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  "Description": "Simulate Mediterranean forest functioning and dynamics\nusing cohort-based description of vegetation [De Caceres et al.\n(2015) <doi:10.1016/j.agrformet.2015.06.012>; De Caceres et al.\n(2021) <doi:10.1016/j.agrformet.2020.108233>].",
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  "Date/Publication": "2026-05-12 11:12:29 UTC",
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    "moisture_turgorLossPoint",
    "mortality_dailyProbability",
    "multiple_runs",
    "optimization_evaluation_function",
    "optimization_evaluation_multicohort_function",
    "optimization_function",
    "optimization_multicohort_function",
    "pheno_leafDevelopmentStatus",
    "pheno_leafSenescenceStatus",
    "pheno_updateLeaves",
    "pheno_updatePhenology",
    "photo_electronLimitedPhotosynthesis",
    "photo_GammaTemp",
    "photo_JmaxTemp",
    "photo_KmTemp",
    "photo_leafPhotosynthesisFunction",
    "photo_leafPhotosynthesisFunction2",
    "photo_multilayerPhotosynthesisFunction",
    "photo_photosynthesis",
    "photo_photosynthesisBaldocchi",
    "photo_rubiscoLimitedPhotosynthesis",
    "photo_sunshadePhotosynthesisFunction",
    "photo_VmaxTemp",
    "plant_basalArea",
    "plant_characterParameter",
    "plant_cover",
    "plant_crownBaseHeight",
    "plant_crownLength",
    "plant_crownRatio",
    "plant_density",
    "plant_equilibriumLeafLitter",
    "plant_equilibriumSmallBranchLitter",
    "plant_foliarBiomass",
    "plant_fuelLoading",
    "plant_height",
    "plant_ID",
    "plant_individualArea",
    "plant_LAI",
    "plant_largerTreeBasalArea",
    "plant_parameter",
    "plant_phytovolume",
    "plant_species",
    "plant_speciesName",
    "plant_water",
    "plot.aspwb",
    "plot.fordyn",
    "plot.forest",
    "plot.growth",
    "plot.growth_day",
    "plot.pwb",
    "plot.pwb_day",
    "plot.soil",
    "plot.spwb",
    "plot.spwb_day",
    "print.summary.forest",
    "pwb",
    "regeneration_germination",
    "regeneration_recruitment",
    "regeneration_recruitment_daily",
    "regeneration_resprouting",
    "regeneration_seedlings",
    "regeneration_seedlings_daily",
    "regeneration_seedmortality",
    "regeneration_seedproduction",
    "regeneration_seedrefill",
    "resetInputs",
    "resistances",
    "root_coarseRootLengths",
    "root_coarseRootLengthsFromVolume",
    "root_coarseRootSoilVolume",
    "root_coarseRootSoilVolumeFromConductance",
    "root_conicDistribution",
    "root_fineRootAreaIndex",
    "root_fineRootBiomass",
    "root_fineRootHalfDistance",
    "root_fineRootRadius",
    "root_fineRootSoilVolume",
    "root_horizontalProportions",
    "root_individualRootedGroundArea",
    "root_ldrDistribution",
    "root_rhizosphereMaximumConductance",
    "root_specificRootSurfaceArea",
    "runners",
    "semi_implicit_integration",
    "shinyplot",
    "shinyplot.aspwb",
    "shinyplot.fordyn",
    "shinyplot.forest",
    "shinyplot.growth",
    "shinyplot.growth_day",
    "shinyplot.pwb",
    "shinyplot.pwb_day",
    "shinyplot.spwb",
    "shinyplot.spwb_day",
    "shrub2forest",
    "soil",
    "soil_campbellParamsClappHornberger",
    "soil_capacitance",
    "soil_conductivity",
    "soil_conductivityCurvePlot",
    "soil_psi",
    "soil_psi2cVG",
    "soil_psi2kVG",
    "soil_psi2thetaSX",
    "soil_psi2thetaVG",
    "soil_redefineLayers",
    "soil_retentionCurvePlot",
    "soil_rockWeight2Volume",
    "soil_saturatedConductivitySX",
    "soil_saturatedWaterDepth",
    "soil_temperatureChange",
    "soil_temperatureGradient",
    "soil_thermalCapacity",
    "soil_thermalConductivity",
    "soil_theta",
    "soil_theta2psiSX",
    "soil_theta2psiVG",
    "soil_thetaFC",
    "soil_thetaSAT",
    "soil_thetaSATSX",
    "soil_thetaWP",
    "soil_unsaturatedConductivitySX",
    "soil_USDAType",
    "soil_vanGenuchtenParamsCarsel",
    "soil_vanGenuchtenParamsToth",
    "soil_water",
    "soil_waterExtractable",
    "soil_waterFC",
    "soil_waterPsi",
    "soil_waterSAT",
    "soil_waterWP",
    "species_basalArea",
    "species_characterParameter",
    "species_cover",
    "species_density",
    "species_foliarBiomass",
    "species_fuelLoading",
    "species_LAI",
    "species_parameter",
    "spwb",
    "spwb_day",
    "spwbInput",
    "stand_basalArea",
    "stand_dominantTreeDiameter",
    "stand_dominantTreeHeight",
    "stand_dominantTreeSpecies",
    "stand_foliarBiomass",
    "stand_fuelLoading",
    "stand_hartBeckingIndex",
    "stand_LAI",
    "stand_meanTreeHeight",
    "stand_quadraticMeanTreeDiameter",
    "stand_shrubVolume",
    "stand_treeDensity",
    "summary.aspwb",
    "summary.fordyn",
    "summary.forest",
    "summary.growth",
    "summary.pwb",
    "summary.soil",
    "summary.spwb",
    "trait_family_means",
    "transp_maximumTranspirationModel",
    "transp_profitMaximization",
    "transp_transpirationGranier",
    "transp_transpirationSperry",
    "transp_transpirationSureau",
    "tree2forest",
    "utils_ldrExploration",
    "utils_ldrOptimization",
    "utils_rockOptimization",
    "vprofile_fuelBulkDensity",
    "vprofile_leafAreaDensity",
    "vprofile_PARExtinction",
    "vprofile_rootDistribution",
    "vprofile_SWRExtinction",
    "vprofile_windExtinction",
    "waterUseEfficiency",
    "wind_canopyTurbulence",
    "wind_canopyTurbulenceModel",
    "woodformation_growRing",
    "woodformation_initRing",
    "woodformation_relativeExpansionRate",
    "woodformation_relativeGrowthRate",
    "woodformation_temperatureEffect"
  ],
  "_datasets": [
    {
      "name": "exampleforest",
      "title": "Description of a forest stand.",
      "object": "exampleforest",
      "class": [
        "forest",
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "exampleforest2",
      "title": "Description of a forest stand.",
      "object": "exampleforest2",
      "class": [
        "forest",
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "examplemeteo",
      "title": "Example daily meteorology data",
      "object": "examplemeteo",
      "class": [
        "data.frame"
      ],
      "fields": [
        "dates",
        "MinTemperature",
        "MaxTemperature",
        "Precipitation",
        "MinRelativeHumidity",
        "MaxRelativeHumidity",
        "Radiation",
        "WindSpeed"
      ],
      "rows": 365,
      "table": true,
      "tojson": true
    },
    {
      "name": "exampleobs",
      "title": "Example observed data",
      "object": "exampleobs",
      "class": [
        "data.frame"
      ],
      "fields": [
        "dates",
        "SWC",
        "ETR",
        "E_T1_148",
        "E_T2_168",
        "FMC_T1_148",
        "FMC_T2_168",
        "BAI_T1_148",
        "BAI_T2_168",
        "DI_T1_148",
        "DI_T2_168"
      ],
      "rows": 365,
      "table": true,
      "tojson": true
    },
    {
      "name": "poblet_trees",
      "title": "Example forest inventory data",
      "object": "poblet_trees",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Plot.Code",
        "Indv.Ref",
        "Species",
        "Diameter.cm"
      ],
      "rows": 717,
      "table": true,
      "tojson": true
    },
    {
      "name": "SFM_metric",
      "title": "Standard fuel models (Albini 1976, Scott & Burgan 2005)",
      "object": "SFM_metric",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Fuel_Model_Type",
        "Load_1h",
        "Load_10h",
        "Load_100h",
        "Load_Live_Herb",
        "Load_Live_Woody",
        "SA/V_1h",
        "SA/V_10h",
        "SA/V_100h",
        "SA/V_Live_Herb",
        "SA/V_Live_Woody",
        "Fuel_Bed_Depth",
        "Mx_dead",
        "Heat_1h",
        "Heat_10h",
        "Heat_100h",
        "Heat_Live_Herb",
        "Heat_Live_Woody"
      ],
      "rows": 53,
      "table": true,
      "tojson": true
    },
    {
      "name": "SpParamsDefinition",
      "title": "Data tables with species parameter definitions and values",
      "object": "SpParamsDefinition",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ParameterName",
        "ParameterGroup",
        "Definition",
        "Type",
        "Units",
        "Strict"
      ],
      "rows": 154,
      "table": true,
      "tojson": true
    },
    {
      "name": "SpParamsMED",
      "title": "Data tables with species parameter definitions and values",
      "object": "SpParamsMED",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Name",
        "IFNcodes",
        "SpIndex",
        "AcceptedName",
        "Species",
        "Genus",
        "Family",
        "Order",
        "Group",
        "GrowthForm",
        "LifeForm",
        "LeafShape",
        "LeafSize",
        "PhenologyType",
        "DispersalType",
        "Hmed",
        "Hmax",
        "Dmax",
        "Z50",
        "Z95",
        "fHDmin",
        "fHDmax",
        "a_ash",
        "b_ash",
        "a_bsh",
        "b_bsh",
        "a_btsh",
        "b_btsh",
        "cr",
        "BTsh",
        "a_fbt",
        "b_fbt",
        "c_fbt",
        "a_cr",
        "b_1cr",
        "b_2cr",
        "b_3cr",
        "c_1cr",
        "c_2cr",
        "a_cw",
        "b_cw",
        "a_bt",
        "b_bt",
        "LeafDuration",
        "t0gdd",
        "Sgdd",
        "Tbgdd",
        "Ssen",
        "Phsen",
        "Tbsen",
        "xsen",
        "ysen",
        "SLA",
        "LeafDensity",
        "WoodDensity",
        "FineRootDensity",
        "conduit2sapwood",
        "r635",
        "pDead",
        "Al2As",
        "Ar2Al",
        "LeafWidth",
        "SRL",
        "RLD",
        "maxFMC",
        "minFMC",
        "LeafPI0",
        "LeafEPS",
        "LeafAF",
        "StemPI0",
        "StemEPS",
        "StemAF",
        "SAV",
        "HeatContent",
        "LigninPercent",
        "LeafAngle",
        "LeafAngleSD",
        "ClumpingIndex",
        "gammaSWR",
        "alphaSWR",
        "kPAR",
        "g",
        "Tmax_LAI",
        "Tmax_LAIsq",
        "Psi_Extract",
        "Exp_Extract",
        "WUE",
        "WUE_par",
        "WUE_co2",
        "WUE_vpd",
        "Gswmin",
        "Gswmax",
        "Gsw_AC_slope",
        "Gs_Toptim",
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        "Gs_P50",
        "Gs_slope",
        "VCleaf_kmax",
        "VCleaf_P12",
        "VCleaf_P50",
        "VCleaf_P88",
        "VCleaf_slope",
        "Kmax_stemxylem",
        "VCstem_P12",
        "VCstem_P50",
        "VCstem_P88",
        "VCstem_slope",
        "Kmax_rootxylem",
        "VCroot_P12",
        "VCroot_P50",
        "VCroot_P88",
        "VCroot_slope",
        "Vmax298",
        "Jmax298",
        "Nleaf",
        "Nsapwood",
        "Nfineroot",
        "WoodC",
        "RERleaf",
        "RERsapwood",
        "RERfineroot",
        "CCleaf",
        "CCsapwood",
        "CCfineroot",
        "RGRleafmax",
        "RGRsapwoodmax",
        "RGRcambiummax",
        "RGRfinerootmax",
        "SRsapwood",
        "SRfineroot",
        "RSSG",
        "MortalityBaselineRate",
        "SurvivalModelStep",
        "SurvivalB0",
        "SurvivalB1",
        "SeedProductionHeight",
        "SeedProductionDiameter",
        "SeedMass",
        "SeedLongevity",
        "DispersalDistance",
        "DispersalShape",
        "ProbRecr",
        "MinTempRecr",
        "MinMoistureRecr",
        "MinFPARRecr",
        "RecrAge",
        "RecrTreeDBH",
        "RecrTreeHeight",
        "RecrShrubHeight",
        "RecrTreeDensity",
        "RecrShrubCover",
        "RespFire",
        "RespDist",
        "RespClip",
        "IngrowthTreeDensity",
        "IngrowthTreeDBH"
      ],
      "rows": 217,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "defaultControl",
      "title": "Control parameters for simulation models",
      "topics": [
        "defaultControl"
      ]
    },
    {
      "page": "defaultManagementFunction",
      "title": "Default forest management actions",
      "topics": [
        "defaultManagementArguments",
        "defaultManagementFunction"
      ]
    },
    {
      "page": "defaultSoilParams",
      "title": "Default soil parameters",
      "topics": [
        "defaultSoilParams"
      ]
    },
    {
      "page": "droughtStress",
      "title": "Drought stress indicators",
      "topics": [
        "droughtStress"
      ]
    },
    {
      "page": "emptyforest",
      "title": "Creation of an empty forest",
      "topics": [
        "emptyforest"
      ]
    },
    {
      "page": "evaluation",
      "title": "Evaluation of simulations results",
      "topics": [
        "evaluation",
        "evaluation_metric",
        "evaluation_plot",
        "evaluation_stats",
        "evaluation_table"
      ]
    },
    {
      "page": "examplemeteo",
      "title": "Example daily meteorology data",
      "topics": [
        "examplemeteo"
      ]
    },
    {
      "page": "exampleobs",
      "title": "Example observed data",
      "topics": [
        "exampleobs"
      ]
    },
    {
      "page": "extract",
      "title": "Extracts model outputs",
      "topics": [
        "extract"
      ]
    },
    {
      "page": "fire_behaviour",
      "title": "Fire behaviour functions",
      "topics": [
        "fire_behaviour",
        "fire_FCCS",
        "fire_Rothermel"
      ]
    },
    {
      "page": "fireHazard",
      "title": "Fire hazard",
      "topics": [
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      ]
    },
    {
      "page": "fordyn",
      "title": "Forest dynamics",
      "topics": [
        "fordyn"
      ]
    },
    {
      "page": "forest",
      "title": "Description of a forest stand.",
      "topics": [
        "exampleforest",
        "exampleforest2",
        "forest"
      ]
    },
    {
      "page": "forest_mapWoodyTables",
      "title": "Map forest plot data",
      "topics": [
        "forest_mapShrubTable",
        "forest_mapTreeTable",
        "forest_mapWoodyTables"
      ]
    },
    {
      "page": "forest_simplification",
      "title": "Forest complexity reduction",
      "topics": [
        "forest_mergeHerbs",
        "forest_mergeShrubs",
        "forest_mergeTrees",
        "forest_reduceToDominant",
        "forest_simplification"
      ]
    },
    {
      "page": "fuel_properties",
      "title": "Fuel stratification and fuel characteristics",
      "topics": [
        "fuel_FCCS",
        "fuel_properties",
        "fuel_stratification"
      ]
    },
    {
      "page": "growth",
      "title": "Forest growth",
      "topics": [
        "growth"
      ]
    },
    {
      "page": "growth_day",
      "title": "Single-day forest growth",
      "topics": [
        "growth_day"
      ]
    },
    {
      "page": "modelInput",
      "title": "Input for simulation models",
      "topics": [
        "growthInput",
        "modelInput",
        "spwbInput"
      ]
    },
    {
      "page": "modifyParams",
      "title": "Modify parameters",
      "topics": [
        "modifyCohortParams",
        "modifyInputParams",
        "modifyParams",
        "modifySpParams"
      ]
    },
    {
      "page": "optimization",
      "title": "Multiple model runs and function factories for optimization routines",
      "topics": [
        "multiple_runs",
        "optimization",
        "optimization_evaluation_function",
        "optimization_evaluation_multicohort_function",
        "optimization_function",
        "optimization_multicohort_function"
      ]
    },
    {
      "page": "TaxonTraitMeans",
      "title": "Parameter average values",
      "topics": [
        "trait_family_means"
      ]
    },
    {
      "page": "plot.forest",
      "title": "Plot forest attributes",
      "topics": [
        "plot.forest",
        "shinyplot.forest"
      ]
    },
    {
      "page": "plot.soil",
      "title": "Soil water curves",
      "topics": [
        "plot.soil"
      ]
    },
    {
      "page": "plot.spwb",
      "title": "Plots simulation results",
      "topics": [
        "plot.aspwb",
        "plot.fordyn",
        "plot.growth",
        "plot.pwb",
        "plot.spwb"
      ]
    },
    {
      "page": "plot.spwb_day",
      "title": "Plots simulation results for one day",
      "topics": [
        "plot.growth_day",
        "plot.pwb_day",
        "plot.spwb_day"
      ]
    },
    {
      "page": "poblet_trees",
      "title": "Example forest inventory data",
      "topics": [
        "poblet_trees"
      ]
    },
    {
      "page": "resetInputs",
      "title": "Reset simulation inputs",
      "topics": [
        "resetInputs"
      ]
    },
    {
      "page": "resistances",
      "title": "Soil-plant resistances",
      "topics": [
        "resistances"
      ]
    },
    {
      "page": "runners-module",
      "title": "Rcpp module: Running simulations",
      "topics": [
        "runners"
      ]
    },
    {
      "page": "SFM_metric",
      "title": "Standard fuel models (Albini 1976, Scott & Burgan 2005)",
      "topics": [
        "SFM_metric"
      ]
    },
    {
      "page": "shinyplot",
      "title": "Shiny app with interactive plots",
      "topics": [
        "shinyplot",
        "shinyplot.aspwb",
        "shinyplot.fordyn",
        "shinyplot.growth",
        "shinyplot.growth_day",
        "shinyplot.pwb",
        "shinyplot.pwb_day",
        "shinyplot.spwb",
        "shinyplot.spwb_day"
      ]
    },
    {
      "page": "soil",
      "title": "Soil initialization",
      "topics": [
        "soil",
        "summary.soil"
      ]
    },
    {
      "page": "soil_redefineLayers",
      "title": "Redefine soil layer widths",
      "topics": [
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      ]
    },
    {
      "page": "SpParams",
      "title": "Data tables with species parameter definitions and values",
      "topics": [
        "SpParams",
        "SpParamsDefinition",
        "SpParamsMED"
      ]
    },
    {
      "page": "spwb",
      "title": "Soil-plant water balance",
      "topics": [
        "spwb"
      ]
    },
    {
      "page": "spwb_day",
      "title": "Single-day soil-plant water balance",
      "topics": [
        "spwb_day"
      ]
    },
    {
      "page": "summary.forest",
      "title": "Summary of forest structure",
      "topics": [
        "print.summary.forest",
        "summary.forest"
      ]
    },
    {
      "page": "summary.spwb",
      "title": "Summarize simulation results",
      "topics": [
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        "summary.fordyn",
        "summary.growth",
        "summary.pwb",
        "summary.spwb"
      ]
    },
    {
      "page": "tree2forest",
      "title": "Single-cohort forests",
      "topics": [
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        "tree2forest"
      ]
    },
    {
      "page": "utils_ldrOptimization",
      "title": "Optimization of root distribution",
      "topics": [
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    },
    {
      "page": "utils_rockOptimization",
      "title": "Optimization of rock fragment content",
      "topics": [
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      ]
    },
    {
      "page": "waterUseEfficiency",
      "title": "Water use efficiency",
      "topics": [
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      ]
    }
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