{
  "_id": "6acb69a0fe5cc25786e8f9cb",
  "Package": "jjmR",
  "Type": "Package",
  "Title": "Graphics and diagnostics tools for SPRFMO's Joint Jack Mackerel\nmodel",
  "Version": "1.2020.1",
  "Date": "2020-10-13",
  "Description": "Graphics and diagnostics tools for SPRFMO's Joint Jack\nMackerel model.",
  "Authors@R": "c( person(\"Ricardo\", \"Oliveros-Ramos\", email = \"roliveros@imarpe.gob.pe\", role = c(\"cre\", \"aut\")), person(\"Wencheng\",\n\"Lau-Medrano\", role = \"aut\"), person(\"Giancarlo\", \"Moron\", role = \"aut\"), person(\"Josymar\", \"Torrejon-Magallanes\", role = \"aut\"),\nperson(\"Niels\", \"Hintzen\", email = \"niels.hintzen@wur.nl\", role = \"aut\"),\nperson(\"Enrique\", \"Ramos-Vasquez\", role = \"ctb\"),     person(\"Jim\", \"Ianelli\", email = \"jim.ianelli@gmail.com\", role = \"aut\"))",
  "Author": "Ricardo Oliveros-Ramos [cre, aut], Wencheng Lau-Medrano [aut],\nGiancarlo Moron [aut], Josymar Torrejon-Magallanes [aut], Niels\nHintzen [aut], Enrique Ramos-Vasquez [ctb], Jim Ianelli [aut]",
  "Maintainer": "Ricardo Oliveros-Ramos <roliveros@imarpe.gob.pe>",
  "License": "GPL-2",
  "Encoding": "UTF-8",
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  "Config/pak/sysreqs": "bwidget cmake make libicu-dev libjpeg-dev\nlibpng-dev libuv1-dev libxml2-dev",
  "Repository": "https://jimianelli.r-universe.dev",
  "Date/Publication": "2026-09-11 20:55:52 UTC",
  "RemoteUrl": "https://github.com/SPRFMO/jjmr",
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  "NeedsCompilation": "no",
  "Packaged": {
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    "User": "root"
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  "_user": "jimianelli",
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  "_expires": "2027-01-19T10:49:02.000Z",
  "_created": "2026-10-11T10:41:43.000Z",
  "_published": "2026-10-11T10:49:04.328Z",
  "_buildurl": "https://github.com/r-universe/jimianelli/actions/runs/38132629643",
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  "_commit": {
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    "author": "lee-qi <leeqi@uw.edu>",
    "committer": "lee-qi <leeqi@uw.edu>",
    "message": "update docs\n",
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  "_maintainer": {
    "name": "Ricardo Oliveros-Ramos",
    "email": "roliveros@imarpe.gob.pe"
  },
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      "package": "icesAdvice",
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      "package": "magrittr",
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      "package": "rmarkdown",
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    {
      "package": "methods",
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    },
    {
      "package": "stats",
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    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    }
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  "_owner": "sprfmo",
  "_selfowned": false,
  "_usedby": 1,
  "_updates": [
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      "week": "2026-11",
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      "uuid": 5052457
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  "_userbio": {
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    "type": "user",
    "name": "Jim Ianelli",
    "followers": 84
  },
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  "_devurl": "https://github.com/sprfmo/jjmr",
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  "_rbuild": "4.6.1",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/jjmR.html",
    "extra/manual.pdf",
    "extra/readme.html",
    "extra/readme.md"
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  "_cranurl": false,
  "_exports": [
    ".getJjmConfig",
    "%>%",
    "annotate_cohorts",
    "calc_mohn_rho",
    "changeNameModel",
    "combineModels",
    "comp_fig_height",
    "compareModels",
    "diagnostics",
    "extr_agefits_fsh",
    "extr_agefits_srv",
    "extr_catch",
    "extr_catch_cv",
    "extr_cv",
    "extr_effn",
    "extr_fished_unfished",
    "extr_francis",
    "extr_indices",
    "extr_kobe",
    "extr_lenfits_fsh",
    "extr_meanage_fsh",
    "extr_meanage_srv",
    "extr_meanlen_fsh",
    "extr_q_breaks",
    "extr_q_trajectory",
    "extr_retro",
    "extr_sel_breaks",
    "extr_sel_fsh",
    "extr_sel_srv",
    "extr_sr",
    "extr_survey_skill",
    "extr_wtat_fsh",
    "extr_wtat_srv",
    "facet_fig_height",
    "fixed_bmsy",
    "get_age_fits",
    "get_catchabilities",
    "get_fishing_mortality",
    "get_index_fits",
    "get_len_fits",
    "get_msy_mt",
    "get_recruits",
    "get_selectivities",
    "get_totals",
    "geth",
    "getter",
    "gray_ramp",
    "has_comp",
    "jjm_label",
    "jjm_pfa_palette",
    "kobe",
    "melt_matrix",
    "plot_catch_age_fits",
    "plot_catch_age_residuals",
    "plot_catch_fleet",
    "plot_comp_fits",
    "plot_comp_ridge",
    "plot_effn",
    "plot_fished_unfished",
    "plot_fishery_weight",
    "plot_fit_diagnostics",
    "plot_francis",
    "plot_historic_retro",
    "plot_indices_v2",
    "plot_kobe",
    "plot_meanstat",
    "plot_metadata_overview",
    "plot_q_trajectory",
    "plot_retro",
    "plot_sel_ridge",
    "plot_selectivities",
    "plot_sr",
    "plot_summary_sheet",
    "plot_survey_skill",
    "plot_wtat",
    "plot_wtat_cohort",
    "read_historic_retro",
    "readExFiles",
    "readJJM",
    "readJJMConfig",
    "report",
    "retro",
    "runit",
    "runJJM",
    "strong_cohorts",
    "theme_jjm",
    "tidy_JJM",
    "writeJJM"
  ],
  "_help": [
    {
      "page": "dot-getJjmConfig",
      "title": "Create a jjm.config object",
      "topics": [
        ".getJjmConfig"
      ]
    },
    {
      "page": "annex_diagnostics",
      "title": "Annex diagnostic plotting helpers",
      "topics": [
        "annex_diagnostics",
        "annotate_cohorts",
        "calc_mohn_rho",
        "comp_fig_height",
        "extr_agefits_fsh",
        "extr_agefits_srv",
        "extr_catch",
        "extr_catch_cv",
        "extr_cv",
        "extr_effn",
        "extr_fished_unfished",
        "extr_francis",
        "extr_indices",
        "extr_kobe",
        "extr_lenfits_fsh",
        "extr_meanage_fsh",
        "extr_meanage_srv",
        "extr_meanlen_fsh",
        "extr_q_breaks",
        "extr_q_trajectory",
        "extr_retro",
        "extr_sel_breaks",
        "extr_sel_fsh",
        "extr_sel_srv",
        "extr_sr",
        "extr_survey_skill",
        "extr_wtat_fsh",
        "extr_wtat_srv",
        "facet_fig_height",
        "has_comp",
        "jjm_label",
        "jjm_pfa_palette",
        "plot_catch_fleet",
        "plot_comp_fits",
        "plot_comp_ridge",
        "plot_effn",
        "plot_fished_unfished",
        "plot_fit_diagnostics",
        "plot_francis",
        "plot_historic_retro",
        "plot_indices_v2",
        "plot_kobe",
        "plot_meanstat",
        "plot_metadata_overview",
        "plot_q_trajectory",
        "plot_retro",
        "plot_sel_ridge",
        "plot_sr",
        "plot_summary_sheet",
        "plot_survey_skill",
        "plot_wtat",
        "plot_wtat_cohort",
        "read_historic_retro",
        "strong_cohorts"
      ]
    },
    {
      "page": "annotate_cohorts",
      "title": "Annotate strong cohort years on a ggplot",
      "topics": [
        "annotate_cohorts"
      ]
    },
    {
      "page": "calc_mohn_rho",
      "title": "Calculate Mohn's rho",
      "topics": [
        "calc_mohn_rho"
      ]
    },
    {
      "page": "changeNameModel",
      "title": "Change the internal name of a model",
      "topics": [
        "changeNameModel"
      ]
    },
    {
      "page": "coerce",
      "title": "Coerce a vector to character or numeric",
      "topics": [
        "coerce"
      ]
    },
    {
      "page": "combineModels",
      "title": "Combine outputs",
      "topics": [
        "combineModels"
      ]
    },
    {
      "page": "comp_fig_height",
      "title": "Calculate figure height for composition fits",
      "topics": [
        "comp_fig_height"
      ]
    },
    {
      "page": "compareModels",
      "title": "Compare combined JJM outputs",
      "topics": [
        "compareModels"
      ]
    },
    {
      "page": "diagnostics",
      "title": "Generate Assessment plots from single model",
      "topics": [
        "diagnostics"
      ]
    },
    {
      "page": "extr_agefits_fsh",
      "title": "Extract fishery age-composition fits",
      "topics": [
        "extr_agefits_fsh"
      ]
    },
    {
      "page": "extr_agefits_srv",
      "title": "Extract survey age-composition fits",
      "topics": [
        "extr_agefits_srv"
      ]
    },
    {
      "page": "extr_catch",
      "title": "Extract observed catch by fleet",
      "topics": [
        "extr_catch"
      ]
    },
    {
      "page": "extr_catch_cv",
      "title": "Extract catch observation CVs",
      "topics": [
        "extr_catch_cv"
      ]
    },
    {
      "page": "extr_cv",
      "title": "Extract index CVs",
      "topics": [
        "extr_cv"
      ]
    },
    {
      "page": "extr_effn",
      "title": "Extract input composition sample sizes",
      "topics": [
        "extr_effn"
      ]
    },
    {
      "page": "extr_fished_unfished",
      "title": "Extract fished and unfished total biomass",
      "topics": [
        "extr_fished_unfished"
      ]
    },
    {
      "page": "extr_francis",
      "title": "Calculate Francis T1.8 effective sample sizes",
      "topics": [
        "extr_francis"
      ]
    },
    {
      "page": "extr_indices",
      "title": "Extract standardised survey index fits",
      "topics": [
        "extr_indices"
      ]
    },
    {
      "page": "extr_kobe",
      "title": "Extract Kobe phase-plot data",
      "topics": [
        "extr_kobe"
      ]
    },
    {
      "page": "extr_lenfits_fsh",
      "title": "Extract fishery length-composition fits",
      "topics": [
        "extr_lenfits_fsh"
      ]
    },
    {
      "page": "extr_meanage_fsh",
      "title": "Extract fishery mean age fits",
      "topics": [
        "extr_meanage_fsh"
      ]
    },
    {
      "page": "extr_meanage_srv",
      "title": "Extract survey mean age fits",
      "topics": [
        "extr_meanage_srv"
      ]
    },
    {
      "page": "extr_meanlen_fsh",
      "title": "Extract fishery mean length fits",
      "topics": [
        "extr_meanlen_fsh"
      ]
    },
    {
      "page": "extr_q_breaks",
      "title": "Extract q break years",
      "topics": [
        "extr_q_breaks"
      ]
    },
    {
      "page": "extr_q_trajectory",
      "title": "Extract q trajectories",
      "topics": [
        "extr_q_trajectory"
      ]
    },
    {
      "page": "extr_retro",
      "title": "Extract retrospective data",
      "topics": [
        "extr_retro"
      ]
    },
    {
      "page": "extr_sel_breaks",
      "title": "Extract selectivity block break years",
      "topics": [
        "extr_sel_breaks"
      ]
    },
    {
      "page": "extr_sel_fsh",
      "title": "Extract fishery selectivity-at-age",
      "topics": [
        "extr_sel_fsh"
      ]
    },
    {
      "page": "extr_sel_srv",
      "title": "Extract survey selectivity-at-age",
      "topics": [
        "extr_sel_srv"
      ]
    },
    {
      "page": "extr_sr",
      "title": "Extract stock-recruitment pairs and curve",
      "topics": [
        "extr_sr"
      ]
    },
    {
      "page": "extr_survey_skill",
      "title": "Extract survey skill data",
      "topics": [
        "extr_survey_skill"
      ]
    },
    {
      "page": "extr_wtat_fsh",
      "title": "Extract fishery weight-at-age data",
      "topics": [
        "extr_wtat_fsh"
      ]
    },
    {
      "page": "extr_wtat_srv",
      "title": "Extract survey weight-at-age data",
      "topics": [
        "extr_wtat_srv"
      ]
    },
    {
      "page": "facet_fig_height",
      "title": "Calculate figure height for faceted plots",
      "topics": [
        "facet_fig_height"
      ]
    },
    {
      "page": "fixed_bmsy",
      "title": "Calculate or input a fixed Bmsy value for the jjm model Updates the msy_mt table in the jjm output with new B/Bmsy ratios.",
      "topics": [
        "fixed_bmsy"
      ]
    },
    {
      "page": "get_age_fits",
      "title": "Get fits to indices",
      "topics": [
        "get_age_fits"
      ]
    },
    {
      "page": "get_catchabilities",
      "title": "Get estimated catchability coefficients",
      "topics": [
        "get_catchabilities"
      ]
    },
    {
      "page": "get_fishing_mortality",
      "title": "Get fishing mortality at age",
      "topics": [
        "get_fishing_mortality"
      ]
    },
    {
      "page": "get_index_fits",
      "title": "Get fits to indices",
      "topics": [
        "get_index_fits"
      ]
    },
    {
      "page": "get_len_fits",
      "title": "Get fits to length compositions",
      "topics": [
        "get_len_fits"
      ]
    },
    {
      "page": "get_msy_mt",
      "title": "Get and tidy msy_my table",
      "topics": [
        "get_msy_mt"
      ]
    },
    {
      "page": "get_recruits",
      "title": "Get estimated recruits",
      "topics": [
        "get_recruits"
      ]
    },
    {
      "page": "get_selectivities",
      "title": "Get and tidy selectivity-at-age ogives over time by model and fleet",
      "topics": [
        "get_selectivities"
      ]
    },
    {
      "page": "get_totals",
      "title": "Get total metrics (biomass, spawning biomass, and recruitment)",
      "topics": [
        "get_totals"
      ]
    },
    {
      "page": "geth",
      "title": "Add hypothesis number to a model name",
      "topics": [
        "geth"
      ]
    },
    {
      "page": "getter",
      "title": "Get elements of a list by string matching on name",
      "topics": [
        "getter"
      ]
    },
    {
      "page": "gray_ramp",
      "title": "Compute a gray color ramp",
      "topics": [
        "gray_ramp"
      ]
    },
    {
      "page": "has_comp",
      "title": "Check whether composition data are available",
      "topics": [
        "has_comp"
      ]
    },
    {
      "page": "jjm_label",
      "title": "Build a publication label from a JJM model name",
      "topics": [
        "jjm_label"
      ]
    },
    {
      "page": "jjm_pfa_palette",
      "title": "JJM annex diagnostic palettes",
      "topics": [
        "jjm_pfa_palette"
      ]
    },
    {
      "page": "kobe",
      "title": "Kobe plot",
      "topics": [
        "kobe"
      ]
    },
    {
      "page": "melt_matrix",
      "title": "Melt an age-or-length matrix into a long tibble",
      "topics": [
        "melt_matrix"
      ]
    },
    {
      "page": "plot_catch_age_fits",
      "title": "Bar+line plot of observed vs predicted catch-at-age",
      "topics": [
        "plot_catch_age_fits"
      ]
    },
    {
      "page": "plot_catch_age_residuals",
      "title": "Bubble plot of catch-at-age residuals",
      "topics": [
        "plot_catch_age_residuals"
      ]
    },
    {
      "page": "plot_catch_fleet",
      "title": "Plot catch by fleet",
      "topics": [
        "plot_catch_fleet"
      ]
    },
    {
      "page": "plot_comp_fits",
      "title": "Plot composition fits and residuals",
      "topics": [
        "plot_comp_fits"
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    },
    {
      "page": "plot_comp_ridge",
      "title": "Plot observed composition ridges",
      "topics": [
        "plot_comp_ridge"
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    },
    {
      "page": "plot_effn",
      "title": "Plot input composition sample sizes",
      "topics": [
        "plot_effn"
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    },
    {
      "page": "plot_fished_unfished",
      "title": "Plot fished and unfished biomass",
      "topics": [
        "plot_fished_unfished"
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    },
    {
      "page": "plot_fishery_weight",
      "title": "Plot weight at age in the fishery",
      "topics": [
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    },
    {
      "page": "plot_fit_diagnostics",
      "title": "Plot standard index fit diagnostics",
      "topics": [
        "plot_fit_diagnostics"
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    },
    {
      "page": "plot_francis",
      "title": "Plot Francis T1.8 reweighting diagnostics",
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    },
    {
      "page": "plot_historic_retro",
      "title": "Plot historical retrospective diagnostics",
      "topics": [
        "plot_historic_retro"
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    },
    {
      "page": "plot_indices_v2",
      "title": "Plot index fits with input CVs",
      "topics": [
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    },
    {
      "page": "plot_kobe",
      "title": "Plot Kobe phase plot",
      "topics": [
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    },
    {
      "page": "plot_meanstat",
      "title": "Plot mean age or mean length fits",
      "topics": [
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    {
      "page": "plot_metadata_overview",
      "title": "Plot metadata overview",
      "topics": [
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    },
    {
      "page": "plot_q_trajectory",
      "title": "Plot q trajectories",
      "topics": [
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    {
      "page": "plot_retro",
      "title": "Plot retrospective peels",
      "topics": [
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    {
      "page": "plot_sel_ridge",
      "title": "Plot selectivity ridges",
      "topics": [
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    },
    {
      "page": "plot_selectivities",
      "title": "Plot selectivities by age, year, fleet, and model",
      "topics": [
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    },
    {
      "page": "plot_sr",
      "title": "Plot stock-recruitment relationship",
      "topics": [
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    },
    {
      "page": "plot_summary_sheet",
      "title": "Plot a summary diagnostics sheet",
      "topics": [
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    },
    {
      "page": "plot_survey_skill",
      "title": "Plot survey skill ROC curves",
      "topics": [
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    },
    {
      "page": "plot_wtat",
      "title": "Plot weight-at-age over time",
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    },
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      "page": "plot_wtat_cohort",
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      "topics": [
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      "page": "plot.jjm.diag",
      "title": "Plot method for jjm.diag objects",
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      "title": "Plot diagnostics",
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      "title": "Plot method for jjm.output objects",
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      "topics": [
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