": 19176506 } ], "_userbio": { "uuid": 20533792, "type": "organization", "name": "ICES tools (production)", "followers": 24, "description": "Tools that are operational and maintained by the ICES Secretariat" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ss3diags" }, "_devurl": "https://github.com/nmfs-ost/ss3diags", "_pkgdown": "https://nmfs-ost.github.io/ss3diags", "_searchresults": 428, "_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/ss3diags.html", "manual.pdf" ], "_cranurl": false, "_exports": [ "SScompsTA1.8", "SSdeltaMVLN", "SSdeltaMVLN_old", "SSdiagsMCMC", "SSdiagsMCMC_ancient", "SShcbias", "SSmase", "SSplotEnsemble", "SSplotHCxval", "SSplotJABBAres", "SSplotKobe", "SSplotModelcomp", "SSplotRetro", "SSplotRunstest", "SSreadMCMC", "SSretroComps", "SSrmse", "ssruns_sig3", "SSrunstest", "SSsettingsBratioF" ], "_help": [ { "page": "SScompsTA1.8", "title": "Francis Weighting for compositional data", "topics": [ "SScompsTA1.8" ] }, { "page": "SSdeltaMVLN", "title": "Joint Distributions for Stock Status Ratios", "topics": [ "SSdeltaMVLN" ] }, { "page": "SSdeltaMVLN_old", "title": "Joint Distributions for Stock Status Ratios", "topics": [ "SSdeltaMVLN_old" ] }, { "page": "SSdiagsMCMC", "title": "MCMC Joint Distributions", "topics": [ "SSdiagsMCMC" ] }, { "page": "SSdiagsMCMC_ancient", "title": "MCMC Joint Distributions", "topics": [ "SSdiagsMCMC_ancient" ] }, { "page": "SShcbias", "title": "Mohn's Rho and Forecast Bias", "topics": [ "SShcbias" ] }, { "page": "SSmase", "title": "Mean Absolute Scaled Error", "topics": [ "SSmase" ] }, { "page": "SSplotEnsemble", "title": "Model ensemble plots", "topics": [ "SSplotEnsemble" ] }, { "page": "SSplotHCxval", "title": "Hindcasting Cross-Validations of Multiple Models", "topics": [ "SSplotHCxval" ] }, { "page": "SSplotJABBAres", "title": "Residual plot", "topics": [ "SSplotJABBAres" ] }, { "page": "SSplotKobe", "title": "KOBE phase plot", "topics": [ "SSplotKobe" ] }, { "page": "SSplotModelcomp", "title": "Compare Multiple SS Model Estimates", "topics": [ "SSplotModelcomp" ] }, { "page": "SSplotRetro", "title": "Retrospective-Forecast with One-Step Ahead Hindcasting", "topics": [ "SSplotRetro" ] }, { "page": "SSplotRunstest", "title": "Residual Diagnostics", "topics": [ "SSplotRunstest" ] }, { "page": "SSreadMCMC", "title": "Read SS MCMC", "topics": [ "SSreadMCMC" ] }, { "page": "SSretroComps", "title": "Retrieve Composition Data from Multiple SS Models", "topics": [ "SSretroComps" ] }, { "page": "SSrmse", "title": "Function for calculating RMSE used for 'SSplotJABBAres()'", "topics": [ "SSrmse" ] }, { "page": "ssruns_sig3", "title": "Runs Test for Residuals", "topics": [ "ssruns_sig3" ] }, { "page": "SSrunstest", "title": "Residual Diagnostics Plot", "topics": [ "SSrunstest" ] }, { "page": "SSsettingsBratioF", "title": "Get Stock Status Settings", "topics": [ "SSsettingsBratioF" ] } ], "_pkglogo": "https://github.com/PIFSCstockassessments/ss3diags/raw/HEAD/man/figures/logo.svg", "_readme": "https://github.com/PIFSCstockassessments/ss3diags/raw/HEAD/README.md", "_rundeps": [ "askpass", "base64enc", "bitops", "bslib", "cachem", "caTools", "cli", "coda", "codetools", "corpcor", "cpp11", "curl", "digest", "dplyr", "evaluate", "farver", "fastmap", "fontawesome", "forcats", "fs", "furrr", "future", "generics", "ggplot2", "gitcreds", "globals", "glue", "gplots", "gridExtra", "gtable", "gtools", "highr", "htmltools", "httr2", "ini", "isoband", "jquerylib", "jsonlite", "kableExtra", "KernSmooth", "knitr", "labeling", "lattice", "lifecycle", "listenv", "magrittr", "memoise", "mime", "mvtnorm", "openssl", "parallelly", "pillar", "pkgconfig", "plyr", "purrr", "r4ss", "R6", "randtests", "rappdirs", "RColorBrewer", "Rcpp", "reshape2", "rlang", "rmarkdown", "rstudioapi", "S7", "sass", "scales", "stringi", "stringr", "svglite", "sys", "systemfonts", "textshaping", "tibble", "tidyr", "tidyselect", "tinytex", "utf8", "vctrs", "viridis", "viridisLite", "withr", "xfun", "xml2", "yaml" ], "_score": 5.351603072419129, "_indexed": false, "_nocasepkg": "ss3diags", "_universes": [ "ices-tools-prod" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.2.2", "date": "2026-06-17T00:35:36.000Z", "distro": "noble", "commit": "d8773e0ac9040e9f8771596a1db54945760f923f", "fileid": "a0da628f57fbd9bd1256068c64007e857f5de5c56f949cf01a7760d03eece7a1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/27657411280" }, { "r": "4.6.0", "os": "linux", "version": "2.2.2", "date": "2026-06-17T00:36:17.000Z", "distro": "noble", "commit": "d8773e0ac9040e9f8771596a1db54945760f923f", "fileid": "127a7eaadd3af9680b4c50a77f0dba038862a16a22556334cc92cd7f0abcae09", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/27657411280" }, { "r": "4.5.3", "os": "mac", "version": "2.2.2", "date": "2026-06-17T00:34:30.000Z", "commit": "d8773e0ac9040e9f8771596a1db54945760f923f", "fileid": "c7ae048287c31fc96188b50102effb1162d8422227a92ff534e4958aacafc6d0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/27657411280" }, { "r": "4.6.0", "os": "mac", "version": "2.2.2", "date": "2026-06-17T00:34:50.000Z", "commit": "d8773e0ac9040e9f8771596a1db54945760f923f", "fileid": "57ab61e27e049c41ea2b7538c2836ef3e6f51c0065c3cf7a6a4a875bb76836b0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/27657411280" }, { "r": "4.6.0", "os": "wasm", "version": "2.2.2", "date": "2026-06-17T00:35:49.000Z", "commit": "d8773e0ac9040e9f8771596a1db54945760f923f", "fileid": "61000298067d47b4d4392582f768a6d50aa0dc1f898c5bb5127c937b2eabd33d", "status": "success", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/27657411280" }, { "r": "4.7.0", "os": "win", "version": "2.2.2", "date": "2026-06-17T00:34:27.000Z", "commit": "d8773e0ac9040e9f8771596a1db54945760f923f", "fileid": "53c4fd746eb4d70104df4461766003a998ec67156a540b8b32667529a868c8e4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/27657411280" }, { "r": "4.5.3", "os": "win", "version": "2.2.2", "date": "2026-06-17T00:34:43.000Z", "commit": "d8773e0ac9040e9f8771596a1db54945760f923f", "fileid": "af8be5570f0df15cb60de9e6e83b961010b4b7faae55faf284b54cabea16d44f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/27657411280" }, { "r": "4.6.0", "os": "win", "version": "2.2.2", "date": "2026-06-17T00:34:52.000Z", "commit": "d8773e0ac9040e9f8771596a1db54945760f923f", "fileid": "7988345d11bd1ff0c0f25c59bb08792cbe031f8f7b43116ae0139d85995373b3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/27657411280" } ] }