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  "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>",
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  "Repository": "https://sprfmo.r-universe.dev",
  "Date/Publication": "2026-05-22 10:22:01 UTC",
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    "message": "Merge pull request #26 from SPRFMO/codex/annex-diagnostics-repairs\n\nAdd annex diagnostics plotting helpers",
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  "_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",
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    "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_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": "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": "compareModels",
      "title": "Compare combined JJM outputs",
      "topics": [
        "compareModels"
      ]
    },
    {
      "page": "diagnostics",
      "title": "Generate Assessment plots from single model",
      "topics": [
        "diagnostics"
      ]
    },
    {
      "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": "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_fishery_weight",
      "title": "Plot weight at age in the fishery",
      "topics": [
        "plot_fishery_weight"
      ]
    },
    {
      "page": "plot_selectivities",
      "title": "Plot selectivities by age, year, fleet, and model",
      "topics": [
        "plot_selectivities"
      ]
    },
    {
      "page": "plot.jjm.diag",
      "title": "Plot method for jjm.diag objects",
      "topics": [
        "plot.jjm.diag"
      ]
    },
    {
      "page": "plot.jjm.diagnostics",
      "title": "Plot diagnostics",
      "topics": [
        "plot.jjm.diagnostics"
      ]
    },
    {
      "page": "plot.jjm.output",
      "title": "Plot method for jjm.output objects",
      "topics": [
        "plot.jjm.output"
      ]
    },
    {
      "page": "print.jjm.config",
      "title": "Print a jjm.config object",
      "topics": [
        "print.jjm.config"
      ]
    },
    {
      "page": "print.jjm.diag",
      "title": "Print method for jjm.diag objects",
      "topics": [
        "print.jjm.diag"
      ]
    },
    {
      "page": "print.jjm.output",
      "title": "Print method for jjm.output objects",
      "topics": [
        "print.jjm.output"
      ]
    },
    {
      "page": "print.summary.jjm.config",
      "title": "Print a summary of jjm.config",
      "topics": [
        "print.summary.jjm.config"
      ]
    },
    {
      "page": "print.summary.jjm.diag",
      "title": "Print method for summary.jjm.diag objects",
      "topics": [
        "print.summary.jjm.diag"
      ]
    },
    {
      "page": "print.summary.jjm.output",
      "title": "Print method for summary.jjm.output objects",
      "topics": [
        "print.summary.jjm.output"
      ]
    },
    {
      "page": "readExFiles",
      "title": "Read external files",
      "topics": [
        "readExFiles"
      ]
    },
    {
      "page": "readJJM",
      "title": "Read a model or list of models",
      "topics": [
        "readJJM"
      ]
    },
    {
      "page": "readJJMConfig",
      "title": "Read dat and ctl files from disk to create a jjm.config object.",
      "topics": [
        "readJJMConfig"
      ]
    },
    {
      "page": "report",
      "title": "Create a report from JJM outputs",
      "topics": [
        "report"
      ]
    },
    {
      "page": "retro",
      "title": "Run a retrospective analysis diagnostic for a JJM model",
      "topics": [
        "retro"
      ]
    },
    {
      "page": "runit",
      "title": "Fit, run, read and plot a JJM model",
      "topics": [
        "runit"
      ]
    },
    {
      "page": "runJJM",
      "title": "Run a JJM model",
      "topics": [
        "runJJM"
      ]
    },
    {
      "page": "runJJM.default",
      "title": "Run JJM models (default method)",
      "topics": [
        "runJJM.default"
      ]
    },
    {
      "page": "runJJM.jjm.config",
      "title": "Run JJM models for jjm.config",
      "topics": [
        "runJJM.jjm.config"
      ]
    },
    {
      "page": "runJJM.jjm.output",
      "title": "Run JJM models for jjm.output",
      "topics": [
        "runJJM.jjm.output"
      ]
    },
    {
      "page": "summary.jjm.config",
      "title": "Summarize a jjm.config object",
      "topics": [
        "summary.jjm.config"
      ]
    },
    {
      "page": "summary.jjm.diag",
      "title": "Summary method for jjm.diag objects",
      "topics": [
        "summary.jjm.diag"
      ]
    },
    {
      "page": "summary.jjm.diagnostics",
      "title": "Summarize all diagnostics from a jjm run",
      "topics": [
        "summary.jjm.diagnostics"
      ]
    },
    {
      "page": "summary.jjm.output",
      "title": "Summary method for jjm.output objects",
      "topics": [
        "summary.jjm.output"
      ]
    },
    {
      "page": "theme_jjm",
      "title": "ggplot2 theme for jjmR",
      "topics": [
        "theme_jjm"
      ]
    },
    {
      "page": "tidy_JJM",
      "title": "Tidy results of JJM model",
      "topics": [
        "tidy_JJM"
      ]
    },
    {
      "page": "writeJJM",
      "title": "Write dat and ctl files from a JJM model stored in R",
      "topics": [
        "writeJJM"
      ]
    }
  ],
  "_readme": "https://github.com/SPRFMO/jjmr/raw/HEAD/README.md",
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