{
  "_id": "6aca3ec6fe5cc25786e85d3b",
  "Package": "LeMaRns",
  "Title": "Length-Based Multispecies Analysis by Numerical Simulation",
  "Version": "0.1.2",
  "Date": "2019-12-09",
  "Authors@R": "c(person(\"Michael A.\", \"Spence\", email = \"michael.spence@cefas.co.uk\", role = c(\"aut\", \"cre\"),comment = c(ORCID = \"0000-0002-3445-7979\")), person(\"Hayley J.\", \"Bannister\", email = \"hayley.bannister@cefas.co.uk\", role = c(\"aut\"),comment = c(ORCID = \"0000-0002-2546-5168\")), person(\"Johnathan E.\", \"Ball\", email = \"johnathan.ball@cefas.co.uk\", role = c(\"aut\")), person(\"Paul J.\", \"Dolder\", email = \"paul.dolder@cefas.co.uk\", role = c(\"aut\"),comment = c(ORCID = \"0000-0002-4179-712X\")), person(\"Robert B.\", \"Thorpe\", email = \"robert.thorpe@cefas.co.uk\", role = c(\"aut\"),comment = c(ORCID = \"0000-0001-8193-6932\")),person(\"Christopher A.\", \"Griffiths\", email = \"chris.griffiths@cefas.co.uk\", role = c(\"ctb\")))",
  "Description": "Set up, run and explore the outputs of the Length-based\nMulti-species model (LeMans; Hall et al. 2006\n<doi:10.1139/f06-039>), focused on the marine environment.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.0.0",
  "VignetteBuilder": "knitr",
  "Collate": "'NS_par.R' 'RcppExports.R' 'calc_M1.R' 'calc_Q.R'\n'calc_growth.R' 'calc_indicators.R' 'calc_mature.R'\n'param_setup.R' 'run_LeMans.R' 'calc_output.R' 'calc_phi.R'\n'calc_prefs.R' 'calc_ration_growthfac.R' 'calc_recruits.R'\n'calc_suit_vect.R' 'get_Catch.R' 'get_SSB.R' 'get_indicators.R'\n'other.R' 'plot_SSB.R' 'plot_indicators.R'",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-10-10 13:27:01 UTC",
    "User": "root"
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  "Author": "Michael A. Spence [aut, cre]\n(<https://orcid.org/0000-0002-3445-7979>), Hayley J. Bannister\n[aut] (<https://orcid.org/0000-0002-2546-5168>), Johnathan E.\nBall [aut], Paul J. Dolder [aut]\n(<https://orcid.org/0000-0002-4179-712X>), Robert B. Thorpe\n[aut] (<https://orcid.org/0000-0001-8193-6932>), Christopher A.\nGriffiths [ctb]",
  "Maintainer": "Michael A. Spence <michael.spence@cefas.co.uk>",
  "Repository": "https://michaelspence.r-universe.dev",
  "Date/Publication": "2019-12-09 14:10:02 UTC",
  "RemoteUrl": "https://github.com/cran/LeMaRns",
  "RemoteRef": "HEAD",
  "RemoteSha": "1486684c4b9e4031eaf81f186efad8d94d4712a8",
  "_user": "michaelspence",
  "_type": "src",
  "_file": "LeMaRns_0.1.2.tar.gz",
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  "_expires": "2027-01-18T13:33:56.000Z",
  "_created": "2026-10-10T13:27:01.000Z",
  "_published": "2026-10-10T13:33:58.076Z",
  "_buildurl": "https://github.com/r-universe/michaelspence/actions/runs/38055570963",
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  "_commit": {
    "id": "1486684c4b9e4031eaf81f186efad8d94d4712a8",
    "author": "Michael A. Spence <michael.spence@cefas.co.uk>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 0.1.2\n",
    "time": 1575900602
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    "email": "michael.spence@cefas.co.uk",
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    "orcid": "0000-0002-3445-7979"
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  "_topics": [
    "cpp"
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  "_rbuild": "4.6.1",
  "_assets": [
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    "extra/citation.json",
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    "extra/contents.json",
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      "date": "2019-06-03"
    },
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      "version": "0.1.1",
      "date": "2019-10-08"
    },
    {
      "version": "0.1.2",
      "date": "2019-12-09"
    }
  ],
  "_exports": [
    "calc_biomass",
    "calc_growth",
    "calc_LFI",
    "calc_LQ",
    "calc_M1",
    "calc_M1_constRNM",
    "calc_M1_lin",
    "calc_M1_stdRNM",
    "calc_M2",
    "calc_mature",
    "calc_phi",
    "calc_prefs",
    "calc_Q",
    "calc_ration_growthfac",
    "calc_recruits",
    "calc_SSB",
    "calc_suit_vect",
    "calc_TyL",
    "comb_LeMans_run",
    "get_annual_catch",
    "get_biomass",
    "get_CPG",
    "get_CPUE",
    "get_indicators",
    "get_LFI",
    "get_LQ",
    "get_M1",
    "get_MML",
    "get_N0",
    "get_Q",
    "get_rec_fun",
    "get_SSB",
    "get_TyL",
    "knife_edge_catch",
    "LeMansParam",
    "log_gaussian_catch",
    "logistic_catch",
    "make_rec_fun",
    "plot_biomass",
    "plot_indicators",
    "plot_LFI",
    "plot_LQ",
    "plot_MML",
    "plot_SSB",
    "plot_TyL",
    "rec_BH",
    "rec_const",
    "rec_hockey",
    "rec_linear",
    "rec_Ricker",
    "run_LeMans"
  ],
  "_datasets": [
    {
      "name": "NS_eta",
      "title": "The steepness of the slope of the catchability curve",
      "object": "gear",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "NS_L50",
      "title": "The length at 50% of the maximum catchability of the catchability curve",
      "object": "gear",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "NS_mixed_fish",
      "title": "Gear selectivity data frame",
      "object": "gear",
      "class": [
        "data.frame"
      ],
      "fields": [
        "catch_species",
        "curve",
        "gear_name",
        "max_catchability"
      ],
      "rows": 21,
      "table": true,
      "tojson": true
    },
    {
      "name": "NS_other",
      "title": "Other food for the North Sea",
      "object": "NS_par",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "NS_par",
      "title": "North Sea data",
      "object": "NS_par",
      "class": [
        "data.frame"
      ],
      "fields": [
        "species_names",
        "Linf",
        "W_a",
        "W_b",
        "k",
        "Lmat",
        "a",
        "b"
      ],
      "rows": 21,
      "table": true,
      "tojson": true
    },
    {
      "name": "NS_tau",
      "title": "North Sea interaction matrix",
      "object": "NS_tau",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "Sprat",
        "Npout",
        "Sandeel",
        "Poor cod",
        "Long rough dab",
        "Dab",
        "Herring",
        "Horse mackerel",
        "Lemon sole",
        "Sole",
        "Mackerel",
        "Whiting",
        "Witch",
        "Gurnard",
        "Plaice",
        "Starry ray",
        "Haddock",
        "Cuckoo ray",
        "Monkfish",
        "Cod",
        "Saithe"
      ],
      "rows": 21,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "calc_growth",
      "title": "Calculate growth",
      "topics": [
        "calc_growth"
      ]
    },
    {
      "page": "calc_LFI",
      "title": "Calculate community indicators",
      "topics": [
        "calc_LFI",
        "calc_LQ",
        "calc_TyL"
      ]
    },
    {
      "page": "calc_M1",
      "title": "Calculate background mortality",
      "topics": [
        "calc_M1",
        "calc_M1_constRNM",
        "calc_M1_lin",
        "calc_M1_stdRNM",
        "get_M1"
      ]
    },
    {
      "page": "calc_M2",
      "title": "Calculate predation mortality",
      "topics": [
        "calc_M2"
      ]
    },
    {
      "page": "calc_mature",
      "title": "Calculate the proportion of mature individuals",
      "topics": [
        "calc_mature"
      ]
    },
    {
      "page": "calc_phi",
      "title": "Calculate the proportion of individuals that leave each length class for each species each length class each time step.",
      "topics": [
        "calc_phi"
      ]
    },
    {
      "page": "calc_prefs",
      "title": "Calculate predator-prey size preferences",
      "topics": [
        "calc_prefs"
      ]
    },
    {
      "page": "calc_Q",
      "title": "Calculate gear catchability",
      "topics": [
        "calc_Q",
        "get_Q",
        "knife_edge_catch",
        "logistic_catch",
        "log_gaussian_catch"
      ]
    },
    {
      "page": "calc_ration_growthfac",
      "title": "Calculate growth increments",
      "topics": [
        "calc_ration_growthfac"
      ]
    },
    {
      "page": "calc_recruits",
      "title": "Calculate the number of recruits",
      "topics": [
        "calc_recruits"
      ]
    },
    {
      "page": "calc_SSB",
      "title": "Calculate Spawning Stock Biomass (SSB) or total biomass",
      "topics": [
        "calc_biomass",
        "calc_SSB"
      ]
    },
    {
      "page": "calc_suit_vect",
      "title": "Combines prey preference and prey suitability",
      "topics": [
        "calc_suit_vect"
      ]
    },
    {
      "page": "comb_LeMans_run",
      "title": "Combine two 'LeMans_outputs' objects",
      "topics": [
        "comb_LeMans_run"
      ]
    },
    {
      "page": "get_annual_catch",
      "title": "Get annual catch for each species, catch per unit effort or catch per gear",
      "topics": [
        "get_annual_catch",
        "get_annual_catch,LeMans_param,LeMans_outputs-method",
        "get_annual_catch,LeMans_param,missing-method",
        "get_annual_catch,missing,LeMans_outputs-method",
        "get_annual_catch,missing,missing-method",
        "get_CPG",
        "get_CPG,LeMans_param,LeMans_outputs-method",
        "get_CPG,LeMans_param,missing-method",
        "get_CPG,missing,LeMans_outputs-method",
        "get_CPG,missing,missing-method",
        "get_CPUE",
        "get_CPUE,LeMans_param,LeMans_outputs-method",
        "get_CPUE,LeMans_param,missing-method",
        "get_CPUE,missing,LeMans_outputs-method",
        "get_CPUE,missing,missing-method"
      ]
    },
    {
      "page": "get_indicators",
      "title": "Calculate indicators",
      "topics": [
        "get_indicators",
        "get_indicators,LeMans_param,LeMans_outputs-method",
        "get_indicators,LeMans_param,missing-method",
        "get_indicators,missing,LeMans_outputs-method",
        "get_indicators,missing,missing-method",
        "get_LFI",
        "get_LFI,LeMans_param,LeMans_outputs-method",
        "get_LFI,LeMans_param,missing-method",
        "get_LFI,missing,LeMans_outputs-method",
        "get_LFI,missing,missing-method",
        "get_LQ",
        "get_LQ,LeMans_param,LeMans_outputs-method",
        "get_LQ,LeMans_param,missing-method",
        "get_LQ,missing,LeMans_outputs-method",
        "get_LQ,missing,missing-method",
        "get_MML",
        "get_MML,LeMans_param,LeMans_outputs-method",
        "get_MML,LeMans_param,missing-method",
        "get_MML,missing,LeMans_outputs-method",
        "get_MML,missing,missing-method",
        "get_TyL",
        "get_TyL,LeMans_param,LeMans_outputs-method",
        "get_TyL,LeMans_param,missing-method",
        "get_TyL,missing,LeMans_outputs-method",
        "get_TyL,missing,missing-method"
      ]
    },
    {
      "page": "get_N0",
      "title": "Generate a starting value for N",
      "topics": [
        "get_N0"
      ]
    },
    {
      "page": "get_rec_fun",
      "title": "Collate the stock recruitment functions",
      "topics": [
        "get_rec_fun"
      ]
    },
    {
      "page": "get_SSB",
      "title": "Calculate Spawning Stock Biomass (SSB) or total biomass",
      "topics": [
        "get_biomass",
        "get_biomass,LeMans_param,LeMans_outputs-method",
        "get_biomass,LeMans_param,missing-method",
        "get_biomass,missing,LeMans_outputs-method",
        "get_biomass,missing,missing-method",
        "get_SSB",
        "get_SSB,LeMans_param,LeMans_outputs-method",
        "get_SSB,LeMans_param,missing-method",
        "get_SSB,missing,LeMans_outputs-method",
        "get_SSB,missing,missing-method"
      ]
    },
    {
      "page": "LeMans_outputs-class",
      "title": "An S4 class representing the outputs of the LeMans model",
      "topics": [
        "LeMans_outputs-class"
      ]
    },
    {
      "page": "LeMans_param-class",
      "title": "An S4 class representing the inputs of the LeMans model",
      "topics": [
        "LeMans_param-class"
      ]
    },
    {
      "page": "LeMansParam",
      "title": "A constructor for the 'LeMansParam' class",
      "topics": [
        "LeMansParam",
        "LeMansParam,ANY,ANY-method",
        "LeMansParam,missing,ANY-method",
        "LeMansParam,missing,missing-method"
      ]
    },
    {
      "page": "make_rec_fun",
      "title": "Generate the stock recruitment functions",
      "topics": [
        "make_rec_fun"
      ]
    },
    {
      "page": "NS_eta",
      "title": "The steepness of the slope of the catchability curve",
      "topics": [
        "NS_eta"
      ]
    },
    {
      "page": "NS_L50",
      "title": "The length at 50% of the maximum catchability of the catchability curve",
      "topics": [
        "NS_L50"
      ]
    },
    {
      "page": "NS_mixed_fish",
      "title": "Gear selectivity data frame",
      "topics": [
        "NS_mixed_fish"
      ]
    },
    {
      "page": "NS_other",
      "title": "Other food for the North Sea",
      "topics": [
        "NS_other"
      ]
    },
    {
      "page": "NS_par",
      "title": "North Sea data",
      "topics": [
        "NS_par"
      ]
    },
    {
      "page": "NS_tau",
      "title": "North Sea interaction matrix",
      "topics": [
        "NS_tau"
      ]
    },
    {
      "page": "plot_indicators",
      "title": "Plot indicators",
      "topics": [
        "plot_indicators",
        "plot_indicators,LeMans_param,LeMans_outputs-method",
        "plot_indicators,LeMans_param,missing-method",
        "plot_indicators,missing,LeMans_outputs-method",
        "plot_indicators,missing,missing-method",
        "plot_LFI",
        "plot_LFI,LeMans_param,LeMans_outputs-method",
        "plot_LFI,LeMans_param,missing-method",
        "plot_LFI,missing,LeMans_outputs-method",
        "plot_LFI,missing,missing-method",
        "plot_LQ",
        "plot_LQ,LeMans_param,LeMans_outputs-method",
        "plot_LQ,LeMans_param,missing-method",
        "plot_LQ,missing,LeMans_outputs-method",
        "plot_LQ,missing,missing-method",
        "plot_MML",
        "plot_MML,LeMans_param,LeMans_outputs-method",
        "plot_MML,LeMans_param,missing-method",
        "plot_MML,missing,LeMans_outputs-method",
        "plot_MML,missing,missing-method",
        "plot_TyL",
        "plot_TyL,LeMans_param,LeMans_outputs-method",
        "plot_TyL,LeMans_param,missing-method",
        "plot_TyL,missing,LeMans_outputs-method",
        "plot_TyL,missing,missing-method"
      ]
    },
    {
      "page": "plot_SSB",
      "title": "Plot Spawning Stock Biomass (SSB)",
      "topics": [
        "plot_biomass",
        "plot_biomass,LeMans_param,LeMans_outputs-method",
        "plot_biomass,LeMans_param,missing-method",
        "plot_biomass,missing,LeMans_outputs-method",
        "plot_biomass,missing,missing-method",
        "plot_SSB",
        "plot_SSB,LeMans_param,LeMans_outputs-method",
        "plot_SSB,LeMans_param,missing-method",
        "plot_SSB,missing,LeMans_outputs-method",
        "plot_SSB,missing,missing-method"
      ]
    },
    {
      "page": "rec_BH",
      "title": "The Beverton-Holt stock recruitment function",
      "topics": [
        "rec_BH"
      ]
    },
    {
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      "author": "Michael A. Spence, Hayley J. Bannister, Johnathan E. Ball and Robert B. Thorpe",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Setting up the model",
        "Dataset for the North Sea",
        "Setting the species-independent parameters",
        "Setting the species-specific parameters",
        "Size, growth and maturity",
        "Recruitment",
        "Mortality",
        "LeMans_param objects",
        "Running the model",
        "Initialising the model",
        "The model run",
        "Growth",
        "run_LeMans function",
        "Exploring the outputs",
        "Biomass",
        "Spawning Stock Biomass (SSB)",
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        "Catch",
        "Case Study",
        "Fishing fleets",
        "Dynamic fishing",
        "Nash equilibrium",
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      "modified": "2019-10-08 16:00:02",
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