{
  "_id": "6ad4684d8b78ae42bccc4d5a",
  "Package": "mpb",
  "Title": "Management Procedures",
  "Version": "3.5.4",
  "Date": "2026-10-15",
  "Authors@R": "person(given = \"Laurence\", family = \"Kell\", role = c(\"aut\", \"cre\"), \nemail = \"laurie@seaplusplus.co.uk\")",
  "Maintainer": "Laurence Kell <laurie@seaplusplus.co.uk>",
  "Description": "mpb is an R package for running and simulation testing\nbiomass based stock assessment models.",
  "VignetteBuilder": "knitr",
  "License": "GPL-2",
  "Collate": "generics.R biodyn-fit.R aspic-fit.R biodyn-class.R biodyns.R\naspic-class.R aspics.R aspic-biodyns.R biodyn-control.R\nbiodyn-methods.R FLQuantJKs.R hrate.R biodyn-accessors.R\naspic-accessors.R aspic-readU.R aspic-io.R aspic-index.R\nbiodyn-admb.R biodyn-F.R biodyn-constructors.R aspic-setIndex.R\nbiodyn-coerce.R aspic-control.R aspic-constructors.R\naspic-coerce.R biodyn-fwd.R biodyn-fwdWindow.R\nbiodyn-setParams.R aspic-plot.R biodyn-msy.R aspic-refpts.R\nbiodyn-profile.R aspic-profile.R FLBRP-production.R objFn.R\nbiodyn-xval.R biodyn-rand.R biodyn-jackSummary.R biodyn-boot.R\nbiodyn-sim.R biodyn-feasible.R biodyn-kobe.R biodyn-nll.R\nbiodyn-profile-Cpp.R biodyn-plot.R biodyn-func.R\nbiodyn-rebuild.R pellat.R iRate.R lk-methods.R lk-mfcl.R\nmng-methods.R plural2iters.R resample.R rjm-series.R\nbiodyn-mse.R biodyn-jack.R biodyn-mvn.R data.R econ-ee.R r2b.R\nrwalk.R aspic-xval.R weighted.var.se.R biodyn-FLBRP2biodyn.R\nplotIndex.R msy.R biodyn-hcr.R nmc.R FLStock-hcr.R\nbiodyn-statusErr.R doc.R hcr.R pellam.R setMP.R biodyn-sra.R\nscale.R jabba-coerce.R spict.R jabbaBuild.R getBiodyn.R\njabba-com.R biodyn-FLPar.R jabba-coerce2.R cmp-plots.R\ncmp-convert.R spict-plots.R spict-helpers.R",
  "LazyLoad": "Yes",
  "LazyData": "Yes",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.3",
  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://flr.r-universe.dev",
  "Date/Publication": "2026-10-15 18:50:23 UTC",
  "RemoteUrl": "https://github.com/lauriekell/mpb",
  "RemoteRef": "HEAD",
  "RemoteSha": "e40abde185eba43d6b85874a66142e99277217e5",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-18 06:20:39 UTC",
    "User": "root"
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  "Author": "Laurence Kell [aut, cre]",
  "_user": "flr",
  "_type": "src",
  "_file": "mpb_3.5.4.tar.gz",
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  "_expires": "2027-01-26T06:33:47.000Z",
  "_created": "2026-10-18T06:20:39.000Z",
  "_published": "2026-10-18T06:33:49.473Z",
  "_buildurl": "https://github.com/r-universe/flr/actions/runs/38802017449",
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    "author": "lauriekell <laurie@kell.es>",
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    "message": "spict vignette uses the ggplotFL plotSpict* plots; assessment-comparison drops the biodyn fit; 3.5.4\n\nAssisted by Cursor (Auto)\n\nCo-authored-by: Cursor <cursoragent@cursor.com>\n",
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  "_exports": [
    "aspic",
    "aspics",
    "biodyn",
    "biodyn2cmp",
    "bmsy",
    "boot",
    "chkIters",
    "cmpACF",
    "cmpAssess",
    "cmpFit",
    "cmpHindcast",
    "cmpHindcastDF",
    "cmpKobe",
    "cmpMASE",
    "cmpPriors",
    "cmpProcess",
    "cmpProduction",
    "cmpQQ",
    "cmpRetro",
    "cmpRuns",
    "cmpStatus",
    "cmpTS",
    "control",
    "control<-",
    "controlFn",
    "diags",
    "diagsFn",
    "fapexAge",
    "feasible",
    "fit",
    "flbrp2cmp",
    "fmsy",
    "fnProfile",
    "fwd",
    "harvest",
    "hcr",
    "hcrParam",
    "hrate",
    "is.aspic",
    "is.biodyn",
    "jabba2biodyn",
    "jabba2cmp",
    "jk",
    "K",
    "kobe",
    "mfclGrw",
    "mixnorm",
    "mohnsRho",
    "mseBiodyn",
    "msy",
    "mvn",
    "nll",
    "nmcFn",
    "p",
    "plot",
    "plotCcf",
    "plotEql",
    "plotHcr",
    "plotIndex",
    "plotIndexResidual",
    "plotJack",
    "plotMSEfn",
    "plotPE",
    "plotProduction",
    "plotSpictACF",
    "plotSpictFit",
    "plotSpictHindcast",
    "plotSpictKobe",
    "plotSpictPriors",
    "plotSpictProcess",
    "plotSpictProduction",
    "plotSpictQQ",
    "plotSpictRetro",
    "plotSpictRuns",
    "plotSpictStatus",
    "plotSpictTS",
    "prdResid",
    "production",
    "profileFn",
    "randFn",
    "randJackFn",
    "readAspic",
    "rebuildTime",
    "recoverBD",
    "refpts",
    "refptSD",
    "resample",
    "runsTest",
    "setControl<-",
    "setMP",
    "setParams<-",
    "sim",
    "spict2biodyn",
    "spict2cmp",
    "spict2FLQuants",
    "spictInp",
    "spictPar",
    "spictPrd",
    "spictPriors",
    "spictTS",
    "tac",
    "timeSeries",
    "writeAspic",
    "xval"
  ],
  "_datasets": [
    {
      "name": "object",
      "title": "",
      "object": "jabba",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "swon",
      "title": "",
      "object": "swon",
      "class": [
        "biodyn"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "alkMFCL",
      "title": "Returns length age data from Multifan-CL as a list with four data frames",
      "topics": [
        "alkMFCL"
      ]
    },
    {
      "page": "as",
      "title": "as(\"biodyn\", \"FLStock\")",
      "concept": [
        "biodyn"
      ],
      "topics": [
        "as"
      ]
    },
    {
      "page": "aspicConstructors",
      "title": "aspic constructor",
      "topics": [
        "aspic",
        "aspic,ANY,ANY-method",
        "aspic,ANY-method",
        "aspic,character-method",
        "aspic,data.frame-method",
        "aspic,missing-method",
        "aspic-method"
      ]
    },
    {
      "page": "aspicClass",
      "title": "ASPIC Biomass Dynamic Model Class",
      "topics": [
        "aspic,biodyn,FLQuant-method",
        "aspic,biodyn,FLQuants,FLQuant-method",
        "aspic,biodyn,FLQuants-method",
        "aspic,character,missing,FLQuant-method",
        "aspic,character,missing-method",
        "aspic,data.frame,missing,FLQuant-method",
        "aspic,data.frame,missing-method",
        "aspic,FLQuant-method",
        "aspic,FLStock,missing-method",
        "aspic,missing,missing,FLQuant-method",
        "aspic,missing,missing-method",
        "aspic-class",
        "catch,aspic-method",
        "catch<-"
      ]
    },
    {
      "page": "aspicsConstructors",
      "title": "aspics",
      "topics": [
        "aspics",
        "aspics,ANY-method",
        "aspics,aspic-method",
        "aspics,character-method",
        "aspics,list-method",
        "aspics,missing-method",
        "aspics-method",
        "aspics-methods"
      ]
    },
    {
      "page": "aspics-class",
      "title": "aspics a class that contains a list of ASPIC biomass dynamic stock assessment model classes",
      "topics": [
        "aspics-class"
      ]
    },
    {
      "page": "biodynConstructors",
      "title": "biodyn constructor",
      "topics": [
        "biodyn"
      ]
    },
    {
      "page": "biodynClass",
      "title": "biodyn class",
      "topics": [
        "biodyn,character,FLPar-method",
        "biodyn,character,missing-method",
        "biodyn,factor,FLPar-method",
        "biodyn,factor,missing-method",
        "biodyn,FLQuant,FLPar-method",
        "biodyn,FLQuant,missing-method",
        "biodyn,FLStock,FLPar-method",
        "biodyn,FLStock,missing-method",
        "biodyn,missing,FLPar-method",
        "biodyn,missing,missing-method",
        "biodyn-class"
      ]
    },
    {
      "page": "biodyn-FLPar-missing-method",
      "title": "Create biodyn Object from FLPar Parameters",
      "topics": [
        "biodyn,FLPar,missing-method"
      ]
    },
    {
      "page": "biodyn2cmp",
      "title": "Convert a biodyn to a cmpAssess",
      "topics": [
        "biodyn2cmp"
      ]
    },
    {
      "page": "biodyns-biodyn-method",
      "title": "biodyns creates a list of biodyn objects",
      "topics": [
        "biodyns,biodyn-method"
      ]
    },
    {
      "page": "aspic-fit",
      "title": "fit",
      "topics": [
        "boot",
        "fit,aspic,missing-method"
      ]
    },
    {
      "page": "boot",
      "title": "boot, Bootstraps biodyn.",
      "topics": [
        "boot,aspic-method",
        "boot,aspics-method",
        "boot,biodyn-method",
        "boot-method"
      ]
    },
    {
      "page": "cmpACF",
      "title": "Autocorrelation of residuals for one or more assessments",
      "topics": [
        "cmpACF"
      ]
    },
    {
      "page": "cmpAssess",
      "title": "Common assessment summary for comparing methods",
      "topics": [
        "cmpAssess"
      ]
    },
    {
      "page": "cmpFit",
      "title": "Observed and fitted values of one or more assessments",
      "topics": [
        "cmpFit"
      ]
    },
    {
      "page": "cmpHindcast",
      "title": "Hindcast cross-validation of one or more assessments",
      "topics": [
        "cmpHindcast"
      ]
    },
    {
      "page": "cmpHindcastDF",
      "title": "Hindcast predictions from retrospective peels",
      "topics": [
        "cmpHindcastDF"
      ]
    },
    {
      "page": "cmpKobe",
      "title": "Kobe phase plot for one or more assessments",
      "topics": [
        "cmpKobe"
      ]
    },
    {
      "page": "cmpMASE",
      "title": "Mean absolute scaled error",
      "topics": [
        "cmpMASE"
      ]
    },
    {
      "page": "cmpPriors",
      "title": "Prior and posterior densities for one or more assessments",
      "topics": [
        "cmpPriors"
      ]
    },
    {
      "page": "cmpProcess",
      "title": "Process residuals with runs tests for one or more assessments",
      "topics": [
        "cmpProcess"
      ]
    },
    {
      "page": "cmpProduction",
      "title": "Production functions of one or more assessments",
      "topics": [
        "cmpProduction"
      ]
    },
    {
      "page": "cmpQQ",
      "title": "Normal QQ plot of residuals for one or more assessments",
      "topics": [
        "cmpQQ"
      ]
    },
    {
      "page": "cmpRetro",
      "title": "Retrospective analysis of one or more assessments",
      "topics": [
        "cmpRetro"
      ]
    },
    {
      "page": "cmpRuns",
      "title": "Observation residuals with runs tests for one or more assessments",
      "topics": [
        "cmpRuns"
      ]
    },
    {
      "page": "cmpStatus",
      "title": "Stock status of one or more assessments",
      "topics": [
        "cmpStatus"
      ]
    },
    {
      "page": "cmpTS",
      "title": "Time series of one or more assessments",
      "topics": [
        "cmpTS"
      ]
    },
    {
      "page": "control-biodyn-method",
      "title": "control",
      "topics": [
        "control,biodyn-method"
      ]
    },
    {
      "page": "biodynAccessors",
      "title": "control<-",
      "topics": [
        "control<-,biodyn,FLPar-method"
      ]
    },
    {
      "page": "controlFn",
      "title": "controlFn",
      "topics": [
        "controlFn"
      ]
    },
    {
      "page": "params",
      "title": "params",
      "topics": [
        "diags",
        "setParams<-,aspic,data.frame-method",
        "setParams<-,biodyn,data.frame-method",
        "setParams<-,biodyn,FLPar-method",
        "setParams<-,biodyn,FLQuant-method",
        "setParams<-,biodyn,FLQuants-method"
      ]
    },
    {
      "page": "biodyn-fit",
      "title": "fit",
      "topics": [
        "diagsFn",
        "fit,aspics,missing-method",
        "fit,biodyn,FLQuantJK-method",
        "fit,biodyn,FLQuantJKs-method",
        "fit,FLPar,FLQuant-method"
      ]
    },
    {
      "page": "timeSeries1",
      "title": "mng",
      "topics": [
        "aspic,missing",
        "biodyn,missing",
        "fapexAge",
        "timeSeries",
        "timeSeries,aspic,missing-method",
        "timeSeries,biodyn,missing-method",
        "timeSeries,FLStock,FLBRP-method",
        "timeSeries,FLStocks,FLBRP-method",
        "timeSeries,FLStocks,FLBRPs-method",
        "timeSeries-method"
      ]
    },
    {
      "page": "feasible",
      "title": "feasible",
      "topics": [
        "feasible",
        "feasible,biodyn,missing-method",
        "feasible,data.frame,FLQuant-method",
        "feasible,FLPar,FLQuant-method"
      ]
    },
    {
      "page": "fit",
      "title": "fit",
      "topics": [
        "fit",
        "fit,aspic-method",
        "fit,aspics-method",
        "fit,biodyn,FLQuant-method",
        "fit,biodyn,FLQuants-method"
      ]
    },
    {
      "page": "fitPella",
      "title": "-mcmc 100000 -mcsave 100'",
      "topics": [
        "fitPella"
      ]
    },
    {
      "page": "flbrp2cmp",
      "title": "Convert an age-structured assessment (FLStock and FLBRP) to a cmpAssess",
      "topics": [
        "flbrp2cmp"
      ]
    },
    {
      "page": "FLQuantJKs",
      "title": "Class FLQuantJKs",
      "topics": [
        "FLQuantJKs",
        "FLQuantJKs,ANY-method",
        "FLQuantJKs,FLQuantJKs-method",
        "FLQuantJKs,list-method",
        "FLQuantJKs,missing-method",
        "FLQuantJKs-class",
        "FLQuantJKs-methods"
      ]
    },
    {
      "page": "fnProfile",
      "title": "fnProfile",
      "topics": [
        "fnProfile"
      ]
    },
    {
      "page": "fwd",
      "title": "fwd",
      "topics": [
        "fwd,biodyn,FLQuants,missing",
        "fwd,biodyn,FLQuants-method",
        "fwd,biodyn,missing,missing",
        "fwd,biodyn,missing,missing-method",
        "fwd,biodyn,missing-method",
        "fwd,FLPar,missing,missing",
        "fwd,FLPar,missing-method",
        "fwd-method"
      ]
    },
    {
      "page": "harvest",
      "title": "harvest",
      "topics": [
        "harvest",
        "harvest,aspic-method",
        "harvest,biodyn,missing-method",
        "harvest,biodyn-method"
      ]
    },
    {
      "page": "hcr",
      "title": "hcr",
      "topics": [
        "hcr,biodyn,FLPar-method",
        "hcr,biodyn-method",
        "hcr,FLStock,FLBRP-method"
      ]
    },
    {
      "page": "hcrParam",
      "title": "hcrParam",
      "topics": [
        "hcrParam"
      ]
    },
    {
      "page": "hrate",
      "title": "hrate",
      "topics": [
        "hrate",
        "hrate,aspic-method",
        "hrate,biodyn-method"
      ]
    },
    {
      "page": "is.aspic",
      "title": "is.aspic",
      "topics": [
        "is.aspic"
      ]
    },
    {
      "page": "is.biodyn",
      "title": "is.biodyn",
      "topics": [
        "is.biodyn"
      ]
    },
    {
      "page": "jabba2biodyn",
      "title": "Coerce a JABBA fit to a biodyn",
      "topics": [
        "jabba2biodyn"
      ]
    },
    {
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