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  "Package": "LandWebUtils",
  "Title": "Helper functions for the LandWeb project",
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  "Authors@R": "c(\nperson(\"Eliot J B\", \"McIntire\", , \"eliot.mcintire@NRCan-RNCan.gc.ca\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-6914-8316\")),\nperson(\"Alex M\", \"Chubaty\", , \"achubaty@for-cast.ca\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-7146-8135\")),\nperson(\"His Majesty the Queen in Right of Canada, as represented by the Minister of Natural Resources Canada\", role = \"cph\")\n)",
  "Description": "Additional utilities for LandWeb analyses.",
  "License": "GPL-3",
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      "topics": [
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      "page": "cleanAreaName",
      "title": "Extract study area name from run name",
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    {
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      "topics": [
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    {
      "page": "landbaseLayers",
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      "topics": [
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      "page": "landmine_attach_identity",
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    {
      "page": "landmine-burn",
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        "landmine_burn1"
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      "page": "landmine_calibration_plots",
      "title": "LandMine calibration diagnostic plots",
      "topics": [
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        "landmine_plot_calibConvergence",
        "landmine_plot_calibDiscrimination",
        "landmine_plot_calibIslands",
        "landmine_plot_calibParams",
        "landmine_plot_calibShape"
      ]
    },
    {
      "page": "landmine_draw_num_fires",
      "title": "Draw the number of fires per FRI zone for one period",
      "topics": [
        "landmine_draw_num_fires"
      ]
    },
    {
      "page": "landmine_estimate_kBest",
      "title": "Fit the truncated-Pareto shape for the fire-size distribution",
      "topics": [
        "landmine_estimate_kBest"
      ]
    },
    {
      "page": "landmine_fire_attainment",
      "title": "Per-fire target attainment from a LandMine 'fireSizes' table",
      "topics": [
        "landmine_fire_attainment"
      ]
    },
    {
      "page": "landmine_fire_ros",
      "title": "Assign a rate of spread to every pixel",
      "topics": [
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      ]
    },
    {
      "page": "landmine_fri_metrics",
      "title": "Per-zone fire-return-interval diagnostics",
      "topics": [
        "landmine_fri_metrics"
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    },
    {
      "page": "landmine_fri_summary",
      "title": "Summarize achieved fire return interval by FRI zone",
      "topics": [
        "landmine_fri_summary"
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    {
      "page": "landmine_fri_verdict",
      "title": "One-line verdict on fire-return-interval attainment",
      "topics": [
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    {
      "page": "landmine_fuel_types",
      "title": "Reporting group to fuel type, for LandMine",
      "topics": [
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    },
    {
      "page": "landmine_ignition_budget",
      "title": "Ignition budget per FRI zone",
      "topics": [
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      "title": "Leading-species to fuel-type lookup used by LandMine",
      "topics": [
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      "title": "LandMine burn optimization function",
      "topics": [
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      "page": "landmine_optim_calibrate",
      "title": "Run the LandMine fire-spread calibration",
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      "title": "Export objects used for optimization and load packages on cluster",
      "topics": [
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      "page": "landmine_optim_clusterSetup",
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      "topics": [
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      "topics": [
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      "page": "landmine_optim_fitAndison",
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    {
      "page": "landmine_fitSN",
      "title": "LandMine objective functions",
      "topics": [
        "landmine_optim_fitSN",
        "landmine_optim_fitSN2"
      ]
    },
    {
      "page": "landmine_optim_islands",
      "title": "Remnant islands within a simulated fire",
      "topics": [
        "landmine_optim_islands"
      ]
    },
    {
      "page": "landmine_optim_islandTarget",
      "title": "Andison island-remnant target",
      "topics": [
        "landmine_optim_islandTarget"
      ]
    },
    {
      "page": "landmine_optim_islandWeight",
      "title": "Resolution-dependent weight for the remnant-island term",
      "topics": [
        "landmine_optim_islandWeight"
      ]
    },
    {
      "page": "landmine_optim_landscape",
      "title": "Build the synthetic landscape used for LandMine calibration",
      "topics": [
        "landmine_optim_landscape"
      ]
    },
    {
      "page": "landmine_optim_shapeIndex",
      "title": "Andison's shape index",
      "topics": [
        "landmine_optim_shapeIndex"
      ]
    },
    {
      "page": "landmine_optim_shapeTarget",
      "title": "Andison's expected shape index for a given fire area",
      "topics": [
        "landmine_optim_shapeTarget"
      ]
    },
    {
      "page": "landmine_optim_params",
      "title": "Unpack LandMine fire-spread calibration parameters",
      "topics": [
        "landmine_optim_params_append",
        "landmine_optim_params_read",
        "landmine_optim_unpack"
      ]
    },
    {
      "page": "landmine_plot_fri_drivers",
      "title": "Plot what separates the failing zones from the rest",
      "topics": [
        "landmine_plot_fri_drivers"
      ]
    },
    {
      "page": "landmine_plot_fri_zones",
      "title": "Map fire-return-interval zones and their attainment",
      "topics": [
        "landmine_plot_fri_zones"
      ]
    },
    {
      "page": "landmine_plots",
      "title": "LandMine diagnostic plots",
      "topics": [
        "landmine_plots",
        "landmine_plot_areaBurnedOverTime",
        "landmine_plot_FRI",
        "landmine_plot_LTHFC"
      ]
    },
    {
      "page": "landmine_reburn_budget",
      "title": "Rebuild the per-zone fire budget for the next reburn round",
      "topics": [
        "landmine_reburn_budget"
      ]
    },
    {
      "page": "landmine_reburn_ceiling",
      "title": "Summarize FRI zones still short of target at the reburn ceiling",
      "topics": [
        "landmine_reburn_ceiling"
      ]
    },
    {
      "page": "landmine_ros_table",
      "title": "LandMine's rate-of-spread table",
      "topics": [
        "landmine_ros_table"
      ]
    },
    {
      "page": "landmine_sizes_to_pixels",
      "title": "Convert fire sizes in hectares to whole pixels, preserving the expectation",
      "topics": [
        "landmine_sizes_to_pixels"
      ]
    },
    {
      "page": "landweb_add_report_column",
      "title": "Add the LandWeb reporting groups to a species equivalency table",
      "topics": [
        "landweb_add_report_column"
      ]
    },
    {
      "page": "landweb_anpp_area",
      "title": "Ecological units that touch an area, for fitting growth curves",
      "topics": [
        "landweb_anpp_area"
      ]
    },
    {
      "page": "landweb_area",
      "title": "The outline of the LandWeb area",
      "topics": [
        "landweb_area"
      ]
    },
    {
      "page": "landweb_bec_zones",
      "title": "BC BEC zones over the BC plots of a growth-curve fitting area",
      "topics": [
        "landweb_bec_zones"
      ]
    },
    {
      "page": "landweb_damage_codes",
      "title": "Damage agent codes to exclude from growth-curve plots, by plot source",
      "topics": [
        "landweb_damage_codes"
      ]
    },
    {
      "page": "landweb_dominant_sppEquiv",
      "title": "Give each merged LandWeb species group its dominant member's traits",
      "topics": [
        "landweb_dominant_sppEquiv"
      ]
    },
    {
      "page": "landweb_growth_sppEquiv",
      "title": "Species table for the shared growth-curve fit",
      "topics": [
        "landweb_growth_sppEquiv"
      ]
    },
    {
      "page": "landweb_growth_trait_frequency",
      "title": "How often refits on resampled plots chose each species' growth-curve traits",
      "topics": [
        "landweb_growth_trait_frequency"
      ]
    },
    {
      "page": "landweb_growth_traits",
      "title": "The growth-curve traits of each species, from the shared fit",
      "topics": [
        "landweb_growth_traits"
      ]
    },
    {
      "page": "landweb_lthfc",
      "title": "The LandWeb long-term historic fire cycle (LTHFC) map",
      "topics": [
        "landweb_lthfc"
      ]
    },
    {
      "page": "landweb_member_cover",
      "title": "Total SCANFI cover of each member species in a study area",
      "topics": [
        "landweb_member_cover"
      ]
    },
    {
      "page": "landweb_report_colours",
      "title": "Colours for the LandWeb reporting groups",
      "topics": [
        "landweb_report_colours"
      ]
    },
    {
      "page": "landweb_report_groups",
      "title": "LandWeb reporting groups",
      "topics": [
        "landweb_report_groups"
      ]
    },
    {
      "page": "landweb_report_map",
      "title": "Simulated species and groups to LandWeb reporting groups",
      "topics": [
        "landweb_report_map"
      ]
    },
    {
      "page": "landweb_require_species",
      "title": "Stop when a species input is empty",
      "topics": [
        "landweb_require_species"
      ]
    },
    {
      "page": "landweb_resample_psp",
      "title": "Resample the plots of a growth-curve fit, whole plots with replacement",
      "topics": [
        "landweb_resample_psp"
      ]
    },
    {
      "page": "landweb_species_map",
      "title": "SCANFI species to LandWeb species groups",
      "topics": [
        "landweb_species_map"
      ]
    },
    {
      "page": "landweb_species_sppEquiv",
      "title": "SCANFI species to LandWeb species, one code per species",
      "topics": [
        "landweb_species_sppEquiv"
      ]
    },
    {
      "page": "landweb_species_units",
      "title": "Which species LandWeb simulates on its own in a study area",
      "topics": [
        "landweb_species_units"
      ]
    },
    {
      "page": "landweb_sppEquiv",
      "title": "Add the LandWeb species groups to a species equivalency table",
      "topics": [
        "landweb_sppEquiv"
      ]
    },
    {
      "page": "landweb_sum_layers",
      "title": "Sum species cover layers into the units LandWeb simulates",
      "topics": [
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    {
      "page": "landweb_unit_growth_traits",
      "title": "Give each simulated unit the growth-curve traits of a member species",
      "topics": [
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    {
      "page": "LandWebCRS",
      "title": "Target CRS (projection) to use with LandWeb",
      "topics": [
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      ]
    },
    {
      "page": "LandWebStudyAreas",
      "title": "Study areas available for LandWeb simulations",
      "topics": [
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        "studyAreaIn",
        "studyAreaProv"
      ]
    },
    {
      "page": "LargePatches",
      "title": "Calculate proportion of large patches in NRV",
      "topics": [
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      ]
    },
    {
      "page": "lcc2020_classes",
      "title": "Canada LCC 2020 class groups used by LandWeb",
      "topics": [
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      ]
    },
    {
      "page": "lcc2020_remap_table",
      "title": "Remap table for overlaying LCC 2020 onto the simulation land cover",
      "topics": [
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    },
    {
      "page": "LeadingVegTypeByAgeClass",
      "title": "Calculate proportion of landscape occupied by each vegetation class",
      "topics": [
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    {
      "page": "loadCASFRI",
      "title": "Load CASFRI data for LandWeb",
      "topics": [
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    {
      "page": "meanTruncPareto",
      "title": "Calculate the mean of a truncated Pareto distribution",
      "topics": [
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      ]
    },
    {
      "page": "plotFMA",
      "title": "Plot boundary polygon(s) for forest management areas",
      "topics": [
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        "plotGG",
        "plotLandWeb"
      ]
    },
    {
      "page": "polygonClean",
      "title": "Do an arbitrary set of operations on a polygon",
      "topics": [
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    },
    {
      "page": "prepReportingPolygons",
      "title": "Prepare reporting polygons",
      "topics": [
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        "prepEcoprovinceLayer",
        "prepEcoregionLayer",
        "prepFMAs",
        "prepFMUs"
      ]
    },
    {
      "page": "prepSpeciesLayers_CASFRI",
      "title": "Prepare species layers from CASFRI v4",
      "topics": [
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      "page": "prepStudyArea",
      "title": "Extract boundary polygon(s) for a LandWeb study area",
      "topics": [
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        "prepTestStudyArea"
      ]
    },
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      "page": "rasterListByPoly",
      "title": "Create a list of rasters in each rep, at each timestep, for each polygon area",
      "topics": [
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      ]
    },
    {
      "page": "recode_cohorts",
      "title": "Recode cohorts' species to their groups",
      "topics": [
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    {
      "page": "refCodeFor",
      "title": "Output key ('refCode') for one analysis kind and reporting layer",
      "topics": [
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    },
    {
      "page": "reportingPolygonLayers",
      "title": "Candidate reporting-polygon source layers",
      "topics": [
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    },
    {
      "page": "runBoxPlotsVegCover",
      "title": "Generate box and whisker plots for leading vegetation cover",
      "topics": [
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    },
    {
      "page": "runHistsLargePatches",
      "title": "Generate histograms for large patches",
      "topics": [
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    },
    {
      "page": "runHistsVegCover",
      "title": "Generate histograms for leading vegetation cover",
      "topics": [
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    {
      "page": "shortNameFor",
      "title": "Look up curated short names",
      "topics": [
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    {
      "page": "sppEquiv_groups",
      "title": "Group the simulated species of a species table",
      "topics": [
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      "page": "studyAreaCrosswalk",
      "title": "Build (or load a cached) LandWeb study-area grouping crosswalk",
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      "page": "tenureShortNames",
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      "page": "validateShortNames",
      "title": "Validate a set of curated short names",
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