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  "Package": "StrathE2E2",
  "Version": "3.3.1",
  "Title": "End-to-End Marine Food Web Model",
  "Author": "Michael Heath [aut], Ian Thurlbeck [ctb]",
  "Maintainer": "Michael Heath <m.heath@strath.ac.uk>",
  "Description": "A dynamic model of the big-picture, whole ecosystem\neffects of hydrodynamics, temperature, nutrients, and fishing\non continental shelf marine food webs. The package is described\nin: Heath, M.R., Speirs, D.C., Thurlbeck, I. and Wilson, R.J.\n(2021) <doi:10.1111/2041-210X.13510> StrathE2E2: An R package\nfor modelling the dynamics of marine food webs and fisheries.\nMethods in Ecology and Evolution 12, 280-287.",
  "License": "GPL (>= 2)",
  "NeedsCompilation": "yes",
  "Date": "2021-02-14",
  "URL": "https://gitlab.com/MarineResourceModelling/StrathE2E/StrathE2E2,\nhttps://marineresourcemodelling.gitlab.io/",
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    "extra/citation.json",
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  "_realowner": "mrheath",
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      "date": "2020-09-02"
    },
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      "date": "2021-01-23"
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    "e2e_calculate_hrscale",
    "e2e_compare_obs",
    "e2e_compare_runs_bar",
    "e2e_compare_runs_box",
    "e2e_copy",
    "e2e_extract_hr",
    "e2e_extract_start",
    "e2e_get_parmdoc",
    "e2e_get_senscrit",
    "e2e_ls",
    "e2e_merge_sens_mc",
    "e2e_optimize_act",
    "e2e_optimize_eco",
    "e2e_optimize_hr",
    "e2e_plot_biomass",
    "e2e_plot_catch",
    "e2e_plot_eco",
    "e2e_plot_edrivers",
    "e2e_plot_fdrivers",
    "e2e_plot_migration",
    "e2e_plot_opt_diagnostics",
    "e2e_plot_sens_mc",
    "e2e_plot_trophic",
    "e2e_plot_ts",
    "e2e_plot_ycurve",
    "e2e_process_sens_mc",
    "e2e_read",
    "e2e_run",
    "e2e_run_mc",
    "e2e_run_sens",
    "e2e_run_ycurve"
  ],
  "_help": [
    {
      "page": "e2e_calculate_hrscale",
      "title": "Calculate initial values of the scaling parameters for the fishing fleet model which link effort to harvest ratios.",
      "topics": [
        "e2e_calculate_hrscale"
      ]
    },
    {
      "page": "e2e_compare_obs",
      "title": "Box and whisker plots comparing annual or monthly observational data with corresponding model outputs.",
      "topics": [
        "e2e_compare_obs"
      ]
    },
    {
      "page": "e2e_compare_runs_bar",
      "title": "Create tornado bar-plots of the differences between two model runs.",
      "topics": [
        "e2e_compare_runs_bar"
      ]
    },
    {
      "page": "e2e_compare_runs_box",
      "title": "Box and whisker plots comparing annual or monthly outputs from single or Monte Carlo baseline and scenario model runs.",
      "topics": [
        "e2e_compare_runs_box"
      ]
    },
    {
      "page": "e2e_copy",
      "title": "Make a copy of a named model/variant and documentation in a user defined workspace",
      "topics": [
        "e2e_copy"
      ]
    },
    {
      "page": "e2e_extract_hr",
      "title": "Extract the values of harvest ratios generated by the fleet model.",
      "topics": [
        "e2e_extract_hr"
      ]
    },
    {
      "page": "e2e_extract_start",
      "title": "Extract the values of all the state variables at the end of a model run and format for use as new initial conditions.",
      "topics": [
        "e2e_extract_start"
      ]
    },
    {
      "page": "e2e_get_parmdoc",
      "title": "Get documentation on the parameters in the model.",
      "topics": [
        "e2e_get_parmdoc"
      ]
    },
    {
      "page": "e2e_get_senscrit",
      "title": "Get documentation on the model outputs available as the basis for sensitivity analysis.",
      "topics": [
        "e2e_get_senscrit"
      ]
    },
    {
      "page": "e2e_ls",
      "title": "List the available models in a designated workspace.",
      "topics": [
        "e2e_ls"
      ]
    },
    {
      "page": "e2e_merge_sens_mc",
      "title": "Combine two or more sets of raw output data from parallel sensitivity or Monte Carlo analysis runs performed on separate machines/processors.",
      "topics": [
        "e2e_merge_sens_mc"
      ]
    },
    {
      "page": "e2e_optimize_act",
      "title": "Optimize StrathE2E fishing gear activity multipliers to maximumize the likelihood of either observed ecosystem target data or know harvest ratios.",
      "topics": [
        "e2e_optimize_act"
      ]
    },
    {
      "page": "e2e_optimize_eco",
      "title": "Optimize StrathE2E ecology model parameters to maximise the likelihood of observed ecosystem target data.",
      "topics": [
        "e2e_optimize_eco"
      ]
    },
    {
      "page": "e2e_optimize_hr",
      "title": "Optimize StrathE2E harvest ratio multipliers to maximum the likelihood of observed ecosystem target data.",
      "topics": [
        "e2e_optimize_hr"
      ]
    },
    {
      "page": "e2e_plot_biomass",
      "title": "Plot showing the annual annual average biomass densities of each guild in the inshore and offshore zones, optionally with credible intervals.",
      "topics": [
        "e2e_plot_biomass"
      ]
    },
    {
      "page": "e2e_plot_catch",
      "title": "Plot the distribution and composition of annual catches across guild, zones and gears in the final year of a model run.",
      "topics": [
        "e2e_plot_catch"
      ]
    },
    {
      "page": "e2e_plot_eco",
      "title": "Plot daily data on ecological outputs from the model over the final year of a run, optionally with credible intervals.",
      "topics": [
        "e2e_plot_eco"
      ]
    },
    {
      "page": "e2e_plot_edrivers",
      "title": "Plot climatological year of environmental driving data.",
      "topics": [
        "e2e_plot_edrivers"
      ]
    },
    {
      "page": "e2e_plot_fdrivers",
      "title": "Plot shaded-grid-cell diagrams of the distributions of fishing-related drivers across gears, guilds and seabed habitats.",
      "topics": [
        "e2e_plot_fdrivers"
      ]
    },
    {
      "page": "e2e_plot_migration",
      "title": "Plot daily data on migration fluxes by actively mobile guilds during the final year of a run, optionally with credible intervals.",
      "topics": [
        "e2e_plot_migration"
      ]
    },
    {
      "page": "e2e_plot_opt_diagnostics",
      "title": "Plot diagnostic data on the performance of parameter optimization functions.",
      "topics": [
        "e2e_plot_opt_diagnostics"
      ]
    },
    {
      "page": "e2e_plot_sens_mc",
      "title": "Plot diagnostic data from sensitivity and Monte Carlo analyses.",
      "topics": [
        "e2e_plot_sens_mc"
      ]
    },
    {
      "page": "e2e_plot_trophic",
      "title": "Plot showing the annual mean trophic level index, and the omnivory index of each guild during the final year of a model run, optionally with credible intervals.",
      "topics": [
        "e2e_plot_trophic"
      ]
    },
    {
      "page": "e2e_plot_ts",
      "title": "Plot ecology model state variables or fishery catches for the full duration of a model run.",
      "topics": [
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      ]
    },
    {
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      "title": "Plot fishery yield curve data for planktivorous or demersal fish.",
      "topics": [
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      ]
    },
    {
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      "title": "Post-process already-created data from sensitivity or Monte Carlo analysis runs.",
      "topics": [
        "e2e_process_sens_mc"
      ]
    },
    {
      "page": "e2e_read",
      "title": "Read all the configuration, driving and parameter files for a designated model and compile the data into a list object.",
      "topics": [
        "e2e_read"
      ]
    },
    {
      "page": "e2e_run",
      "title": "Run the StrathE2E model with a given configuration.",
      "topics": [
        "e2e_run"
      ]
    },
    {
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      "title": "Run a Monte Carlo simulation with StrathE2E and derive centiles of credible values of model outputs.",
      "topics": [
        "e2e_run_mc"
      ]
    },
    {
      "page": "e2e_run_sens",
      "title": "Perform a parameter sensitivity analysis on the StrathE2E model.",
      "topics": [
        "e2e_run_sens"
      ]
    },
    {
      "page": "e2e_run_ycurve",
      "title": "Run a set of models to generate fishery yield curve data for either planktivorous or demersal fish.",
      "topics": [
        "e2e_run_ycurve"
      ]
    },
    {
      "page": "StrathE2E2-package",
      "title": "StrathE2E2 Package",
      "topics": [
        "StrathE2E2"
      ]
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