{ "_id": "6a4c1d4907c3fd5c3260d610", "Package": "FLjjm", "Title": "Running the JJM Stock Assessment Model Inside the MSE FLR System", "Version": "0.3.10", "AuthorR": "c( person(given = 'Iago', family = 'Mosqueira', role =\nc('aut', 'cre'), email = 'iago.mosqueira@wur.nl'), person(given\n= 'Karolina', family = 'Molla Gazi', role = c('aut'), email =\n'karolina.mollagazi@wur.nl'))", "Description": "Runs the JJM stock assessment model for Chilean Jack\nMackerel inside the MSE system of FLR's mse package.", "Additional_repositories": "https://sprfmo.r-universe.dev,\nhttps://flr.r-universe.dev", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "License": "EUPL", "LazyLoad": "Yes", "LazyData": "No", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-06 21:17:10 UTC", "User": "root" }, "Author": "Iago Mosqueira [aut, cre], Karolina Molla Gazi [aut]", "Maintainer": "Iago Mosqueira ", "Config/pak/sysreqs": "bwidget cmake make libicu-dev libjpeg-dev\nlibpng-dev libuv1-dev libxml2-dev", "Repository": "https://sprfmo.r-universe.dev", "Date/Publication": "2026-06-25 07:45:01 UTC", "RemoteUrl": "https://github.com/SPRFMO/FLjjm", "RemoteRef": "HEAD", "RemoteSha": "732a89da2056e4e0533ecae2d552fdb0674dda79", "_user": "sprfmo", "_type": "src", "_file": "FLjjm_0.3.10.tar.gz", "_fileid": "https://r2.ropensci.org/f6187643a73648af6508b2d71d8f64c3ccb46f0933451f7dc6f9519f5ad5e6d0", "_filesize": 7770369, "_sha256": "f6187643a73648af6508b2d71d8f64c3ccb46f0933451f7dc6f9519f5ad5e6d0", "_expires": "2026-10-14T21:25:27.000Z", "_created": "2026-07-06T21:17:10.000Z", "_published": "2026-07-06T21:25:29.563Z", "_jobs": [ { "job": 85482225708, "time": 379, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "8121954739" }, { "job": 85482225700, "time": 414, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "8121966987" }, { "job": 85482225676, "time": 210, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "8121894932" }, { "job": 85482225693, "time": 183, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "8121885341" }, { "job": 85481367519, "time": 276, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8121819836" }, { "job": 85482225718, "time": 199, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8121891154" }, { "job": 85482225705, "time": 218, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "8121898544" }, { "job": 85482225731, "time": 262, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "8121914788" }, { "job": 85482225702, "time": 232, "config": "windows-release", "r": "4.6.1", "check": "WARNING", "artifact": "8121903470" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/sprfmo/actions/runs/28823668727", "_status": "success", "_upstream": "https://github.com/SPRFMO/FLjjm", "_commit": { "id": "732a89da2056e4e0533ecae2d552fdb0674dda79", "author": "Iago Mosqueira ", "committer": "Iago Mosqueira ", "message": "Updated perf stats and metrics\n", "time": 1782373501 }, "_maintainer": { "name": "Iago Mosqueira", "email": "iago.mosqueira@wur.nl", "login": "iagomosqueira", "description": "", "uuid": 1029847 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "FLCore", "role": "Depends" }, { "package": "ggplotFL", "role": "Depends" }, { "package": "jjmR", "version": ">= 1.2018.02", "role": "Depends" }, { "package": "mse", "role": "Imports" }, { "package": "FLFishery", "role": "Imports" }, { "package": "FLasher", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "progressr", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "sprfmo", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-28", "n": 3 }, { "week": "2025-50", "n": 5 }, { "week": "2026-10", "n": 4 }, { "week": "2026-11", "n": 7 }, { "week": "2026-17", "n": 1 }, { "week": "2026-20", "n": 2 }, { "week": "2026-21", "n": 2 }, { "week": "2026-22", "n": 6 }, { "week": "2026-23", "n": 1 }, { "week": "2026-24", "n": 9 }, { "week": "2026-25", "n": 3 }, { "week": "2026-26", "n": 2 } ], "_tags": [], "_stars": 0, "_contributors": [ { "user": "iagomosqueira", "count": 101, "uuid": 1029847 }, { "user": "jimianelli", "count": 8, "uuid": 2715618 } ], "_userbio": { "uuid": 5023653, "type": "organization", "name": "SPRFMO", "followers": 16, "description": "South Pacific Regional Fisheries Management Organisation" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/FLjjm" }, "_devurl": "https://github.com/sprfmo/fljjm", "_searchresults": 8, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/FLjjm.html", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_cranurl": false, "_exports": [ "buildFLBjjm", "buildFLBsjjm", "buildFLFsjjm", "buildFLIsjjm", "buildFLRPsjjm", "buildFLSjjm", "buildFLSsjjm", "buildjjmctl", "buildjjmdata", "calljjms", "cjm.iem", "cjm.oem", "cjmage2len", "exejjms", "fwdmov", "fwdmov.om", "get_os", "getjjms", "jjms", "jjms.sa", "jmets", "loadJJMS", "perfect.oem", "readFLBjjm", "readFLFsjjm", "readFLIsjjm", "readFLoemjjm", "readFLomjjm", "readFLRPsjjm", "readFLSjjm", "readFLSsjjm", "readMod", "readRep", "runjjms", "slick_performance" ], "_datasets": [ { "name": "biol", "title": "", "object": "cjm", "file": "cjm.RData", "class": [ "FLBiol" ], "fields": [], "table": false, "tojson": false }, { "name": "fiss", "title": "", "object": "cjm", "file": "cjm.RData", "class": [ "FLFisheries" ], "fields": [], "table": false, "tojson": false }, { "name": "idx", "title": "", "object": "cjmstk", "file": "cjmstk.RData", "class": [ "FLIndices" ], "fields": [], "table": false, "tojson": false }, { "name": "idxs", "title": "", "object": "cjmstks", "file": "cjmstks.RData", "class": [ "FLIndices" ], "fields": [], "table": false, "tojson": false }, { "name": "indicators", "title": "", "object": "indicators", "file": "indicators.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "inds", "title": "", "object": "cjm", "file": "cjm.RData", "class": [ "FLIndices" ], "fields": [], "table": false, "tojson": false }, { "name": "mod", "title": "", "object": "cjmstk", "file": "cjmstk.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "mods", "title": "", "object": "cjmstks", "file": "cjmstks.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "oem", "title": "", "object": "ombf", "file": "ombf.RData", "class": [ "FLoem" ], "fields": [], "table": false, "tojson": false }, { "name": "om", "title": "", "object": "ombf", "file": "ombf.RData", "class": [ "FLombf" ], "fields": [], "table": false, "tojson": false }, { "name": "statistics", "title": "", "object": "statistics", "file": "statistics.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "stk", "title": "", "object": "cjmstk", "file": "cjmstk.RData", "class": [ "FLStock" ], "fields": [], "table": false, "tojson": false }, { "name": "stks", "title": "", "object": "cjmstks", "file": "cjmstks.RData", "class": [ "FLStocks" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "dot-combinejjmsout", "title": "Combine Fisheries Model Results", "topics": [ ".combinejjmsout" ] }, { "page": "AgeToLengthComp", "title": "Convert Age Composition to Length Composition", "topics": [ "AgeToLengthComp" ] }, { "page": "build", "title": "Build Functions for FLjjm Package", "topics": [ "build" ] }, { "page": "buildFLBjjm", "title": "Build an FLBiol from a jjm.output object", "topics": [ "buildFLBjjm" ] }, { "page": "buildFLFsjjm", "title": "Build FLFisheries from JJMS Model Output", "topics": [ "buildFLFsjjm" ] }, { "page": "buildFLIsjjm", "title": "Construct FLIndices from a jjm.output object", "topics": [ "buildFLIsjjm" ] }, { "page": "buildFLRPsjjm", "title": "Build reference points (FLPar) from jjm.output", "topics": [ "buildFLRPsjjm" ] }, { "page": "buildFLSjjm", "title": "Build FLStock from jjm.output", "topics": [ "buildFLSjjm" ] }, { "page": "buildFLSojjm", "title": "Build FLStock with areas from jjm.output", "topics": [ "buildFLSojjm" ] }, { "page": "buildFLSsjjm", "title": "Build multiple FLStock objects from jjm.output", "topics": [ "buildFLSsjjm" ] }, { "page": "buildjjmctl", "title": "Updating dat and ctl file lists from FLstock(s) and FLIndices", "topics": [ "buildjjmctl" ] }, { "page": "catch-FLStocks-method", "title": "Calculate Total Catch across FLStocks", "topics": [ "catch,FLStocks-method" ] }, { "page": "cjm.oem", "title": "Observation Error Model wrapper for CJM within MSE workflows", "topics": [ "cjm.oem" ] }, { "page": "cjmage2len", "title": "Convert Age Composition to Length Composition for Landings", "topics": [ "cjmage2len" ] }, { "page": "cjmfwc", "title": "Converts FLQuants with Fleets as Areas into a fwdControl Object", "topics": [ "cjmfwc" ] }, { "page": "exejjms", "title": "Execute JJMS Model", "topics": [ "exejjms" ] }, { "page": "fbar-FLStocks-method", "title": "Calculate Average Fishing Mortality across FLStocks", "topics": [ "fbar,FLStocks-method" ] }, { "page": "FLjjm", "title": "FLjjm: An R Package for Interacting with JJMS Stock Assessment Model in FLR", "topics": [ "FLjjm" ] }, { "page": "fwdmov", "title": "Forward Movement Simulation", "topics": [ "fwdmov" ] }, { "page": "fwdmov.om", "title": "Forward Movement Operation Model", "topics": [ "fwdmov.om" ] }, { "page": "jjms", "title": "Run JJMS Model for Fisheries Stock Assessment", "topics": [ "jjms" ] }, { "page": "jjms.sa", "title": "JJMS Stock Assessment", "topics": [ "jjms.sa" ] }, { "page": "loadFLSjjms", "title": "Load FLStocks from JJMS Model", "topics": [ "loadFLSjjms" ] }, { "page": "loadJJMS", "title": "Load JJMS Model Components", "topics": [ "loadJJMS" ] }, { "page": "namejjms", "title": "Get Name of JJMS Model", "topics": [ "namejjms" ] }, { "page": "nStocksjjms", "title": "Get Number of Stocks in JJMS Model", "topics": [ "nStocksjjms" ] }, { "page": "packjjmsrun", "title": "Clean Up JJMS Model Run Directory", "topics": [ "packjjmsrun" ] }, { "page": "readFLBjjm", "title": "Create an FLBiol from a JJMS model run directory", "topics": [ "readFLBjjm" ] }, { "page": "readFLFsjjm", "title": "Create FLFisheries objects from a JJMS model run directory", "topics": [ "readFLFsjjm" ] }, { "page": "readFLIsjjm", "title": "Create an FLIndices object from a JJMS model run directory", "topics": [ "readFLIsjjm" ] }, { "page": "readFLoemjjm", "title": "Read FLIndices with OEM iterations and MC outputs", "topics": [ "readFLoemjjm" ] }, { "page": "readFLomjjm", "title": "Create an FLombf object from a JJMS model run directory", "topics": [ "readFLomjjm" ] }, { "page": "readFLRPsjjm", "title": "Create an FLPar contaning reference points from a JJMS model run directory", "topics": [ "readFLRPsjjm" ] }, { "page": "readFLSjjm", "title": "Create an FLStock from a JJMS model run directory", "topics": [ "readFLSjjm" ] }, { "page": "readFLSsjjm", "title": "Create an FLStocks from a two-stock JJMS model run directory", "topics": [ "readFLSsjjm" ] }, { "page": "runjjms", "title": "Run JJMS Model", "topics": [ "runjjms" ] }, { "page": "slick_performance", "title": "Compute performance metrics for MPs and OM in slick format", "topics": [ "slick_performance" ] }, { "page": "ssb-FLStocks-method", "title": "Calculate Total Spawning Stock Biomass across FLStocks", "topics": [ "ssb,FLStocks-method" ] }, { "page": "yourFunctionName", "title": "Construct Components of Fisheries Model", "topics": [ "yourFunctionName" ] } ], "_rundeps": [ "backports", "base64enc", "boot", "broom", "bslib", "cachem", "cli", "codetools", "colorspace", "cowplot", "cpp11", "data.table", "deldir", "Deriv", "digest", "doBy", "doFuture", "dplyr", "evaluate", "farver", "fastmap", "FLasher", "FLBRP", "FLCore", "FLFishery", "fontawesome", "forcats", "foreach", "forecast", "fracdiff", "fs", "future", "future.apply", "generics", "ggplot2", "ggplotFL", "ggrepel", "ggridges", "globals", "glue", "gridExtra", "gtable", "highr", "htmltools", "icesAdvice", "interp", "isoband", "iterators", "jjmR", "jpeg", "jquerylib", "jsonlite", "knitr", "labeling", "lattice", "latticeExtra", "lifecycle", "listenv", "lmtest", "magrittr", "MASS", "Matrix", "memoise", "mime", "modelr", "mse", "nlme", "nnet", "parallelly", "patchwork", "PBSmodelling", "pillar", "pkgconfig", "png", "progressr", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "rlang", "rmarkdown", "S7", "sass", "scales", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "timeDate", "tinytex", "urca", "utf8", "vctrs", "viridisLite", "withr", "xfun", "XML", "yaml", "zoo" ], "_vignettes": [ { "source": "FLjjm.Rmd", "filename": "FLjjm.html", "title": "Description of the FLjjm package", "author": "Name SURNAME", "engine": "knitr::rmarkdown", "headings": [ "Using the FLjjm package", "Loading jjms outputs", "Running jjms", "jjms.sa", "Observation Error Model (oem)", "Indices of abundance to generate in MP:", "Example / Workflow 1", "Example / Workflow 2", "Reference", "buildjjmdata", "buildFLIsjjm", "FLIndex", "More information", "Software Versions", "Author information", "References" ], "created": "2024-01-19 17:41:21", "modified": "2026-05-31 08:45:04", "commits": 3 } ], "_score": 3.079181246047625, "_indexed": true, "_nocasepkg": "fljjm", "_universes": [ "sprfmo", "iagomosqueira" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.3.10", "date": "2026-07-06T21:20:29.000Z", "distro": "resolute", "commit": "732a89da2056e4e0533ecae2d552fdb0674dda79", "fileid": "https://r2.ropensci.org/bfae0921f020affea5135fafa509ec1e7f86ac1943d426e5795b3de8186d5483", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/sprfmo/actions/runs/28823668727" }, { "r": "4.6.1", "os": "linux", "version": "0.3.10", "date": "2026-07-06T21:21:20.000Z", "distro": "resolute", "commit": "732a89da2056e4e0533ecae2d552fdb0674dda79", "fileid": "https://r2.ropensci.org/164dbe3d0bec09cbe5694d68c0b8f8b21bb2e398b918e82bea243c27ece76937", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/sprfmo/actions/runs/28823668727" }, { "r": "4.5.3", "os": "mac", "version": "0.3.10", "date": "2026-07-06T21:19:40.000Z", "commit": "732a89da2056e4e0533ecae2d552fdb0674dda79", "fileid": "https://r2.ropensci.org/df8521e4aa733a0bb36e239924e22801f833743bbb5d36d30a53d24123cad682", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/sprfmo/actions/runs/28823668727" }, { "r": "4.6.1", "os": "mac", "version": "0.3.10", "date": "2026-07-06T21:19:24.000Z", "commit": "732a89da2056e4e0533ecae2d552fdb0674dda79", "fileid": "https://r2.ropensci.org/76ff3ddba7cdbb6f1b9595f26c69f8adce58dbcd3df6331baa5b162a576d8ba0", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/sprfmo/actions/runs/28823668727" }, { "r": "4.6.0", "os": "wasm", "version": "0.3.10", "date": "2026-07-06T21:21:16.000Z", "commit": "732a89da2056e4e0533ecae2d552fdb0674dda79", "fileid": "https://r2.ropensci.org/bb106d9d9fe672f6e538aabf6795e9119f5fdaaa2d62662751677a1e0480f50d", "status": "success", "buildurl": "https://github.com/r-universe/sprfmo/actions/runs/28823668727" }, { "r": "4.7.0", "os": "win", "version": "0.3.10", "date": "2026-07-06T21:19:12.000Z", "commit": "732a89da2056e4e0533ecae2d552fdb0674dda79", "fileid": "https://r2.ropensci.org/ed8357425a954d4548eb003ff56d8a3be362f61f5a7bbf300320b252ddb46164", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/sprfmo/actions/runs/28823668727" }, { "r": "4.5.3", "os": "win", "version": "0.3.10", "date": "2026-07-06T21:19:20.000Z", "commit": "732a89da2056e4e0533ecae2d552fdb0674dda79", "fileid": "https://r2.ropensci.org/c6161f856bfe16f1d3f9a244613f3c178349cfe7926e0ea565e001b05bed3dce", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/sprfmo/actions/runs/28823668727" }, { "r": "4.6.1", "os": "win", "version": "0.3.10", "date": "2026-07-06T21:19:20.000Z", "commit": "732a89da2056e4e0533ecae2d552fdb0674dda79", "fileid": "https://r2.ropensci.org/c469d7916f7b53ffddf42da8a505acb56d3f4f693ac24f34551c5fe69d4e05e0", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/sprfmo/actions/runs/28823668727" } ] }