{
  "_id": "6aae56b13d719c1f8407b788",
  "Package": "SAMtool",
  "Type": "Package",
  "Title": "Stock Assessment Methods Toolkit",
  "Version": "1.9.3",
  "Authors@R": "c(person(\"Quang\", \"Huynh\", email = \"quang@bluematterscience.com\", role = c(\"aut\", \"cre\")), \nperson(\"Tom\", \"Carruthers\", email = \"tom@bluematterscience.com\", role = \"aut\"),\nperson(\"Adrian\", \"Hordyk\", email = \"adrian@bluematterscience.com\", role = \"aut\"))",
  "Date": "2026-08-20",
  "Maintainer": "Quang Huynh <quang@bluematterscience.com>",
  "Description": "Simulation tools for closed-loop simulation are provided\nfor the 'MSEtool' operating model to inform data-rich\nfisheries. 'SAMtool' provides a conditioning model, assessment\nmodels of varying complexity with standardized reporting,\nmodel-based management procedures, and diagnostic tools for\nevaluating assessments inside closed-loop simulation.",
  "License": "GPL-3",
  "LazyData": "yes",
  "LazyLoad": "yes",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "Encoding": "UTF-8",
  "URL": "https://openmse.com, https://samtool.openmse.com,\nhttps://github.com/Blue-Matter/SAMtool",
  "BugReports": "https://github.com/Blue-Matter/SAMtool/issues",
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev",
  "Repository": "https://blue-matter.r-universe.dev",
  "Date/Publication": "2026-08-20 21:21:55 UTC",
  "RemoteUrl": "https://github.com/Blue-Matter/SAMtool",
  "RemoteRef": "HEAD",
  "RemoteSha": "c2c3f1b0568bf195f90285a0bb9a6691a6da5c87",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-09-19 09:21:06 UTC",
    "User": "root"
  },
  "Author": "Quang Huynh [aut, cre],\nTom Carruthers [aut],\nAdrian Hordyk [aut]",
  "_user": "blue-matter",
  "_type": "src",
  "_file": "SAMtool_1.9.3.tar.gz",
  "_fileid": "https://r2.ropensci.org/2381b15db045fbeba44463a5b1a253e5e7189546c63f2e4ceb3ee5b1e5f973b7",
  "_filesize": 745212,
  "_sha256": "2381b15db045fbeba44463a5b1a253e5e7189546c63f2e4ceb3ee5b1e5f973b7",
  "_expires": "2026-12-28T09:32:31.000Z",
  "_created": "2026-09-19T09:21:06.000Z",
  "_published": "2026-09-19T09:32:32.948Z",
  "_jobs": [
    {
      "job": 105874788207,
      "time": 259,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "10581668300"
    },
    {
      "job": 105874788172,
      "time": 298,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "10581543756"
    },
    {
      "job": 105874788163,
      "time": 268,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "10581808177"
    },
    {
      "job": 105874788203,
      "time": 328,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "10581502500"
    },
    {
      "job": 105874788127,
      "time": 179,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "10582017896"
    },
    {
      "job": 105874788129,
      "time": 587,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "10581278138"
    },
    {
      "job": 105874788200,
      "time": 252,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "10581613440"
    },
    {
      "job": 105874788198,
      "time": 514,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "10581558843"
    },
    {
      "job": 105874173981,
      "time": 309,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10581577103"
    },
    {
      "job": 105874788131,
      "time": 208,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "10581818130"
    },
    {
      "job": 105874788151,
      "time": 362,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "10581567315"
    },
    {
      "job": 105874788205,
      "time": 324,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "10581357793"
    },
    {
      "job": 105874788141,
      "time": 272,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "10582296471"
    },
    {
      "job": 105874788165,
      "time": 310,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "10581322694"
    },
    {
      "job": 105874788147,
      "time": 281,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "10582042855"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/blue-matter/actions/runs/35434252291",
  "_status": "success",
  "_upstream": "https://github.com/Blue-Matter/SAMtool",
  "_commit": {
    "id": "c2c3f1b0568bf195f90285a0bb9a6691a6da5c87",
    "author": "Quang Huynh <quang@bluematterscience.com>",
    "committer": "Quang Huynh <quang@bluematterscience.com>",
    "message": "Add na.rm = TRUE\n",
    "time": 1787260915
  },
  "_maintainer": {
    "name": "Quang Huynh",
    "email": "quang@bluematterscience.com",
    "login": "quang-huynh",
    "description": "",
    "uuid": 15094006
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "MSEtool",
      "version": ">= 3.0.0",
      "role": "Depends"
    },
    {
      "package": "TMB",
      "role": "LinkingTo"
    },
    {
      "package": "RcppEigen",
      "role": "LinkingTo"
    },
    {
      "package": "TMB",
      "version": ">= 1.9.0",
      "role": "Imports"
    },
    {
      "package": "abind",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "gplots",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "pbapply",
      "role": "Imports"
    },
    {
      "package": "rmarkdown",
      "role": "Imports"
    },
    {
      "package": "snowfall",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "vars",
      "role": "Imports"
    },
    {
      "package": "caret",
      "role": "Suggests"
    },
    {
      "package": "corpcor",
      "role": "Suggests"
    },
    {
      "package": "covr",
      "role": "Suggests"
    },
    {
      "package": "extraDistr",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    },
    {
      "package": "Gmisc",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "mvtnorm",
      "role": "Suggests"
    },
    {
      "package": "numDeriv",
      "role": "Suggests"
    },
    {
      "package": "reshape2",
      "role": "Suggests"
    },
    {
      "package": "shiny",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "tmbstan",
      "role": "Suggests"
    },
    {
      "package": "usethis",
      "role": "Suggests"
    }
  ],
  "_owner": "blue-matter",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-42",
      "n": 1
    },
    {
      "week": "2025-43",
      "n": 1
    },
    {
      "week": "2026-03",
      "n": 1
    },
    {
      "week": "2026-14",
      "n": 5
    },
    {
      "week": "2026-15",
      "n": 4
    },
    {
      "week": "2026-18",
      "n": 1
    },
    {
      "week": "2026-19",
      "n": 2
    },
    {
      "week": "2026-23",
      "n": 2
    },
    {
      "week": "2026-25",
      "n": 2
    },
    {
      "week": "2026-34",
      "n": 1
    }
  ],
  "_tags": [],
  "_stars": 3,
  "_contributors": [
    {
      "user": "quang-huynh",
      "count": 484,
      "uuid": 15094006
    },
    {
      "user": "adrianhordyk",
      "count": 9,
      "uuid": 5696790
    }
  ],
  "_userbio": {
    "uuid": 71036379,
    "type": "organization",
    "name": "Blue Matter Science",
    "followers": 41
  },
  "_downloads": {
    "count": 553,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/SAMtool"
  },
  "_mentions": 30,
  "_devurl": "https://github.com/blue-matter/samtool",
  "_pkgdown": "https://samtool.openmse.com",
  "_searchresults": 40,
  "_topics": [
    "cpp"
  ],
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/SAMtool.html"
  ],
  "_homeurl": "https://github.com/blue-matter/samtool",
  "_realowner": "blue-matter",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2021-01-22"
    },
    {
      "version": "1.1.0",
      "date": "2021-02-02"
    },
    {
      "version": "1.1.1",
      "date": "2021-02-17"
    },
    {
      "version": "1.1.2",
      "date": "2021-03-09"
    },
    {
      "version": "1.2.0",
      "date": "2021-07-06"
    },
    {
      "version": "1.2.1",
      "date": "2021-08-12"
    },
    {
      "version": "1.2.2",
      "date": "2021-09-16"
    },
    {
      "version": "1.2.3",
      "date": "2021-11-28"
    },
    {
      "version": "1.2.4",
      "date": "2021-12-15"
    },
    {
      "version": "1.2.5",
      "date": "2022-01-12"
    },
    {
      "version": "1.2.6",
      "date": "2022-03-31"
    },
    {
      "version": "1.3.0",
      "date": "2022-04-08"
    },
    {
      "version": "1.3.1",
      "date": "2022-05-06"
    },
    {
      "version": "1.4.0",
      "date": "2022-06-07"
    },
    {
      "version": "1.4.1",
      "date": "2022-11-16"
    },
    {
      "version": "1.5.0",
      "date": "2023-01-29"
    },
    {
      "version": "1.5.1",
      "date": "2023-02-09"
    },
    {
      "version": "1.5.2",
      "date": "2023-04-05"
    },
    {
      "version": "1.5.3",
      "date": "2023-05-23"
    },
    {
      "version": "1.6.0",
      "date": "2023-07-19"
    },
    {
      "version": "1.6.1",
      "date": "2023-08-24"
    },
    {
      "version": "1.6.2",
      "date": "2023-10-26"
    },
    {
      "version": "1.6.3",
      "date": "2023-11-18"
    },
    {
      "version": "1.6.4",
      "date": "2024-02-15"
    },
    {
      "version": "1.7.0",
      "date": "2024-08-29"
    },
    {
      "version": "1.8.0",
      "date": "2024-11-08"
    },
    {
      "version": "1.8.1",
      "date": "2025-04-28"
    },
    {
      "version": "1.8.2",
      "date": "2025-09-05"
    },
    {
      "version": "1.9.0",
      "date": "2025-10-21"
    },
    {
      "version": "1.9.1",
      "date": "2026-01-15"
    },
    {
      "version": "1.9.2",
      "date": "2026-06-19"
    }
  ],
  "_exports": [
    "Assessment",
    "cDD",
    "cDD_SS",
    "check_RCMdata",
    "compare_models",
    "compare_RCM",
    "DD_SS",
    "DD_TMB",
    "DDSS_4010",
    "DDSS_75MSY",
    "DDSS_MSY",
    "diagnostic",
    "diagnostic_AM",
    "getinds",
    "HCR_escapement",
    "HCR_FB",
    "HCR_fixedF",
    "HCR_MSY",
    "HCR_ramp",
    "HCR_segment",
    "HCR40_10",
    "HCR60_20",
    "HCR80_40MSY",
    "HCRlin",
    "mahplot",
    "make_interim_MP",
    "make_MP",
    "make_projection_MP",
    "Perfect",
    "plot",
    "plot_betavar",
    "plot_composition",
    "plot_crosscorr",
    "plot_lognormalvar",
    "plot_residuals",
    "plot_SR",
    "plot_steepness",
    "plot_timeseries",
    "posterior",
    "PRBcalc",
    "prelim_AM",
    "Probs",
    "prof",
    "profile",
    "project",
    "projection",
    "RCM",
    "RCM_assess",
    "RCM2MOM",
    "RCMdata",
    "RCModel",
    "RCMstan",
    "retro",
    "retrospective",
    "retrospective_AM",
    "SCA",
    "SCA_4010",
    "SCA_75MSY",
    "SCA_CAL",
    "SCA_DDM",
    "SCA_MSY",
    "SCA_Pope",
    "SCA_RWM",
    "SCA2",
    "Shortcut",
    "Shortcut2",
    "sim",
    "simulate",
    "SP",
    "SP_4010",
    "SP_75MSY",
    "SP_Fox",
    "SP_MSY",
    "SP_production",
    "SP_SS",
    "SSS",
    "SSS_4010",
    "SSS_75MSY",
    "SSS_MSY",
    "summary",
    "TAC_MSY",
    "userguide",
    "VPA"
  ],
  "_datasets": [
    {
      "name": "pcod",
      "title": "Pacific cod in Area 5ABCD (Hecate Strait and Queen Charlotte Sound), British Columbia, Canada",
      "object": "pcod",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "swordfish",
      "title": "North Atlantic Swordfish dataset",
      "object": "swordfish",
      "class": [
        "Data"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "SAMtool-package",
      "title": "Stock Assessment Methods Toolkit",
      "topics": [
        "SAMtool-package",
        "SAMtool"
      ]
    },
    {
      "page": "Assessment-class",
      "title": "Class-'Assessment'",
      "topics": [
        "Assessment",
        "Assessment-class"
      ]
    },
    {
      "page": "cDD",
      "title": "Continuous Delay-differential assessment model",
      "topics": [
        "cDD",
        "cDD_SS"
      ]
    },
    {
      "page": "RCM",
      "title": "Rapid Conditioning Model (RCM)",
      "topics": [
        "check_RCMdata",
        "RCM",
        "RCM,list,RCMdata-method",
        "RCM,OM,Data-method",
        "RCM,OM,list-method",
        "RCM,OM,RCMdata-method"
      ]
    },
    {
      "page": "compare_models",
      "title": "Compare output from several assessment models",
      "topics": [
        "compare_models"
      ]
    },
    {
      "page": "DD_TMB",
      "title": "Delay - Difference Stock Assessment in TMB",
      "topics": [
        "DD_SS",
        "DD_TMB"
      ]
    },
    {
      "page": "diagnostic",
      "title": "Diagnostic of assessments in MSE: did Assess models converge during MSE?",
      "topics": [
        "diagnostic",
        "diagnostic_AM"
      ]
    },
    {
      "page": "getinds",
      "title": "Characterize posterior predictive data",
      "topics": [
        "getinds"
      ]
    },
    {
      "page": "HCR_escapement",
      "title": "Fixed escapement harvest control rule",
      "topics": [
        "HCR_escapement"
      ]
    },
    {
      "page": "HCR_FB",
      "title": "A Harvest Control Rule using B/BMSY and F/FMSY to adjust TAC or TAE.",
      "topics": [
        "HCR_FB"
      ]
    },
    {
      "page": "HCR_fixedF",
      "title": "Simple fixed F harvest control rule",
      "topics": [
        "HCR_fixedF"
      ]
    },
    {
      "page": "HCR_MSY",
      "title": "Harvest control rule to fish at some fraction of maximum sustainable yield",
      "topics": [
        "HCR_MSY"
      ]
    },
    {
      "page": "HCR_ramp",
      "title": "Linearly ramped harvest control rules",
      "topics": [
        "HCR40_10",
        "HCR60_20",
        "HCR80_40MSY",
        "HCR_ramp"
      ]
    },
    {
      "page": "HCR_segment",
      "title": "Segmented harvest control rules",
      "topics": [
        "HCR_segment"
      ]
    },
    {
      "page": "HCRlin",
      "title": "Generic linear harvest control rule based on biomass",
      "topics": [
        "HCRlin"
      ]
    },
    {
      "page": "mahplot",
      "title": "Plot statistical power of the indicator with increasing time blocks",
      "topics": [
        "mahplot"
      ]
    },
    {
      "page": "make_MP",
      "title": "Make a custom management procedure (MP)",
      "topics": [
        "make_interim_MP",
        "make_MP",
        "make_projection_MP"
      ]
    },
    {
      "page": "Model-based-MP",
      "title": "Model-based management procedures",
      "topics": [
        "Data-rich-MP",
        "DDSS_4010",
        "DDSS_75MSY",
        "DDSS_MSY",
        "Model-based-MP",
        "MP",
        "SCA_4010",
        "SCA_75MSY",
        "SCA_MSY",
        "SP_4010",
        "SP_75MSY",
        "SP_MSY",
        "SSS_4010",
        "SSS_75MSY",
        "SSS_MSY"
      ]
    },
    {
      "page": "pcod",
      "title": "Pacific cod in Area 5ABCD (Hecate Strait and Queen Charlotte Sound), British Columbia, Canada",
      "topics": [
        "pcod"
      ]
    },
    {
      "page": "plot_betavar",
      "title": "Plots a beta variable",
      "topics": [
        "plot_betavar"
      ]
    },
    {
      "page": "plot_composition",
      "title": "Plot composition data",
      "topics": [
        "plot_composition"
      ]
    },
    {
      "page": "plot_crosscorr",
      "title": "Produce a cross-correlation plot of the derived data arising from getinds(MSE_object)",
      "topics": [
        "plot_crosscorr"
      ]
    },
    {
      "page": "plot_lognormalvar",
      "title": "Plots a lognormal variable",
      "topics": [
        "plot_lognormalvar"
      ]
    },
    {
      "page": "plot_residuals",
      "title": "Plot residuals",
      "topics": [
        "plot_residuals"
      ]
    },
    {
      "page": "plot_SR",
      "title": "Plot stock-recruitment function",
      "topics": [
        "plot_SR"
      ]
    },
    {
      "page": "plot_steepness",
      "title": "Plots probability distribution function of stock-recruit steepness",
      "topics": [
        "plot_steepness"
      ]
    },
    {
      "page": "plot_timeseries",
      "title": "Plot time series of data",
      "topics": [
        "plot_timeseries"
      ]
    },
    {
      "page": "plot.Assessment",
      "title": "Plot Assessment object",
      "topics": [
        "plot,Assessment,missing-method",
        "plot,Assessment,retro-method",
        "plot.Assessment"
      ]
    },
    {
      "page": "plot.prof",
      "title": "Plot profile object",
      "topics": [
        "plot,prof,missing-method",
        "plot.prof"
      ]
    },
    {
      "page": "plot.RCModel",
      "title": "Plot RCM scope output",
      "topics": [
        "compare_RCM",
        "plot,RCModel,missing-method",
        "plot.RCModel"
      ]
    },
    {
      "page": "plot.retro",
      "title": "Methods for retro object",
      "topics": [
        "plot,retro,missing-method",
        "plot.retro",
        "summary,retro-method",
        "summary.retro"
      ]
    },
    {
      "page": "posterior",
      "title": "Sample posterior of TMB models in SAMtool",
      "topics": [
        "posterior",
        "posterior,Assessment-method",
        "posterior,RCModel-method",
        "posterior.Assessment",
        "posterior.RCModel",
        "RCMstan"
      ]
    },
    {
      "page": "PRBcalc",
      "title": "Calculate mahalanobis distance (null and alternative MSEs) and statistical power for all MPs in an MSE",
      "topics": [
        "PRBcalc"
      ]
    },
    {
      "page": "prelim_AM",
      "title": "Preliminary Assessments in MSE",
      "topics": [
        "prelim_AM"
      ]
    },
    {
      "page": "Probs",
      "title": "Calculates mahalanobis distance and rejection of the Null operating model",
      "topics": [
        "Probs"
      ]
    },
    {
      "page": "prof-class",
      "title": "Class-'prof'",
      "topics": [
        "prof",
        "prof-class"
      ]
    },
    {
      "page": "profile",
      "title": "Profile likelihood of assessment models",
      "topics": [
        "profile",
        "profile,Assessment-method",
        "profile,RCModel-method"
      ]
    },
    {
      "page": "project-class",
      "title": "Class-'project'",
      "topics": [
        "project",
        "project-class"
      ]
    },
    {
      "page": "projection",
      "title": "Projections for assessment models",
      "topics": [
        "projection"
      ]
    },
    {
      "page": "RCM_assess",
      "title": "The rapid conditioning model as an assessment function",
      "topics": [
        "RCM_assess"
      ]
    },
    {
      "page": "RCM2MOM",
      "title": "Convert RCM to a multi-fleet operating model (MOM)",
      "topics": [
        "RCM2MOM"
      ]
    },
    {
      "page": "RCMdata-class",
      "title": "Class-'RCMdata'",
      "topics": [
        "RCMdata",
        "RCMdata-class"
      ]
    },
    {
      "page": "RCModel-class",
      "title": "Class-'RCModel'",
      "topics": [
        "RCModel",
        "RCModel-class"
      ]
    },
    {
      "page": "retro-class",
      "title": "Class-'retro'",
      "topics": [
        "retro",
        "retro-class"
      ]
    },
    {
      "page": "retrospective",
      "title": "Retrospective analysis of assessment models",
      "topics": [
        "retrospective",
        "retrospective,Assessment-method",
        "retrospective,RCModel-method"
      ]
    },
    {
      "page": "retrospective_AM",
      "title": "retrospective_AM (retrospective of Assessment model in MSE)",
      "topics": [
        "retrospective_AM"
      ]
    },
    {
      "page": "SCA",
      "title": "Statistical catch-at-age (SCA) model",
      "topics": [
        "SCA",
        "SCA2",
        "SCA_Pope"
      ]
    },
    {
      "page": "SCA_CAL",
      "title": "Age-structured model using fishery length composition",
      "topics": [
        "SCA_CAL"
      ]
    },
    {
      "page": "SCA_DDM",
      "title": "SCA models with time-varying natural mortality",
      "topics": [
        "SCA_DDM"
      ]
    },
    {
      "page": "SCA_RWM",
      "title": "SCA with random walk in M",
      "topics": [
        "SCA_RWM"
      ]
    },
    {
      "page": "Shortcut",
      "title": "Assessment emulator as a shortcut to model fitting in closed-loop simulation",
      "topics": [
        "Perfect",
        "Shortcut",
        "Shortcut2"
      ]
    },
    {
      "page": "sim-class",
      "title": "Class-'sim'",
      "topics": [
        "sim",
        "sim-class"
      ]
    },
    {
      "page": "simulate",
      "title": "Generate simulated data from TMB models in SAMtool",
      "topics": [
        "simulate",
        "simulate,Assessment-method",
        "simulate,RCModel-method",
        "simulate.Assessment",
        "simulate.RCModel"
      ]
    },
    {
      "page": "SP",
      "title": "Surplus production model with FMSY and MSY as leading parameters",
      "topics": [
        "SP",
        "SP_Fox",
        "SP_SS"
      ]
    },
    {
      "page": "SP_production",
      "title": "Find the production parameter based on depletion that produces MSY",
      "topics": [
        "SP_production"
      ]
    },
    {
      "page": "SSS",
      "title": "Simple Stock Synthesis",
      "topics": [
        "SSS"
      ]
    },
    {
      "page": "summary.Assessment",
      "title": "Summary of Assessment object",
      "topics": [
        "summary,Assessment-method",
        "summary.Assessment"
      ]
    },
    {
      "page": "swordfish",
      "title": "North Atlantic Swordfish dataset",
      "topics": [
        "swordfish"
      ]
    },
    {
      "page": "TAC_MSY",
      "title": "Calculate MSY-based TAC from Assessment object",
      "topics": [
        "calculate_TAC",
        "TAC_MSY"
      ]
    },
    {
      "page": "userguide",
      "title": "Get the SAMtool vignettes",
      "topics": [
        "userguide"
      ]
    },
    {
      "page": "VPA",
      "title": "Virtual population analysis (VPA)",
      "topics": [
        "VPA"
      ]
    }
  ],
  "_pkglogo": "https://github.com/Blue-Matter/SAMtool/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/Blue-Matter/SAMtool/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "base64enc",
    "bitops",
    "bslib",
    "cachem",
    "caTools",
    "cli",
    "cpp11",
    "digest",
    "dplyr",
    "evaluate",
    "farver",
    "fastmap",
    "fontawesome",
    "fs",
    "generics",
    "ggplot2",
    "glue",
    "gplots",
    "gtable",
    "gtools",
    "highr",
    "htmltools",
    "isoband",
    "jquerylib",
    "jsonlite",
    "KernSmooth",
    "knitr",
    "labeling",
    "lattice",
    "lifecycle",
    "lmtest",
    "lubridate",
    "magrittr",
    "MASS",
    "Matrix",
    "memoise",
    "mime",
    "MSEtool",
    "nlme",
    "patchwork",
    "pbapply",
    "pillar",
    "pkgconfig",
    "purrr",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "rlang",
    "rmarkdown",
    "S7",
    "sandwich",
    "sass",
    "scales",
    "snow",
    "snowfall",
    "stringi",
    "stringr",
    "strucchange",
    "tibble",
    "tidyr",
    "tidyselect",
    "timechange",
    "tinytex",
    "TMB",
    "urca",
    "utf8",
    "vars",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "yaml",
    "zoo"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_score": 6.2552725051033065,
  "_indexed": true,
  "_nocasepkg": "samtool",
  "_universes": [
    "blue-matter",
    "quang-huynh"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.9.3",
      "date": "2026-09-19T09:24:30.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "c2c3f1b0568bf195f90285a0bb9a6691a6da5c87",
      "fileid": "https://r2.ropensci.org/74438e3d06a9c85b36e53adeaef2f9c7fd6e889269a6dff309f964eb9fe97faa",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/blue-matter/actions/runs/35434252291"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.9.3",
      "date": "2026-09-19T09:25:04.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "c2c3f1b0568bf195f90285a0bb9a6691a6da5c87",
      "fileid": "https://r2.ropensci.org/99db9ac6073203ff830898a89b435d83c189fa43807f8faa7e2cd60270ae06d4",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/blue-matter/actions/runs/35434252291"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.9.3",
      "date": "2026-09-19T09:24:38.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "c2c3f1b0568bf195f90285a0bb9a6691a6da5c87",
      "fileid": "https://r2.ropensci.org/a653343c5e2fe371d30cef2b73b22b53b0079f7ae4cafa6568bd91bcd821837b",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/blue-matter/actions/runs/35434252291"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.9.3",
      "date": "2026-09-19T09:25:08.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "c2c3f1b0568bf195f90285a0bb9a6691a6da5c87",
      "fileid": "https://r2.ropensci.org/d6d2332b84c2bde8273946ab7f6101f77cf35971cacaef0a5c7a1202bb712f53",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/blue-matter/actions/runs/35434252291"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.9.3",
      "date": "2026-09-19T09:23:39.000Z",
      "arch": "aarch64",
      "commit": "c2c3f1b0568bf195f90285a0bb9a6691a6da5c87",
      "fileid": "https://r2.ropensci.org/3b1d1f77057a15cb7df8d030fee4da70ed8f1b866e103bdffcf5e4d11cfae1ed",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/blue-matter/actions/runs/35434252291"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.9.3",
      "date": "2026-09-19T09:26:24.000Z",
      "arch": "x86_64",
      "commit": "c2c3f1b0568bf195f90285a0bb9a6691a6da5c87",
      "fileid": "https://r2.ropensci.org/a78a1e8dfcaa25afd36a62f7aef4ae088fee1aa0c555bb0599f621cd2981f042",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/blue-matter/actions/runs/35434252291"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.9.3",
      "date": "2026-09-19T09:24:36.000Z",
      "arch": "aarch64",
      "commit": "c2c3f1b0568bf195f90285a0bb9a6691a6da5c87",
      "fileid": "https://r2.ropensci.org/003882fb5d9c63f72faf6d402d61f6f9459d435d20816d143c3c8737be6a2a2f",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/blue-matter/actions/runs/35434252291"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.9.3",
      "date": "2026-09-19T09:26:08.000Z",
      "arch": "x86_64",
      "commit": "c2c3f1b0568bf195f90285a0bb9a6691a6da5c87",
      "fileid": "https://r2.ropensci.org/f5c52e0bf1881914fbbe491579d4b54f8f93e5d87010573f89547ea8c66ddf40",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/blue-matter/actions/runs/35434252291"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.9.3",
      "date": "2026-09-19T09:25:14.000Z",
      "arch": "emscripten",
      "commit": "c2c3f1b0568bf195f90285a0bb9a6691a6da5c87",
      "fileid": "https://r2.ropensci.org/5524ad00185e8ba5fc229e122328d174800c01dcee7edfcde75bc1e267f451f7",
      "status": "success",
      "buildurl": "https://github.com/r-universe/blue-matter/actions/runs/35434252291"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.9.3",
      "date": "2026-09-19T09:25:38.000Z",
      "arch": "aarch64",
      "commit": "c2c3f1b0568bf195f90285a0bb9a6691a6da5c87",
      "fileid": "https://r2.ropensci.org/f4a616b72f792dffc51ecdf1f340da571b0befe5a3c9aac84a46715f5948f452",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/blue-matter/actions/runs/35434252291"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.9.3",
      "date": "2026-09-19T09:23:37.000Z",
      "arch": "x86_64",
      "commit": "c2c3f1b0568bf195f90285a0bb9a6691a6da5c87",
      "fileid": "https://r2.ropensci.org/6f154d7651067e6d4ba5d72eaf22d1d8e8c3350997e74412d86494407b17581b",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/blue-matter/actions/runs/35434252291"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.9.3",
      "date": "2026-09-19T09:23:29.000Z",
      "arch": "x86_64",
      "commit": "c2c3f1b0568bf195f90285a0bb9a6691a6da5c87",
      "fileid": "https://r2.ropensci.org/4fa73cc6a9347ce6d6ab35795c638e70adf2d7949d6c9a128ac8c89bb118c444",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/blue-matter/actions/runs/35434252291"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.9.3",
      "date": "2026-09-19T09:25:16.000Z",
      "arch": "aarch64",
      "commit": "c2c3f1b0568bf195f90285a0bb9a6691a6da5c87",
      "fileid": "https://r2.ropensci.org/2b4258e2ac0df0869246edc6bb4923dc78db6ebfec13d184e0089b117a7d7b18",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/blue-matter/actions/runs/35434252291"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.9.3",
      "date": "2026-09-19T09:23:43.000Z",
      "arch": "x86_64",
      "commit": "c2c3f1b0568bf195f90285a0bb9a6691a6da5c87",
      "fileid": "https://r2.ropensci.org/b96cf29c1d30b314af48660c904e1a1da5fbfc59cdb3ed757caf6c2abaa798d8",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/blue-matter/actions/runs/35434252291"
    }
  ]
}