{ "_id": "6a1329d4acfb0bcc41d284a3", "Package": "mse", "Title": "Tools for Running Management Strategy Evaluations using FLR", "Version": "2.4.9", "Authors@R": "c(person(given = \"Iago\", family = \"Mosqueira\",\nrole = c(\"aut\", \"cre\"), email = \"iago.mosqueira@wur.nl\"),\nperson(\"Ernesto\", \"Jardim\", email = \"ernesto.jardim@gmail.com\",\nrole = c(\"aut\")))", "Description": "A set of functions and methods to enable the development\nand running of Management Strategy Evaluation (MSE) analyses,\nusing the FLR packages and classes and the a4a methods and\nalgorithms.", "Additional_repositories": "https://flr.r-universe.dev", "Collate": "'generics.R' 'mseCtrl-class.R' 'mpCtrl-class.R' 'FLo-class.R'\n'FLom-class.R' 'FLombf-class.R' 'oem.R' 'FLoem-class.R'\n'FLiem-class.R' 'FLmse-class.R' 'FLmses-class.R' 'dispatch.R'\n'mp.R' 'tune.R' 'tracking.R' 'performance.R' 'plot.R' 'data.R'\n'utilities.R' 'sa.R' 'ind.R' 'phcr.R' 'hcr.R' 'is.R' 'iem.R'\n'fb.R' 'tm.R' 'om.R' 'statistics.R'", "License": "EUPL", "LazyLoad": "true", "LazyData": "false", "BugReports": "https://github.com/flr/mse/issues", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "Repository": "https://ices-tools-prod.r-universe.dev", "Date/Publication": "2026-05-24 15:47:22 UTC", "RemoteUrl": "https://github.com/flr/mse", "RemoteRef": "HEAD", "RemoteSha": "6c7e81302180d6fe8f4cc7debf2b17c2f3ccd6db", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-24 16:13:38 UTC", "User": "root" }, "Author": "Iago Mosqueira [aut, cre],\nErnesto Jardim [aut]", "Maintainer": "Iago Mosqueira ", "MD5sum": "e958796e75576d36052e68a71fcfc31f", "_user": "ices-tools-prod", "_type": "src", "_file": "mse_2.4.9.tar.gz", "_fileid": "39c4ac3cc8851adf9fe2fb3ed340a07116f7601b17a94f94c75651a814bba298", "_filesize": 49080291, "_sha256": "39c4ac3cc8851adf9fe2fb3ed340a07116f7601b17a94f94c75651a814bba298", "_created": "2026-05-24T16:13:38.000Z", "_published": "2026-05-24T16:39:48.159Z", "_distro": "noble", "_jobs": [ { "job": 77610591240, "time": 893, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7186660377" }, { "job": 77610591223, "time": 966, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7186668810" }, { "job": 77610591237, "time": 483, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7186614518" }, { "job": 77610591233, "time": 572, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7186624234" }, { "job": 77610302790, "time": 300, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7186564751" }, { "job": 77610591222, "time": 137, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7186579108" }, { "job": 77610591229, "time": 1483, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7186724180" }, { "job": 77610591227, "time": 934, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7186664952" }, { "job": 77610591234, "time": 897, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7186660688" } ], "_buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/26366193648", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/flr/mse", "_commit": { "id": "6c7e81302180d6fe8f4cc7debf2b17c2f3ccd6db", "author": "Iago Mosqueira ", "committer": "Iago Mosqueira ", "message": "Version update\n", "time": 1779637642 }, "_maintainer": { "name": "Iago Mosqueira", "email": "iago.mosqueira@wur.nl", "login": "iagomosqueira", "description": "", "uuid": 1029847 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "data.table", "role": "Depends" }, { "package": "FLCore", "version": ">= 2.6.22", "role": "Depends" }, { "package": "FLasher", "version": ">= 0.7.1", "role": "Depends" }, { "package": "future", "role": "Depends" }, { "package": "progressr", "role": "Depends" }, { "package": "doFuture", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "FLFishery", "role": "Imports" }, { "package": "FLBRP", "version": ">= 2.5.8", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "ggplotFL", "version": ">= 2.7.2", "role": "Imports" }, { "package": "ggrepel", "role": "Imports" }, { "package": "patchwork", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "FLa4a", "role": "Suggests" }, { "package": "doParallel", "role": "Suggests" } ], "_owner": "flr", "_selfowned": false, "_usedby": 4, "_updates": [ { "week": "2025-23", "n": 2 }, { "week": "2025-28", "n": 2 }, { "week": "2025-33", "n": 1 }, { "week": "2025-36", "n": 1 }, { "week": "2025-42", "n": 1 }, { "week": "2025-43", "n": 1 }, { "week": "2025-45", "n": 4 }, { "week": "2025-46", "n": 4 }, { "week": "2025-47", "n": 2 }, { "week": "2025-48", "n": 7 }, { "week": "2025-49", "n": 4 }, { "week": "2025-50", "n": 16 }, { "week": "2025-51", "n": 9 }, { "week": "2025-52", "n": 8 }, { "week": "2026-01", "n": 24 }, { "week": "2026-02", "n": 23 }, { "week": "2026-03", "n": 10 }, { "week": "2026-04", "n": 1 }, { "week": "2026-05", "n": 10 }, { "week": "2026-06", "n": 5 }, { "week": "2026-07", "n": 2 }, { "week": "2026-09", "n": 10 }, { "week": "2026-11", "n": 6 }, { "week": "2026-12", "n": 2 }, { "week": "2026-13", "n": 11 }, { "week": "2026-15", "n": 4 }, { "week": "2026-19", "n": 2 }, { "week": "2026-21", "n": 2 } ], "_tags": [ { "name": "v2.3.0", "date": "2025-11-27" }, { "name": "mse_2.4.9", "date": "2026-05-24" } ], "_topics": [ "simulation", "mse", "fisheries", "flr", "a4a", "management-strategy-evaluation" ], "_stars": 4, "_contributors": [ { "user": "iagomosqueira", "count": 999, "uuid": 1029847 }, { "user": "lauriekell", "count": 17, "uuid": 1682087 } ], "_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/mse" }, "_devurl": "https://github.com/flr/mse", "_searchresults": 178, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/mse.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_cranurl": false, "_exports": [ "args", "args<-", "biol", "biol<-", "biols", "biols<-", "catch", "catch.n", "catch.n<-", "catch.wt", "catch.wt<-", "catch<-", "combinations", "control", "cpue.ind", "cpues.ind", "debug", "decisions", "default.oem", "deplete", "deviances", "deviances<-", "dims", "discards", "discards.n", "discards.n<-", "discards.wt", "discards.wt<-", "discards<-", "effortlimit.fb", "est", "est<-", "exists", "FCB", "FCB<-", "fec", "fisheries", "fisheries<-", "fixedC.hcr", "fixedF.hcr", "fleetBehaviour", "fleetBehaviour<-", "FLiem", "FLmse", "FLmses", "FLoem", "FLom", "FLombf", "fwd", "fwd.om", "goFish", "harvest", "harvest<-", "hcr", "hcr<-", "hockeystick.hcr", "hr", "hyperstability.fb", "index.hat", "indicator.is", "initiate", "isys", "isys<-", "iter", "landings", "landings<-", "loadlist", "m", "m.spwn", "m.spwn<-", "m<-", "mat", "mat<-", "merge", "method", "method<-", "metrics", "model", "model<-", "movingF.phcr", "mp", "mpa.tm", "mpCtrl", "mpDispatch", "mps", "mseCtrl", "n", "noise.iem", "observations", "observations<-", "oem", "oem<-", "om", "om<-", "perfect.oem", "perfect.sa", "performance", "performance<-", "phcr", "phcr<-", "plot_hockeystick.hcr", "projection", "projection<-", "rec", "refpts", "refpts<-", "response.fb", "sampling.oem", "seasonal.is", "selectMetric", "setcontrol", "setdeviances", "shortcut.oem", "simulator", "sp.is", "split.is", "sr<-", "ssb", "statistics", "stock", "stock.n", "stock.n<-", "stock.wt", "stock.wt<-", "stock<-", "tac.is", "tm", "tm<-", "track<-", "tracking", "tracking<-", "tsb", "tunebisect", "undebug", "wt" ], "_datasets": [ { "name": "oem", "title": "S4 class 'FLmse'", "object": "plesim", "file": "plesim.rda", "class": [ "FLoem" ], "fields": [], "table": false, "tojson": false }, { "name": "oem", "title": "S4 class 'FLmse'", "object": "sol274", "file": "sol274.rda", "class": [ "FLoem" ], "fields": [], "table": false, "tojson": false }, { "name": "om", "title": "S4 class 'FLmse'", "object": "plesim", "file": "plesim.rda", "class": [ "FLom" ], "fields": [], "table": false, "tojson": false }, { "name": "om", "title": "S4 class 'FLmse'", "object": "sol274", "file": "sol274.rda", "class": [ "FLom" ], "fields": [], "table": false, "tojson": false }, { "name": "statistics", "title": "A complete set of performance statistics", "object": "statistics", "file": "statistics.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "cpue.ind", "title": "Computes CPUE-based Indicators of changes in Stock Abundance", "topics": [ "cpue.ind" ] }, { "page": "debug-mse", "title": "Debugging mse modules", "topics": [ "debug,FLo,ANY-method", "debug,mseCtrl,missing-method", "debug-mse", "undebug,FLo,ANY-method", "undebug,mpCtrl,character-method", "undebug,mpCtrl,missing-method", "undebug,mseCtrl,missing-method" ] }, { "page": "fixedC.hcr", "title": "A fixed target C", "topics": [ "fixedC.hcr" ] }, { "page": "fixedF.hcr", "title": "A fixed target F", "topics": [ "fixedF.hcr" ] }, { "page": "FLiem-class", "title": "S4 class 'FLiem'", "topics": [ "FLiem", "FLiem-class", "FLiem-methods", "initialize,FLiem-method", "iter,FLiem-method" ] }, { "page": "FLmse-class", "title": "S4 class 'FLmse'", "topics": [ "args,FLmse-method", "args<-,FLmse,list-method", "control,FLmse-method", "FLmse", "FLmse-class", "FLmse-methods", "oem", "oem,FLmse-method", "oem-methods", "oem<-", "oem<--methods", "om", "om,FLmse-method", "om-methods", "om<-", "om<--methods", "tracking", "tracking,FLmse-method", "tracking-methods", "tracking<-", "tracking<--methods" ] }, { "page": "FLoem-class", "title": "Specification for the observation error model (OEM).", "topics": [ "combine,FLoem,FLoem-method", "deviances,FLoem-method", "deviances<-,FLoem,list-method", "FLoem", "FLoem-class", "FLoem-methods", "iter,FLoem-method", "observations", "observations,FLoem-method", "observations-methods", "observations<-", "observations<-,FLoem,ANY,FLStock-method", "observations<-,FLoem,missing,list-method", "observations<--methods", "show,FLoem-method" ] }, { "page": "FLom-class", "title": "A class for an operating model (OM)", "topics": [ "combine,FLom,FLom-method", "control<-,FLmse,mpCtrl-method", "FLom", "FLom-class", "FLom-methods", "oem<-,FLmse,FLoem-method", "om<-,FLmse,FLo-method", "sr,FLom-method", "sr<-,FLom,FLSR-method", "stock,FLom-method", "stock<-,FLom,FLStock-method", "tracking<-,FLmse,data.table-method" ] }, { "page": "fwd.om", "title": "A method to project the operating model (OM)", "topics": [ "fwd.om" ] }, { "page": "hockeystick.hcr", "title": "Hockey-stick Harvest Control Rule", "topics": [ "hockeystick.hcr" ] }, { "page": "hr", "title": "hr method for FLombf", "topics": [ "hr,FLombf-method" ] }, { "page": "index.hat-FLIndexBiomass-FLStock-method", "title": "Predicted index of abundance from abundance estimates", "topics": [ "index.hat,FLIndexBiomass,FLStock-method" ] }, { "page": "indicator.is", "title": "Indicator Implementation System Module", "topics": [ "indicator.is" ] }, { "page": "initiate", "title": "Initializes a population for a given virgin biomass.", "topics": [ "initiate" ] }, { "page": "mp", "title": "mp executes a single run of a Management Procedure", "topics": [ "mp" ] }, { "page": "mpCtrl-class", "title": "S4 class 'mpCtrl'", "topics": [ "args,mpCtrl-method", "args<-,mpCtrl,function-method", "args<-,mpCtrl-method", "debug,mpCtrl,character-method", "est,mpCtrl-method", "est<-", "est<-,mpCtrl,function-method", "est<-,mpCtrl,list-method", "est<-,mpCtrl,mseCtrl-method", "est<--methods", "hcr,mpCtrl-method", "hcr<-", "hcr<-,mpCtrl,function-method", "hcr<-,mpCtrl,list-method", "hcr<-,mpCtrl,mseCtrl-method", "hcr<--methods", "initialize,mpCtrl-method", "isys,mpCtrl-method", "isys<-", "isys<-,mpCtrl,function-method", "isys<-,mpCtrl,list-method", "isys<-,mpCtrl,mseCtrl-method", "isys<--methods", "iter,mpCtrl-method", "iters,mpCtrl-method", "method,mpCtrl-method", "method<-,mpCtrl,function-method", "method<-,mpCtrl-method", "mpCtrl", "mpCtrl-class", "mpCtrl-methods", "phcr,mpCtrl-method", "phcr<-", "phcr<-,mpCtrl,function-method", "phcr<-,mpCtrl,list-method", "phcr<-,mpCtrl,mseCtrl-method", "phcr<--methods", "show,mpCtrl-method", "tm,mpCtrl-method", "tm<-", "tm<-,mpCtrl,function-method", "tm<-,mpCtrl,list-method", "tm<-,mpCtrl,mseCtrl-method", "tm<--methods" ] }, { "page": "mpDispatch", "title": "Title", "topics": [ "mpDispatch" ] }, { "page": "mps", "title": "Run Multiple Management Procedure Scenarios", "topics": [ "mps" ] }, { "page": "mseCtrl-class", "title": "S4 class 'mseCtrl'", "topics": [ "args", "args,mseCtrl-method", "args-methods", "args<-", "args<-,mseCtrl,list-method", "args<--methods", "exists", "exists,mseCtrl-method", "initialize,mseCtrl-method", "method", "method,mseCtrl-method", "method-methods", "method<-", "method<-,mseCtrl,function-method", "method<--methods", "mseCtrl", "mseCtrl-class", "mseCtrl-methods", "show,mseCtrl-method" ] }, { "page": "partialHR", "title": "hr", "topics": [ "partialHR" ] }, { "page": "perfect.oem", "title": "A perfect observation of catch and abundances-at-age.", "topics": [ "perfect.oem" ] }, { "page": "perfect.sa", "title": "A perfect 'estimate' of abundances, catches and harvest.", "topics": [ "perfect.sa" ] }, { "page": "performance", "title": "Compute Performance Statistics for Management Procedure Evaluation", "topics": [ "performance", "performance,FLmse-method", "performance,FLmses-method", "performance,FLo-method", "performance,FLombf-method", "performance,FLQuants-method", "performance,FLStock-method", "performance,FLStocks-method", "performance,list-method" ] }, { "page": "plesim", "title": "FLom object", "topics": [ "plesim" ] }, { "page": "sampling.oem", "title": "sampling.oem", "topics": [ "sampling.oem" ] }, { "page": "selectMetric", "title": "Select and/or Compute a Metric from the _stk_ and _ind_ inputs", "topics": [ "selectMetric" ] }, { "page": "setcontrol", "title": "setcontrol Modify on the fly the arguments on any mpCtrl module", "topics": [ "setcontrol" ] }, { "page": "split.is", "title": "Split a biol target across fleets by setting relative 'quant' proportions", "topics": [ "split.is" ] }, { "page": "statistics", "title": "A complete set of performance statistics", "topics": [ "statistics" ] }, { "page": "tac.is", "title": "TAC implementation system module", "topics": [ "tac.is" ] }, { "page": "tunebisect", "title": "Tune Management Procedures Using Bisection Method", "topics": [ "tunebisect" ] } ], "_pkglogo": "https://github.com/flr/mse/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/flr/mse/raw/HEAD/README.md", "_rundeps": [ "cli", "codetools", "cowplot", "cpp11", "data.table", "digest", "doFuture", "farver", "FLasher", "FLBRP", "FLCore", "FLFishery", "foreach", "future", "future.apply", "ggplot2", "ggplotFL", "ggrepel", "globals", "glue", "gridExtra", "gtable", "isoband", "iterators", "labeling", "lattice", "lifecycle", "listenv", "MASS", "Matrix", "parallelly", "patchwork", "progressr", "R6", "RColorBrewer", "Rcpp", "rlang", "S7", "scales", "vctrs", "viridisLite", "withr" ], "_score": 6.077789275362719, "_indexed": false, "_nocasepkg": "mse", "_universes": [ "ices-tools-prod" ], "_indexurl": "https://flr.r-universe.dev/mse", "_previous": "2.4.8", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.4.9", "date": "2026-05-24T16:16:49.000Z", "distro": "noble", "commit": "6c7e81302180d6fe8f4cc7debf2b17c2f3ccd6db", "fileid": "1e79bef6f00d21accbf95648ab33d68a2d7b47db3c972de5d09e4a1247812821", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/26366193648" }, { "r": "4.6.0", "os": "linux", "version": "2.4.9", "date": "2026-05-24T16:17:24.000Z", "distro": "noble", "commit": "6c7e81302180d6fe8f4cc7debf2b17c2f3ccd6db", "fileid": "74a653486b11d1bef340f18cd269b41c5d77bcf6bf79fa68c51b7d26340b147d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/26366193648" }, { "r": "4.5.3", "os": "mac", "version": "2.4.9", "date": "2026-05-24T16:15:51.000Z", "commit": "6c7e81302180d6fe8f4cc7debf2b17c2f3ccd6db", "fileid": "fd14104d30b57ec83e709e408a0e584bd604a9c4c7943ed4dd155891eeccded5", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/26366193648" }, { "r": "4.6.0", "os": "mac", "version": "2.4.9", "date": "2026-05-24T16:15:47.000Z", "commit": "6c7e81302180d6fe8f4cc7debf2b17c2f3ccd6db", "fileid": "d3871bb9e1de09f49e3f6917c03143d9c74ae0f3873bee08feb1d9912ab6a5b1", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/26366193648" }, { "r": "4.6.0", "os": "wasm", "version": "2.4.9", "date": "2026-05-24T16:16:57.000Z", "commit": "6c7e81302180d6fe8f4cc7debf2b17c2f3ccd6db", "fileid": "ac3a3cd3e479bb3949cfc49f4d04922de58d093328214507576c138a6acd2d4e", "status": "success", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/26366193648" }, { "r": "4.7.0", "os": "win", "version": "2.4.9", "date": "2026-05-24T16:16:01.000Z", "commit": "6c7e81302180d6fe8f4cc7debf2b17c2f3ccd6db", "fileid": "38693dca7f8f07ab7b6036f79d149a7be9bf138da23cb3c7652d4f7eabb25524", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/26366193648" }, { "r": "4.5.3", "os": "win", "version": "2.4.9", "date": "2026-05-24T16:15:40.000Z", "commit": "6c7e81302180d6fe8f4cc7debf2b17c2f3ccd6db", "fileid": "1a8c3bcc649ee068225b95073210e8d9aa4ed68cc06dc10ff5c3ac1ca7a1410e", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/26366193648" }, { "r": "4.6.0", "os": "win", "version": "2.4.9", "date": "2026-05-24T16:15:48.000Z", "commit": "6c7e81302180d6fe8f4cc7debf2b17c2f3ccd6db", "fileid": "422e5f36513b72a82d8ae6b7dc0f7a8fe39d38b16fc7a03072b37c6d5ba5a086", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ices-tools-prod/actions/runs/26366193648" } ] }