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  "Title": "Biosphere integrity metrics for LPJmL",
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  "Maintainer": "Fabian Stenzel <stenzel@pik-potsdam.de>",
  "Description": "Functions to compute Biosphere integrity metrics BioCol\nand EcoRisk based on output from LPJmL.",
  "License": "AGPL-3",
  "Encoding": "UTF-8",
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    "calc_biocol",
    "calc_delta_v",
    "calc_ecorisk",
    "calc_roc_data",
    "calculate_within_biome_diffs",
    "classify_biomes",
    "disaggregate_into_biomes",
    "ecorisk_combine_hist_and_scen_data",
    "ecorisk_cross_table",
    "ecorisk_wrapper",
    "get_biome_names",
    "list_outputs",
    "plot_biocol",
    "plot_biocol_map",
    "plot_biocol_ts",
    "plot_biome_averages",
    "plot_biome_internal_distribution",
    "plot_biomes",
    "plot_ecorisk_cross_table",
    "plot_ecorisk_map",
    "plot_ecorisk_maps",
    "plot_ecorisk_over_time_panel",
    "plot_ecorisk_radial",
    "plot_ecorisk_radial_panel",
    "plot_ecorisk_radial_to_screen",
    "plot_global",
    "plot_overtime_to_screen",
    "read_calc_biocol",
    "read_ecorisk_data",
    "replace_ref_data_with_average_ref_biome_cell",
    "roc_plot",
    "roc_plot_paper"
  ],
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    {
      "page": "average_nyear_window",
      "title": "Calculate averages (mean) for defined window sizes",
      "topics": [
        "average_nyear_window"
      ]
    },
    {
      "page": "calc_biocol",
      "title": "Calculate BioCol",
      "topics": [
        "calc_biocol"
      ]
    },
    {
      "page": "calc_delta_v",
      "title": "Calculates changes in vegetation structure (vegetation_structure_change)",
      "topics": [
        "calc_delta_v"
      ]
    },
    {
      "page": "calc_ecorisk",
      "title": "Calculate the ecosystem change metric EcoRisk between 2 sets of states This function is called by the wrapper function (ecorisk_wrapper), unless you know what you are doing, don't use this function directly.",
      "topics": [
        "calc_ecorisk"
      ]
    },
    {
      "page": "calc_roc_data",
      "title": "Calculate ROC curve data",
      "topics": [
        "calc_roc_data"
      ]
    },
    {
      "page": "calculate_within_biome_diffs",
      "title": "Calculate ecorisk with each biomes average cell",
      "topics": [
        "calculate_within_biome_diffs"
      ]
    },
    {
      "page": "classify_biomes",
      "title": "Classify biomes",
      "topics": [
        "classify_biomes"
      ]
    },
    {
      "page": "disaggregate_into_biomes",
      "title": "Averages EcoRisk values across regions",
      "topics": [
        "disaggregate_into_biomes"
      ]
    },
    {
      "page": "ecorisk_combine_hist_and_scen_data",
      "title": "Create modified EcoRisk data combining two time series",
      "topics": [
        "ecorisk_combine_hist_and_scen_data"
      ]
    },
    {
      "page": "ecorisk_cross_table",
      "title": "Create modified EcoRisk data for crosstable",
      "topics": [
        "ecorisk_cross_table"
      ]
    },
    {
      "page": "ecorisk_wrapper",
      "title": "Wrapper for calculating the ecosystem change metric EcoRisk",
      "topics": [
        "ecorisk_wrapper"
      ]
    },
    {
      "page": "get_biome_names",
      "title": "Get biome names",
      "topics": [
        "get_biome_names"
      ]
    },
    {
      "page": "list_outputs",
      "title": "List required output files for given metric",
      "topics": [
        "list_outputs"
      ]
    },
    {
      "page": "plot_biocol",
      "title": "Plot absolute BioCol, overtime, maps, and npp into given folder",
      "topics": [
        "plot_biocol"
      ]
    },
    {
      "page": "plot_biocol_map",
      "title": "Plot global map of BioCol to file",
      "topics": [
        "plot_biocol_map"
      ]
    },
    {
      "page": "plot_biocol_ts",
      "title": "Plot absolute BioCol, overtime, maps, and npp into given folder",
      "topics": [
        "plot_biocol_ts"
      ]
    },
    {
      "page": "plot_biome_averages",
      "title": "Plot radial EcoRisk with 4/16 biomes",
      "topics": [
        "plot_biome_averages"
      ]
    },
    {
      "page": "plot_biome_internal_distribution",
      "title": "Plot distribution of similarity within biomes",
      "topics": [
        "plot_biome_internal_distribution"
      ]
    },
    {
      "page": "plot_biomes",
      "title": "Plot global distribution of lpjml simulated biomes",
      "topics": [
        "plot_biomes"
      ]
    },
    {
      "page": "plot_ecorisk_cross_table",
      "title": "Plot crosstable showing (dis-)similarity between average biome pixels",
      "topics": [
        "plot_ecorisk_cross_table"
      ]
    },
    {
      "page": "plot_ecorisk_map",
      "title": "Plot EcoRisk map to file",
      "topics": [
        "plot_ecorisk_map"
      ]
    },
    {
      "page": "plot_ecorisk_maps",
      "title": "Plot EcoRisk maps",
      "topics": [
        "plot_ecorisk_maps"
      ]
    },
    {
      "page": "plot_ecorisk_over_time_panel",
      "title": "Plot timeline of EcoRisk variables as panel to file with 4/16 biomes",
      "topics": [
        "plot_ecorisk_over_time_panel"
      ]
    },
    {
      "page": "plot_ecorisk_radial",
      "title": "Plot radial EcoRisk plot to file",
      "topics": [
        "plot_ecorisk_radial"
      ]
    },
    {
      "page": "plot_ecorisk_radial_panel",
      "title": "Plot radial EcoRisk panel to file with 4/16 biomes",
      "topics": [
        "plot_ecorisk_radial_panel"
      ]
    },
    {
      "page": "plot_ecorisk_radial_to_screen",
      "title": "Plot radial EcoRisk plot to screen",
      "topics": [
        "plot_ecorisk_radial_to_screen"
      ]
    },
    {
      "page": "plot_global",
      "title": "Plot global LPJmL array",
      "topics": [
        "plot_global"
      ]
    },
    {
      "page": "plot_overtime_to_screen",
      "title": "Plot timeline of EcoRisk variables to screen",
      "topics": [
        "plot_overtime_to_screen"
      ]
    },
    {
      "page": "read_calc_biocol",
      "title": "Calculate BioCol based on file lists from a PNV run and LU run of LPJmL. Do not use this function directly, unless you are instructed to do so, there is a wrapper called calc_biocol() which is for use of endusers.",
      "topics": [
        "read_calc_biocol"
      ]
    },
    {
      "page": "read_ecorisk_data",
      "title": "Read in output data from LPJmL to calculate the ecosystem change metric EcoRisk. This function is called by the wrapper function (ecorisk_wrapper), unless you know what you are doing, don't use this function directly.",
      "topics": [
        "read_ecorisk_data"
      ]
    },
    {
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      "title": "Create modified EcoRisk data file",
      "topics": [
        "replace_ref_data_with_average_ref_biome_cell"
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        "roc_plot"
      ]
    },
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      "page": "roc_plot_paper",
      "title": "Plot ROC curve",
      "topics": [
        "roc_plot_paper"
      ]
    },
    {
      "page": "state_diff_global",
      "title": "c based on Heyder 2011 eq. 10-13",
      "topics": [
        "state_diff_global"
      ]
    },
    {
      "page": "state_diff_local",
      "title": "based on Heyder 2011 eq. 6-9; epsilon case handling from code by Sebastian Ostberg (not documented in papers)",
      "topics": [
        "state_diff_local"
      ]
    }
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      "title": "Computing biospheremetrics",
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      "engine": "knitr::rmarkdown",
      "headings": [
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        "Installation biospheremetrics",
        "Preparations",
        "Demo case",
        "BioCol",
        "EcoRisk",
        "Metrics definitions and file names",
        "Example use"
      ],
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