{ "_id": "6a1f2ea8b401979e73426b5b", "Package": "cat3advice", "Type": "Package", "Title": "ICES category 3 empirical harvest control rules", "Version": "0.1.2", "Authors@R": "c(\nperson(\"Simon H.\", \"Fischer\", email = \"simon.fischer@cefas.gov.uk\",\nrole = c(\"aut\", \"cre\")))", "Maintainer": "Simon Fischer ", "Description": "A package to apply the the ICES category 3 empirical\n(model-free) harvest control rules.", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.2", "Collate": "'generics.R' 'A.R' 'length_data.R' 'f.R' 'F_hr.R' 'I.R' 'b.R'\n'm.R' 'chr.R' 'data.R' 'r.R' 'plotting.R' 'rb.R' 'rfb.R'\n'utils-pipe.R'", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libicu-dev", "Repository": "https://ices-tools-prod.r-universe.dev", "Date/Publication": "2025-06-19 11:19:05 UTC", "RemoteUrl": "https://github.com/shfischer/cat3advice", "RemoteRef": "HEAD", "RemoteSha": "76680ef15123d9b9f0510dee625b2b1b75cd260c", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-15 09:20:28 UTC", "User": "root" }, "Author": "Simon H. Fischer [aut, cre]", "MD5sum": "4b0b0d71301daf275c31870012fea131", "_user": "ices-tools-prod", "_type": "src", "_file": "cat3advice_0.1.2.tar.gz", "_fileid": "e85ad021cb9c21b644ce5073b74818eb81764345b488901f3c9da89aee77b1ad", "_filesize": 855203, "_sha256": "e85ad021cb9c21b644ce5073b74818eb81764345b488901f3c9da89aee77b1ad", "_created": "2026-05-15T09:20:28.000Z", "_published": "2026-06-02T19:27:36.792Z", "_distro": "noble", "_jobs": [ { "job": 79154411152, "time": 157, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7013967626" }, { "job": 79154411143, "time": 149, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7013963603" }, { "job": 79154411169, "time": 132, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7013958494" }, { "job": 79154411172, "time": 121, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7013955073" }, { "job": 79154410181, "time": 276, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7013918893" }, { "job": 79154410053, "time": 108, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7367736455" }, { "job": 79154410613, "time": 119, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7014039977" }, { "job": 79154410803, "time": 109, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7013952529" }, { "job": 79154410402, "time": 129, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7013957233" } ], "_buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/25910074760", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/shfischer/cat3advice", "_commit": { "id": "76680ef15123d9b9f0510dee625b2b1b75cd260c", "author": "Simon Fischer <32540427+shfischer@users.noreply.github.com>", "committer": "Simon Fischer <32540427+shfischer@users.noreply.github.com>", "message": "added r-universe badge\n", "time": 1750331945 }, "_maintainer": { "name": "Simon Fischer", "email": "simon.fischer@cefas.gov.uk", "login": "shfischer", "uuid": 32540427 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "scales", "role": "Imports" }, { "package": "icesAdvice", "role": "Imports" }, { "package": "patchwork", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "shfischer", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-25", "n": 6 } ], "_tags": [], "_stars": 3, "_contributors": [ { "user": "shfischer", "count": 153, "uuid": 32540427 } ], "_userbio": { "uuid": 20533792, "type": "organization", "name": "ICES tools (production)", "description": "Tools that are operational and maintained by the ICES Secretariat" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/cat3advice" }, "_devurl": "https://github.com/shfischer/cat3advice", "_searchresults": 14, "_rbuild": "4.6.0", "_assets": [ "extra/cat3advice.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_cranurl": false, "_exports": [ "%>%", "A", "advice", "b", "chr", "chr_A", "chr_b", "chr_I", "chr_m", "f", "F", "HR", "I", "indicator", "inverse_indicator", "Lc", "Lmean", "Lref", "m", "plot", "r", "rb", "rb_A", "rb_b", "rb_m", "rb_r", "rfb", "rfb_A", "rfb_b", "rfb_f", "rfb_m", "rfb_r", "summary", "value" ], "_datasets": [ { "name": "ple7e_catch", "title": "Western English Channel plaice example data", "object": "ple7e_catch", "class": [ "data.frame" ], "fields": [ "year", "advice", "landings", "discards", "catch" ], "rows": 36, "table": true, "tojson": true }, { "name": "ple7e_f", "title": "Western English Channel plaice example data", "object": "ple7e_f", "class": [ "comp_f" ], "fields": [], "table": false, "tojson": false }, { "name": "ple7e_f2", "title": "Western English Channel plaice example data", "object": "ple7e_f2", "class": [ "f" ], "fields": [], "table": false, "tojson": false }, { "name": "ple7e_hr", "title": "Western English Channel plaice example data", "object": "ple7e_hr", "class": [ "HR" ], "fields": [], "table": false, "tojson": false }, { "name": "ple7e_idx", "title": "Western English Channel plaice example data", "object": "ple7e_idx", "class": [ "data.frame" ], "fields": [ "year", "index" ], "rows": 19, "table": true, "tojson": true }, { "name": "ple7e_length", "title": "Western English Channel plaice example data", "object": "ple7e_length", "class": [ "data.frame" ], "fields": [ "year", "catch_category", "length", "numbers" ], "rows": 777, "table": true, "tojson": true }, { "name": "ple7e_WKBPLAICE", "title": "Western English Channel plaice example data", "object": "ple7e_WKBPLAICE", "class": [ "data.frame" ], "fields": [ "year", "advice", "advice_landings", "advice_discards", "catch", "landings", "discards", "index" ], "rows": 45, "table": true, "tojson": true } ], "_help": [ { "page": "A-class", "title": "A-class", "topics": [ "A-class", "chr_A-class", "rb_A-class", "rfb_A-class" ] }, { "page": "advice", "title": "ICES advice sheet-style output table", "topics": [ "advice", "advice,A-method", "advice,b-method", "advice,chr-method", "advice,chr_A-method", "advice,chr_m-method", "advice,F-method", "advice,f-method", "advice,I-method", "advice,m-method", "advice,r-method", "advice,rb-method", "advice,rb_m-method", "advice,rfb-method", "advice,rfb_f-method", "advice,rfb_m-method" ] }, { "page": "b", "title": "rb/rfb/chr rule - component b (biomass safeguard)", "topics": [ "b", "b,b-method", "b,data.frame-method", "b,I-method", "b,numeric-method", "chr_b", "chr_b,ANY-method", "rb_b", "rb_b,ANY-method", "rfb_b", "rfb_b,ANY-method" ] }, { "page": "b-class", "title": "b-class", "topics": [ "b-class", "chr_b-class", "rb_b-class", "rfb_b-class" ] }, { "page": "chr", "title": "chr rule", "topics": [ "chr", "chr,chr,A,I,F,b,m-method", "chr,chr,missing,missing,missing,missing,missing-method", "chr,missing,A,I,F,b,m-method", "chr,missing,numeric,numeric,numeric,numeric,numeric-method" ] }, { "page": "chr-class", "title": "An S4 class to represent the chr rule.", "topics": [ "chr-class" ] }, { "page": "f", "title": "rfb rule - component f (fishing pressure proxy, length indicator)", "topics": [ "f", "f,f,missing,missing-method", "f,missing,Lmean,Lref-method", "f,numeric,missing,missing-method", "rfb_f", "rfb_f,ANY,missing,missing-method", "rfb_f,missing,ANY,ANY-method" ] }, { "page": "Ftarget", "title": "Calculation of the (relative) harvest rate target", "topics": [ "F", "F,F,missing-method", "F,HR,f-method", "F,HR,missing-method", "F,numeric,missing-method" ] }, { "page": "F-class", "title": "f-class", "topics": [ "f-class", "rfb_f-class" ] }, { "page": "Ftarget-class", "title": "F", "topics": [ "Ftarget-class" ] }, { "page": "HR", "title": "Calculation of the (relative) harvest rate", "topics": [ "HR", "HR,data.frame-method", "HR,HR-method" ] }, { "page": "HR-class", "title": "HR-class", "topics": [ "HR-class" ] }, { "page": "I", "title": "chr rule - component I (biomass index value)", "topics": [ "chr_I", "chr_I,ANY-method", "I", "I,data.frame-method", "I,I-method", "I,vector-method" ] }, { "page": "I-class", "title": "I-class", "topics": [ "chr_I-class", "I-class" ] }, { "page": "chr_indicator", "title": "indicator", "topics": [ "indicator", "indicator,f-method" ] }, { "page": "inverse_indicator", "title": "Return the inverse indicator for component f of the chr rule.", "topics": [ "inverse_indicator" ] }, { "page": "Lc", "title": "Length at first capture Lc", "topics": [ "Lc", "Lc,data.frame-method", "Lc,Lc-method", "Lc,numeric-method" ] }, { "page": "Lc-class", "title": "An S4 class to represent length at first capture", "topics": [ "Lc-class" ] }, { "page": "Lmean", "title": "Mean catch length Lmean", "topics": [ "Lmean", "Lmean,data.frame,data.frame-method", "Lmean,data.frame,Lc-method", "Lmean,data.frame,missing-method", "Lmean,Lmean,missing-method", "Lmean,numeric,missing-method" ] }, { "page": "Lmean-class", "title": "An S4 class to represent mean catch length", "topics": [ "Lmean-class" ] }, { "page": "Lref", "title": "Reference catch length", "topics": [ "Lref" ] }, { "page": "Lref-class", "title": "An S4 class to represent the reference catch length", "topics": [ "Lref-class" ] }, { "page": "m", "title": "rfb/rb/chr rule - component m (multiplier)", "topics": [ "chr_m", "chr_m,ANY-method", "chr_m,missing-method", "m", "m,m-method", "m,missing-method", "m,numeric-method", "rb_m", "rb_m,ANY-method", "rb_m,missing-method", "rfb_m", "rfb_m,ANY-method", "rfb_m,missing-method" ] }, { "page": "m-class", "title": "m-class", "topics": [ "chr_m-class", "m-class", "rb_m-class", "rfb_m-class" ] }, { "page": "ple7e", "title": "Western English Channel plaice example data", "topics": [ "ple7e", "ple7e_catch", "ple7e_f", "ple7e_f2", "ple7e_hr", "ple7e_idx", "ple7e_length", "ple7e_WKBPLAICE" ] }, { "page": "length_freq_plot", "title": "Plot length frequencies", "topics": [ "plot,Lc,ANY-method", "plot,Lmean,ANY-method" ] }, { "page": "r", "title": "rfb/rb rule - component r (index ratio)", "topics": [ "r", "r,data.frame-method", "r,numeric-method", "r,r-method", "rb_r", "rb_r,ANY-method", "rfb_r", "rfb_r,ANY-method" ] }, { "page": "r-class", "title": "r-class", "topics": [ "r-class", "rb_r-class", "rfb_r-class" ] }, { "page": "rb", "title": "rb rule", "topics": [ "rb", "rb,missing,A,r,b,m-method", "rb,rb,A,r,b,m-method", "rb,rb,missing,missing,missing,missing-method" ] }, { "page": "rb-class", "title": "An S4 class to represent the rb rule.", "topics": [ "rb-class" ] }, { "page": "rfb", "title": "rfb rule", "topics": [ "rfb", "rfb,missing,A,r,f,b,m-method", "rfb,missing,numeric,numeric,numeric,numeric,numeric-method", "rfb,rfb,A,r,f,b,m-method", "rfb,rfb,missing,missing,missing,missing,missing-method" ] }, { "page": "rfb_plot", "title": "Plot elements of the rfb/rb/chr rule", "topics": [ "plot,b,missing-method", "plot,b,r-method", "plot,F,missing-method", "plot,f,missing-method", "plot,HR,ANY-method", "plot,I,missing-method", "plot,r,b-method", "plot,r,missing-method", "rfb_plot" ] }, { "page": "rfb-class", "title": "An S4 class to represent the rfb rule.", "topics": [ "rfb-class" ] }, { "page": "show", "title": "show", "topics": [ "show" ] }, { "page": "summary", "title": "summary", "topics": [ "summary", "summary,A-method", "summary,b-method", "summary,HR-method", "summary,Lc-method", "summary,Lmean-method", "summary,m-method", "summary,r-method" ] }, { "page": "value", "title": "value", "topics": [ "value", "value,A-method", "value,b-method", "value,chr-method", "value,F-method", "value,f-method", "value,HR-method", "value,I-method", "value,Lc-method", "value,Lmean-method", "value,Lref-method", "value,m-method", "value,r-method", "value,rb-method", "value,rfb-method" ] } ], "_readme": "https://github.com/shfischer/cat3advice/raw/HEAD/readme.md", "_rundeps": [ "cli", "cpp11", "dplyr", "farver", "generics", "ggplot2", "glue", "gtable", "icesAdvice", "isoband", "labeling", "lifecycle", "magrittr", "patchwork", "pillar", "pkgconfig", "purrr", "R6", "RColorBrewer", "rlang", "S7", "scales", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "cat3advice.Rmd", "filename": "cat3advice.pdf", "title": "cat3advice", "author": "Simon H. Fischer", "engine": "knitr::rmarkdown", "headings": [ "cat3advice", "Vignette change log", "cat3advice R package", "Documentation", "Installation", "Tutorial", "The rfb rule", "Reference catch $A_y$", "Biomass index trend (ratio) $r$", "Biomass safeguard $b$", "Fishing pressure proxy $f$", "Length data", "Length at first capture $L_c$", "Mean length", "Reference length", "Indicator", "Multiplier $m$", "Application of rfb rule", "The rb rule", "Application of rb rule", "The chr rule", "Biomass index value $I_{y-1}$", "Target harvest rate $HR_{\\text{MSYproxy}}$", "Harvest rate", "Harvest rate target $HR_{\\text{MSYproxy}}$", "Application of chr rule", "chr rule with custom parameters and discard survival", "Data", "Biomass index value", "Target harvest rate", "Biomass safeguard", "Multiplier", "Application of the (tuned) chr rule", "References" ], "created": "2023-04-04 16:29:30", "modified": "2025-06-17 10:23:50", "commits": 11 } ], "_score": 3.322219294733919, "_indexed": false, "_nocasepkg": "cat3advice", "_universes": [ "ices-tools-prod" ], "_indexurl": "https://shfischer.r-universe.dev/cat3advice", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.2", "date": "2026-05-15T09:22:50.000Z", "distro": "noble", "commit": "76680ef15123d9b9f0510dee625b2b1b75cd260c", "fileid": "d29edd245fe16b9dc52f650ce62499a0effd0fdcfff38d55f97d04509196c7c6", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/25910074760" }, { "r": "4.6.0", "os": "linux", "version": "0.1.2", "date": "2026-05-15T09:22:39.000Z", "distro": "noble", "commit": "76680ef15123d9b9f0510dee625b2b1b75cd260c", "fileid": "735dcc8ee5943a22e9be12ef38532abcc781144a272f1d66828e07ffd2d82faf", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/25910074760" }, { "r": "4.5.3", "os": "mac", "version": "0.1.2", "date": "2026-05-15T09:22:25.000Z", "commit": "76680ef15123d9b9f0510dee625b2b1b75cd260c", "fileid": "b9c6b6c7574638dbd2756953e2ba4e56fa9fd380488adef0cf9afab4e2a93560", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/25910074760" }, { "r": "4.6.0", "os": "mac", "version": "0.1.2", "date": "2026-05-15T09:22:18.000Z", "commit": "76680ef15123d9b9f0510dee625b2b1b75cd260c", "fileid": "a2d221fe98d47098ae6fa64586ab5bfc05cb69b0975b4a4fd1feec12809dcdbe", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/25910074760" }, { "r": "4.7.0", "os": "win", "version": "0.1.2", "date": "2026-05-15T09:27:02.000Z", "commit": "76680ef15123d9b9f0510dee625b2b1b75cd260c", "fileid": "f19bc5936cbb288c16fb63de4a7d074ce1e4d853c6c63a6a0aa82858134a6201", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/25910074760" }, { "r": "4.5.3", "os": "win", "version": "0.1.2", "date": "2026-05-15T09:21:44.000Z", "commit": "76680ef15123d9b9f0510dee625b2b1b75cd260c", "fileid": "64a4d9c09f1fffd39bd53565b92d1b9a74739ef04478d3016b149e0a6159be6a", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/25910074760" }, { "r": "4.6.0", "os": "win", "version": "0.1.2", "date": "2026-05-15T09:22:02.000Z", "commit": "76680ef15123d9b9f0510dee625b2b1b75cd260c", "fileid": "51f0f25db4712cb9e1d833863e2c48852f1311e81c45a7d91b035df089fdb1f4", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/25910074760" }, { "r": "4.6.0", "os": "wasm", "version": "0.1.2", "date": "2026-06-02T19:27:16.000Z", "commit": "76680ef15123d9b9f0510dee625b2b1b75cd260c", "fileid": "7a4fc43566ac4f81dd1691af00bd3d70149141c659f662256d7608bf4c24a880", "status": "success", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/25910074760" } ] }