{
  "_id": "6a1ed781b401979e7340edb8",
  "Package": "spict",
  "Type": "Package",
  "Title": "Stochastic surplus Production model in Continuous-Time (SPiCT)",
  "Version": "1.3.9",
  "Date": "2026-04-17",
  "Authors@R": "c(person(given=\"Martin Waever\",\nfamily=\"Pedersen\",\nemail=\"wpsgodd@gmail.com\",\nrole=c(\"aut\", \"cre\", \"cph\")),\nperson(given=\"Casper Willestofte\",\nfamily=\"Berg\",\nemail=\"cbe@aqua.dtu.dk\",\nrole=c(\"aut\"),\ncomment=c()),\nperson(given=\"Tobias Karl\",\nfamily=\"Mildenberger\",\nemail=\"tobm@aqua.dtu.dk\",\nrole=c(\"aut\"),\ncomment=c(ORCID=\"0000-0002-6631-7524\")),\nperson(given=\"Alexandros\",\nfamily=\"Kokkalis\",\nemail=\"alko@aqua.dtu.dk\",\nrole=c(\"aut\"),\ncomment=c(ORCID=\"0000-0002-9662-6272\")))",
  "Description": "Fits a surplus production model to fisheries catch and\nbiomass index data.",
  "License": "GPL (>=3)",
  "LazyData": "true",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.3.2",
  "Repository": "https://ices-tools-prod.r-universe.dev",
  "Date/Publication": "2026-04-17 12:06:20 UTC",
  "RemoteUrl": "https://github.com/DTUAqua/spict",
  "RemoteRef": "HEAD",
  "RemoteSha": "0c750002a4f85362ef903108256cf59b72c94250",
  "RemoteSubdir": "spict",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-20 09:52:51 UTC",
    "User": "root"
  },
  "Author": "Martin Waever Pedersen [aut, cre, cph],\nCasper Willestofte Berg [aut],\nTobias Karl Mildenberger [aut] (ORCID:\n<https://orcid.org/0000-0002-6631-7524>),\nAlexandros Kokkalis [aut] (ORCID:\n<https://orcid.org/0000-0002-9662-6272>)",
  "Maintainer": "Martin Waever Pedersen <wpsgodd@gmail.com>",
  "MD5sum": "fe356548cb397d94b64fe776474ed758",
  "_user": "ices-tools-prod",
  "_type": "src",
  "_file": "spict_1.3.9.tar.gz",
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  "_sha256": "cc98aaef914a841e4445a9f4478b37fa425c3d3864cc7c7c431cf6d75d2a128b",
  "_created": "2026-05-20T09:52:51.000Z",
  "_published": "2026-06-02T13:15:45.292Z",
  "_distro": "noble",
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  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/DTUAqua/spict",
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    "author": "Casper W. Berg <casperwberg@gmail.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Merge pull request #214 from DTUAqua/dev\n\nv1.3.9",
    "time": 1776427580
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    "name": "Martin Waever Pedersen",
    "email": "wpsgodd@gmail.com",
    "login": "mawp",
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    "uuid": 4504914
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  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.0",
      "role": "Depends"
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    {
      "package": "TMB",
      "version": ">= 1.7.1",
      "role": "Depends"
    },
    {
      "package": "TMB",
      "role": "LinkingTo"
    },
    {
      "package": "RcppEigen",
      "role": "LinkingTo"
    },
    {
      "package": "ellipse",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Suggests"
    },
    {
      "package": "mgcv",
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    {
      "package": "rjags",
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  "_owner": "dtuaqua",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-16",
      "n": 1
    }
  ],
  "_tags": [],
  "_topics": [
    "fisheries-management",
    "fisheries-stock-assessment",
    "spict",
    "cpp"
  ],
  "_stars": 29,
  "_contributors": [
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    "type": "organization",
    "name": "ICES tools (production)",
    "description": "Tools that are operational and maintained by the ICES Secretariat"
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/spict"
  },
  "_devurl": "https://github.com/dtuaqua/spict",
  "_searchresults": 144,
  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/spict.html",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    "add.man.scenario",
    "add.manlines",
    "annual",
    "calc.bmsyk",
    "calc.gamma",
    "calc.influence",
    "calc.mase",
    "calc.om",
    "calc.osa.resid",
    "calc.process.resid",
    "calc.tac",
    "check.ini",
    "check.inp",
    "check.man.time",
    "extract.simstats",
    "fit.aspic",
    "fit.meyermillar",
    "fit.spict",
    "get.AIC",
    "get.catchindexoverlap",
    "get.cov",
    "get.mfrow",
    "get.msyvec",
    "get.no.active.priors",
    "get.par",
    "get.spline",
    "get.TAC",
    "get.version",
    "guess.m",
    "hindcast",
    "invlogit",
    "invlogp1",
    "likprof.spict",
    "list.possible.priors",
    "list.quantities",
    "make.datin",
    "make.fconvec",
    "make.ffacvec",
    "make.obj",
    "make.report",
    "make.splinemat",
    "man.select",
    "man.tac",
    "man.timeline",
    "manage",
    "mansummary",
    "meanvar2shaperate",
    "modefrac2shaperate",
    "mohns_rho",
    "plot2",
    "plotspict.bbmsy",
    "plotspict.biomass",
    "plotspict.catch",
    "plotspict.ci",
    "plotspict.compare",
    "plotspict.data",
    "plotspict.diagnostic",
    "plotspict.diagnostic.process",
    "plotspict.f",
    "plotspict.fb",
    "plotspict.ffmsy",
    "plotspict.growth",
    "plotspict.hcr",
    "plotspict.hindcast",
    "plotspict.infl",
    "plotspict.inflsum",
    "plotspict.likprof",
    "plotspict.osar",
    "plotspict.priors",
    "plotspict.production",
    "plotspict.retro",
    "plotspict.retro.fixed",
    "plotspict.season",
    "plotspict.tc",
    "read.aspic",
    "read.aspic.res",
    "res.diagn",
    "retape.spict",
    "retro",
    "shaperate2meanvar",
    "shorten.inp",
    "sim.spict",
    "sumspict.diagnostics",
    "sumspict.drefpoints",
    "sumspict.fixedpars",
    "sumspict.ini",
    "sumspict.manage",
    "sumspict.parest",
    "sumspict.predictions",
    "sumspict.priors",
    "sumspict.srefpoints",
    "sumspict.states",
    "test.spict",
    "trans2real",
    "txt.stamp",
    "validate.spict",
    "validation.data.frame",
    "write.aspic"
  ],
  "_datasets": [
    {
      "name": "pol",
      "title": "Fisheries data included in Polacheck et al. (1993).",
      "object": "pol",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "acf.signf",
      "title": "Check whether ACF of residuals is significant in any lags.",
      "topics": [
        "acf.signf"
      ]
    },
    {
      "page": "add.catchunit",
      "title": "Add catch unit to label",
      "topics": [
        "add.catchunit"
      ]
    },
    {
      "page": "add.col.legend",
      "title": "Add a legend explaining colors of points (vertical orientation)",
      "topics": [
        "add.col.legend"
      ]
    },
    {
      "page": "add.col.legend.hor",
      "title": "Add a legend explaining colors of points (horizontal orientation)",
      "topics": [
        "add.col.legend.hor"
      ]
    },
    {
      "page": "add.man.scenario",
      "title": "Define management scenario",
      "topics": [
        "add.man.scenario",
        "get.TAC",
        "get.TAC,",
        "make.man.inp"
      ]
    },
    {
      "page": "add.manlines",
      "title": "Add lines to plot indicating result of management scenarios.",
      "topics": [
        "add.manlines"
      ]
    },
    {
      "page": "annual",
      "title": "Convert from quarterly (or other sub-annual) data to annual means, sums or a custom function.",
      "topics": [
        "annual"
      ]
    },
    {
      "page": "arrow.line",
      "title": "Draw a line with arrow heads.",
      "topics": [
        "arrow.line"
      ]
    },
    {
      "page": "calc.bmsyk",
      "title": "Calculates the Bmsy/K ratio",
      "topics": [
        "calc.bmsyk"
      ]
    },
    {
      "page": "calc.EBinf",
      "title": "Calculate E(Binfinity), i.e. the fished equilibrium.",
      "topics": [
        "calc.EBinf"
      ]
    },
    {
      "page": "calc.gamma",
      "title": "Calculate gamma from n",
      "topics": [
        "calc.gamma"
      ]
    },
    {
      "page": "calc.influence",
      "title": "Calculates influence statistics of observations.",
      "topics": [
        "calc.influence"
      ]
    },
    {
      "page": "calc.mase",
      "title": "Calculate Mean Absolute Scaled Error (MASE)",
      "topics": [
        "calc.mase"
      ]
    },
    {
      "page": "calc.om",
      "title": "Calculates the order of magnitude for the relative reference levels B/Bmsy and F/Fmsy",
      "topics": [
        "calc.om"
      ]
    },
    {
      "page": "calc.osa.resid",
      "title": "Calculate one-step-ahead residuals.",
      "topics": [
        "calc.osa.resid"
      ]
    },
    {
      "page": "calc.process.resid",
      "title": "Calculate process residuals",
      "topics": [
        "calc.process.resid"
      ]
    },
    {
      "page": "calc.tac",
      "title": "Calculate Total Allowable Catch (TAC)",
      "topics": [
        "calc.tac"
      ]
    },
    {
      "page": "check.catchList",
      "title": "Check catch list",
      "topics": [
        "check.catchList"
      ]
    },
    {
      "page": "check.ini",
      "title": "Check sensitivity of fit to initial parameter values",
      "topics": [
        "check.ini"
      ]
    },
    {
      "page": "check.inp",
      "title": "Check list of input variables",
      "topics": [
        "check.inp"
      ]
    },
    {
      "page": "check.man",
      "title": "Check the consistency of management scenarios in rep",
      "topics": [
        "check.man"
      ]
    },
    {
      "page": "check.man.time",
      "title": "Checks and corrects management time to be within model time",
      "topics": [
        "check.man.time"
      ]
    },
    {
      "page": "check.rep",
      "title": "Check rep list",
      "topics": [
        "check.rep"
      ]
    },
    {
      "page": "extract.hindcast.info",
      "title": "Extract hindcast info from a fitted spict object",
      "topics": [
        "extract.hindcast.info"
      ]
    },
    {
      "page": "extract.simstats",
      "title": "Extracts relevant statistics from the estimation of a simulated data set.",
      "topics": [
        "extract.simstats"
      ]
    },
    {
      "page": "fd",
      "title": "Format date",
      "topics": [
        "fd"
      ]
    },
    {
      "page": "fit.aspic",
      "title": "Fits aspic to the data contained in the input file",
      "topics": [
        "fit.aspic"
      ]
    },
    {
      "page": "fit.jags",
      "title": "Fit the Meyer & Millar model using rjags",
      "topics": [
        "fit.jags"
      ]
    },
    {
      "page": "fit.meyermillar",
      "title": "Fit the model of Meyer & Millar (1999)",
      "topics": [
        "fit.meyermillar"
      ]
    },
    {
      "page": "fit.spict",
      "title": "Fit a continuous-time surplus production model to data.",
      "topics": [
        "fit.spict"
      ]
    },
    {
      "page": "get.AIC",
      "title": "Calculate AIC from a rep list.",
      "topics": [
        "get.AIC"
      ]
    },
    {
      "page": "get.catchindexoverlap",
      "title": "Find observations of catch and index that overlap",
      "topics": [
        "get.catchindexoverlap"
      ]
    },
    {
      "page": "get.colnms",
      "title": "Get column names for data.frames.",
      "topics": [
        "get.colnms"
      ]
    },
    {
      "page": "get.cov",
      "title": "Get covariance matrix of two reported quantities not of fixed model parameters. Covariance of fixed model parameters can be found in rep$cov.fixed.",
      "topics": [
        "get.cov"
      ]
    },
    {
      "page": "get.EBinf",
      "title": "Calculate E(Binfinity) the fished equilibrium.",
      "topics": [
        "get.EBinf"
      ]
    },
    {
      "page": "get.ffac",
      "title": "Estimate fishing mortality factor minimising probability of specified model variable hitting a specified reference level under given fishing mortality",
      "topics": [
        "get.ffac"
      ]
    },
    {
      "page": "get.manC",
      "title": "Estimate catch for management period based on last catch observations",
      "topics": [
        "get.manC"
      ]
    },
    {
      "page": "get.manlimits",
      "title": "Get limts of any parameter considering all spict objects in rep$man",
      "topics": [
        "get.manlimits"
      ]
    },
    {
      "page": "get.manmax",
      "title": "Get spict object in rep$man with longest time series",
      "topics": [
        "get.manmax"
      ]
    },
    {
      "page": "get.mfrow",
      "title": "Get mfrow from the number of plots to be plotted",
      "topics": [
        "get.mfrow"
      ]
    },
    {
      "page": "get.msyvec",
      "title": "If multiple growth rates (r) are used (e.g. for a seasonal model), return specified reference point for all instances of r.",
      "topics": [
        "get.msyvec"
      ]
    },
    {
      "page": "get.no.active.priors",
      "title": "Get number of active priors",
      "topics": [
        "get.no.active.priors"
      ]
    },
    {
      "page": "get.order",
      "title": "Get order of printed quantities.",
      "topics": [
        "get.order"
      ]
    },
    {
      "page": "get.osar.pvals",
      "title": "Check whether ACF of catch and index residuals is significant in any lags.",
      "topics": [
        "get.osar.pvals"
      ]
    },
    {
      "page": "get.par",
      "title": "Extract parameters from a result report as generated by fit.spict.",
      "topics": [
        "get.par",
        "list.quantities"
      ]
    },
    {
      "page": "get.spline",
      "title": "Get the values of the seasonal spline for F.",
      "topics": [
        "get.spline"
      ]
    },
    {
      "page": "get.version",
      "title": "Get version of spict including git sha1 version if available.",
      "topics": [
        "get.version"
      ]
    },
    {
      "page": "guess.m",
      "title": "Use a simple linear regression to guess m (MSY).",
      "topics": [
        "guess.m"
      ]
    },
    {
      "page": "hindcast",
      "title": "Conduct hindcasting analysis",
      "topics": [
        "hindcast"
      ]
    },
    {
      "page": "invlogit",
      "title": "Inverse logit transform.",
      "topics": [
        "invlogit"
      ]
    },
    {
      "page": "invlogp1",
      "title": "Inverse log \"plus one\" transform",
      "topics": [
        "invlogp1"
      ]
    },
    {
      "page": "latex.figure",
      "title": "Generate latex code for including a figure.",
      "topics": [
        "latex.figure"
      ]
    },
    {
      "page": "likprof.spict",
      "title": "Create profile likelihood",
      "topics": [
        "likprof.spict"
      ]
    },
    {
      "page": "list.possible.priors",
      "title": "List parameters to which priors can be added",
      "topics": [
        "list.possible.priors"
      ]
    },
    {
      "page": "make.datin",
      "title": "Create data list used as input to TMB::MakeADFun.",
      "topics": [
        "make.datin"
      ]
    },
    {
      "page": "make.fconvec",
      "title": "Make fcon vector",
      "topics": [
        "make.fconvec"
      ]
    },
    {
      "page": "make.ffacvec",
      "title": "Make ffac vector",
      "topics": [
        "make.ffacvec"
      ]
    },
    {
      "page": "make.obj",
      "title": "Create TMB obj using TMB::MakeADFun and squelch screen printing.",
      "topics": [
        "make.obj"
      ]
    },
    {
      "page": "make.report",
      "title": "Creates a pdf file containing the summary output and result plots",
      "topics": [
        "make.report"
      ]
    },
    {
      "page": "make.rpellipse",
      "title": "Calculate confidence ellipsis for reference points.",
      "topics": [
        "make.rpellipse"
      ]
    },
    {
      "page": "make.splinemat",
      "title": "Make a spline design matrix",
      "topics": [
        "make.splinemat"
      ]
    },
    {
      "page": "man.cols",
      "title": "Load color of management scenarios.",
      "topics": [
        "man.cols"
      ]
    },
    {
      "page": "man.select",
      "title": "Select management scenarios",
      "topics": [
        "man.select"
      ]
    },
    {
      "page": "man.tac",
      "title": "Get the TAC for the management scenarios",
      "topics": [
        "man.tac"
      ]
    },
    {
      "page": "man.timeline",
      "title": "Print a schematic to the console visualising the management timeline",
      "topics": [
        "man.timeline"
      ]
    },
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