Mediterranean Forest Simulation
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Documentation for package ‘medfate’ version 2.9.3
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B C D E F G H L M O P R S T V W
-- B --
| biophysics | Physical and biophysical utility functions |
| biophysics_irradianceToPhotonFlux | Physical and biophysical utility functions |
| biophysics_leafTemperature | Physical and biophysical utility functions |
| biophysics_leafTemperature2 | Physical and biophysical utility functions |
| biophysics_leafVapourPressure | Physical and biophysical utility functions |
| biophysics_radiationDiurnalPattern | Physical and biophysical utility functions |
| biophysics_temperatureDiurnalPattern | Physical and biophysical utility functions |
| biophysics_waterDynamicViscosity | Physical and biophysical utility functions |
-- C --
| carbon | Carbon-related functions |
| carbon_carbonCompartments | Carbon-related functions |
| carbon_leafStarchCapacity | Carbon-related functions |
| carbon_leafStructuralBiomass | Carbon-related functions |
| carbon_osmoticWaterPotential | Carbon-related functions |
| carbon_relativeSapViscosity | Carbon-related functions |
| carbon_sapwoodStarchCapacity | Carbon-related functions |
| carbon_sapwoodStructuralBiomass | Carbon-related functions |
| carbon_sapwoodStructuralLivingBiomass | Carbon-related functions |
| carbon_sugarConcentration | Carbon-related functions |
| carbon_sugarStarchDynamicsLeaf | Carbon-related functions |
| carbon_sugarStarchDynamicsStem | Carbon-related functions |
-- D --
| defaultControl | Control parameters for simulation models |
| defaultManagementArguments | Default forest management actions |
| defaultManagementFunction | Default forest management actions |
| defaultSoilParams | Default soil parameters |
| droughtStress | Drought stress indicators |
-- E --
| emptyforest | Forest description |
| evaluation | Evaluation of simulations results |
| evaluation_metric | Evaluation of simulations results |
| evaluation_plot | Evaluation of simulations results |
| evaluation_stats | Evaluation of simulations results |
| evaluation_table | Evaluation of simulations results |
| exampleforestMED | Example forest stands |
| exampleforestUS | Example forest stands |
| examplemeteo | Example daily meteorology data |
| exampleobs | Example observed data |
| extractSubdaily | Extracts subdaily output |
-- F --
| fireHazard | Fire hazard |
| fire_behaviour | Fire behaviour functions |
| fire_FCCS | Fire behaviour functions |
| fire_Rothermel | Fire behaviour functions |
| fordyn | Forest dynamics |
| forest | Forest description |
| forest2aboveground | Input for simulation models |
| forest2belowground | Input for simulation models |
| forest2growthInput | Input for simulation models |
| forest2spwbInput | Input for simulation models |
| forest_mergeShrubs | Forest merge functions |
| forest_mergeTrees | Forest merge functions |
| fuel_FCCS | Fuel stratification and fuel characteristics |
| fuel_properties | Fuel stratification and fuel characteristics |
| fuel_stratification | Fuel stratification and fuel characteristics |
| fuel_windAdjustmentFactor | Fuel stratification and fuel characteristics |
-- G --
| growth | Forest growth |
| growthInput | Input for simulation models |
| growth_day | Single day simulation |
-- H --
| hydraulics_averagePsi | Hydraulic confuctance functions |
| hydraulics_averageRhizosphereResistancePercent | Scaling from conductivity to conductance |
| hydraulics_conductancefunctions | Hydraulic confuctance functions |
| hydraulics_correctConductanceForViscosity | Hydraulic confuctance functions |
| hydraulics_E2psiAboveground | Hydraulic supply functions |
| hydraulics_E2psiBelowground | Hydraulic supply functions |
| hydraulics_E2psiFineRootLeaf | Hydraulic supply functions |
| hydraulics_E2psiNetwork | Hydraulic supply functions |
| hydraulics_E2psiNetworkStem1 | Hydraulic supply functions |
| hydraulics_E2psiTwoElements | Hydraulic supply functions |
| hydraulics_E2psiVanGenuchten | Hydraulic supply functions |
| hydraulics_E2psiXylem | Hydraulic supply functions |
| hydraulics_E2psiXylemUp | Hydraulic supply functions |
| hydraulics_ECapacitance | Hydraulic supply functions |
| hydraulics_ECrit | Hydraulic supply functions |
| hydraulics_EVanGenuchten | Hydraulic supply functions |
| hydraulics_EXylem | Hydraulic supply functions |
| hydraulics_findRhizosphereMaximumConductance | Scaling from conductivity to conductance |
| hydraulics_K2Psi | Hydraulic confuctance functions |
| hydraulics_maximumSoilPlantConductance | Scaling from conductivity to conductance |
| hydraulics_maximumStemHydraulicConductance | Scaling from conductivity to conductance |
| hydraulics_psi2K | Hydraulic confuctance functions |
| hydraulics_psi2Weibull | Hydraulic confuctance functions |
| hydraulics_psiCrit | Hydraulic confuctance functions |
| hydraulics_referenceConductivityHeightFactor | Scaling from conductivity to conductance |
| hydraulics_regulatedPsiTwoElements | Hydraulic supply functions |
| hydraulics_regulatedPsiXylem | Hydraulic supply functions |
| hydraulics_rootxylemConductanceProportions | Scaling from conductivity to conductance |
| hydraulics_scalingconductance | Scaling from conductivity to conductance |
| hydraulics_soilPlantResistances | Scaling from conductivity to conductance |
| hydraulics_supplyFunctionAboveground | Hydraulic supply functions |
| hydraulics_supplyFunctionBelowground | Hydraulic supply functions |
| hydraulics_supplyFunctionFineRootLeaf | Hydraulic supply functions |
| hydraulics_supplyFunctionNetwork | Hydraulic supply functions |
| hydraulics_supplyFunctionNetworkStem1 | Hydraulic supply functions |
| hydraulics_supplyFunctionOneXylem | Hydraulic supply functions |
| hydraulics_supplyFunctionPlot | Hydraulic supply functions |
| hydraulics_supplyfunctions | Hydraulic supply functions |
| hydraulics_supplyFunctionThreeElements | Hydraulic supply functions |
| hydraulics_supplyFunctionTwoElements | Hydraulic supply functions |
| hydraulics_taperFactorSavage | Scaling from conductivity to conductance |
| hydraulics_terminalConduitRadius | Scaling from conductivity to conductance |
| hydraulics_vanGenuchtenConductance | Hydraulic confuctance functions |
| hydraulics_vulnerabilityCurvePlot | Hydraulic confuctance functions |
| hydraulics_xylemConductance | Hydraulic confuctance functions |
| hydraulics_xylemPsi | Hydraulic confuctance functions |
| hydrology_erFactor | Rainfall interception |
| hydrology_infiltrationAmount | Soil infiltration, percolation and bare soil evaporation |
| hydrology_infiltrationRepartition | Soil infiltration, percolation and bare soil evaporation |
| hydrology_interception | Rainfall interception |
| hydrology_interceptionPlot | Rainfall interception |
| hydrology_rainInterception | Rainfall interception |
| hydrology_snowMelt | Soil infiltration, percolation and bare soil evaporation |
| hydrology_soil | Soil infiltration, percolation and bare soil evaporation |
| hydrology_soilEvaporation | Soil infiltration, percolation and bare soil evaporation |
| hydrology_soilEvaporationAmount | Soil infiltration, percolation and bare soil evaporation |
| hydrology_soilInfiltrationPercolation | Soil vertical inputs |
| hydrology_soilWaterInputs | Soil vertical inputs |
| hydrology_verticalInputs | Soil vertical inputs |
-- L --
| light | Radiation transfer functions |
| light_cohortAbsorbedSWRFraction | Radiation transfer functions |
| light_cohortSunlitShadeAbsorbedRadiation | Radiation transfer functions |
| light_instantaneousLightExtinctionAbsortion | Radiation transfer functions |
| light_layerIrradianceFraction | Radiation transfer functions |
| light_layerIrradianceFractionBottomUp | Radiation transfer functions |
| light_layerSunlitFraction | Radiation transfer functions |
| light_longwaveRadiationSHAW | Radiation transfer functions |
| light_PARcohort | Radiation transfer functions |
| light_PARground | Radiation transfer functions |
| light_SWRground | Radiation transfer functions |
-- M --
| modelInput | Input for simulation models |
| modifyCohortParams | Modify parameters |
| modifyInputParams | Modify parameters |
| modifyParams | Modify parameters |
| modifySpParams | Modify parameters |
| moisture | Tissue moisture functions |
| moisture_apoplasticPsi | Tissue moisture functions |
| moisture_apoplasticRWC | Tissue moisture functions |
| moisture_leafWaterCapacity | Tissue moisture functions |
| moisture_pressureVolumeCurvePlot | Tissue moisture functions |
| moisture_sapwoodWaterCapacity | Tissue moisture functions |
| moisture_symplasticPsi | Tissue moisture functions |
| moisture_symplasticRWC | Tissue moisture functions |
| moisture_tissueRWC | Tissue moisture functions |
| moisture_turgorLossPoint | Tissue moisture functions |
| mortality_dailyProbability | Mortality |
| multiple_runs | Multiple model runs and function factories for optimization routines |
-- O --
| optimization | Multiple model runs and function factories for optimization routines |
| optimization_evaluation_function | Multiple model runs and function factories for optimization routines |
| optimization_evaluation_multicohort_function | Multiple model runs and function factories for optimization routines |
| optimization_function | Multiple model runs and function factories for optimization routines |
| optimization_multicohort_function | Multiple model runs and function factories for optimization routines |
-- P --
| pheno_leafDevelopmentStatus | Leaf phenology |
| pheno_leafSenescenceStatus | Leaf phenology |
| pheno_updateLeaves | Leaf phenology |
| pheno_updatePhenology | Leaf phenology |
| photo | Photosynthesis submodel functions |
| photo_electronLimitedPhotosynthesis | Photosynthesis submodel functions |
| photo_GammaTemp | Photosynthesis submodel functions |
| photo_JmaxTemp | Photosynthesis submodel functions |
| photo_KmTemp | Photosynthesis submodel functions |
| photo_leafPhotosynthesisFunction | Photosynthesis submodel functions |
| photo_leafPhotosynthesisFunction2 | Photosynthesis submodel functions |
| photo_multilayerPhotosynthesisFunction | Photosynthesis submodel functions |
| photo_photosynthesis | Photosynthesis submodel functions |
| photo_rubiscoLimitedPhotosynthesis | Photosynthesis submodel functions |
| photo_sunshadePhotosynthesisFunction | Photosynthesis submodel functions |
| photo_VmaxTemp | Photosynthesis submodel functions |
| plant_basalArea | Plant description functions |
| plant_characterParameter | Plant description functions |
| plant_cover | Plant description functions |
| plant_crownBaseHeight | Plant description functions |
| plant_crownLength | Plant description functions |
| plant_crownRatio | Plant description functions |
| plant_density | Plant description functions |
| plant_equilibriumLeafLitter | Plant description functions |
| plant_equilibriumSmallBranchLitter | Plant description functions |
| plant_foliarBiomass | Plant description functions |
| plant_fuel | Plant description functions |
| plant_height | Plant description functions |
| plant_ID | Plant description functions |
| plant_individualArea | Plant description functions |
| plant_LAI | Plant description functions |
| plant_largerTreeBasalArea | Plant description functions |
| plant_parameter | Plant description functions |
| plant_phytovolume | Plant description functions |
| plant_species | Plant description functions |
| plant_speciesName | Plant description functions |
| plant_values | Plant description functions |
| plot.fordyn | Plots simulation results |
| plot.forest | Plot forest attributes |
| plot.growth | Plots simulation results |
| plot.growth_day | Plots simulation results for one day |
| plot.pwb | Plots simulation results |
| plot.pwb_day | Plots simulation results for one day |
| plot.spwb | Plots simulation results |
| plot.spwb_day | Plots simulation results for one day |
| print.soil | Soil initialization |
| print.summary.forest | Forest description |
| pwb | Soil-plant water balance |
-- R --
| recruitment | Plant recruitment |
| resetInputs | Reset simulation inputs |
| resistances | Soil-plant resistances |
| root | Root functions |
| root_coarseRootLengths | Root functions |
| root_coarseRootLengthsFromVolume | Root functions |
| root_coarseRootSoilVolume | Root functions |
| root_coarseRootSoilVolumeFromConductance | Root functions |
| root_conicDistribution | Root functions |
| root_fineRootAreaIndex | Root functions |
| root_fineRootBiomass | Root functions |
| root_fineRootHalfDistance | Root functions |
| root_fineRootRadius | Root functions |
| root_fineRootSoilVolume | Root functions |
| root_horizontalProportions | Root functions |
| root_individualRootedGroundArea | Root functions |
| root_ldrDistribution | Root functions |
| root_rhizosphereMaximumConductance | Root functions |
| root_specificRootSurfaceArea | Root functions |
-- S --
| SFM_metric | Standard fuel models (Albini 1976, Scott & Burgan 2005) |
| shinyplot | Shiny app with interactive plots |
| shinyplot.fordyn | Shiny app with interactive plots |
| shinyplot.forest | Plot forest attributes |
| shinyplot.growth | Shiny app with interactive plots |
| shinyplot.growth_day | Shiny app with interactive plots |
| shinyplot.pwb | Shiny app with interactive plots |
| shinyplot.pwb_day | Shiny app with interactive plots |
| shinyplot.spwb | Shiny app with interactive plots |
| shinyplot.spwb_day | Shiny app with interactive plots |
| soil | Soil initialization |
| soil_conductivity | Soil texture and hydraulics |
| soil_psi | Soil texture and hydraulics |
| soil_psi2thetaSX | Soil texture and hydraulics |
| soil_psi2thetaVG | Soil texture and hydraulics |
| soil_retentionCurvePlot | Soil texture and hydraulics |
| soil_rockWeight2Volume | Soil texture and hydraulics |
| soil_saturatedConductivitySX | Soil texture and hydraulics |
| soil_temperatureChange | Soil thermodynamic functions |
| soil_temperatureGradient | Soil thermodynamic functions |
| soil_texture | Soil texture and hydraulics |
| soil_thermalCapacity | Soil thermodynamic functions |
| soil_thermalConductivity | Soil thermodynamic functions |
| soil_thermodynamics | Soil thermodynamic functions |
| soil_theta | Soil texture and hydraulics |
| soil_theta2psiSX | Soil texture and hydraulics |
| soil_theta2psiVG | Soil texture and hydraulics |
| soil_thetaFC | Soil texture and hydraulics |
| soil_thetaSAT | Soil texture and hydraulics |
| soil_thetaSATSX | Soil texture and hydraulics |
| soil_thetaWP | Soil texture and hydraulics |
| soil_unsaturatedConductivitySX | Soil texture and hydraulics |
| soil_USDAType | Soil texture and hydraulics |
| soil_vanGenuchtenParamsCarsel | Soil texture and hydraulics |
| soil_vanGenuchtenParamsToth | Soil texture and hydraulics |
| soil_water | Soil texture and hydraulics |
| soil_waterExtractable | Soil texture and hydraulics |
| soil_waterFC | Soil texture and hydraulics |
| soil_waterSAT | Soil texture and hydraulics |
| soil_waterTableDepth | Soil texture and hydraulics |
| soil_waterWP | Soil texture and hydraulics |
| species_basalArea | Species description functions |
| species_characterParameter | Species description functions |
| species_cover | Species description functions |
| species_density | Species description functions |
| species_foliarBiomass | Species description functions |
| species_fuel | Species description functions |
| species_LAI | Species description functions |
| species_parameter | Species description functions |
| species_phytovolume | Species description functions |
| species_values | Species description functions |
| SpParams | Data tables with species parameter definition and values for Mediterranean and US |
| SpParamsDefinition | Data tables with species parameter definition and values for Mediterranean and US |
| SpParamsMED | Data tables with species parameter definition and values for Mediterranean and US |
| SpParamsUS | Data tables with species parameter definition and values for Mediterranean and US |
| spwb | Soil-plant water balance |
| spwbInput | Input for simulation models |
| spwb_day | Single day simulation |
| spwb_ldrCalibration | Calibration of root distribution |
| spwb_ldrExploration | Optimization of root distribution |
| spwb_ldrOptimization | Optimization of root distribution |
| spwb_sensitivity | Sensitivity analysis for soil plant water balance simulations |
| stand_basalArea | Stand values |
| stand_dominantTreeDiameter | Stand values |
| stand_dominantTreeHeight | Stand values |
| stand_foliarBiomass | Stand values |
| stand_fuel | Stand values |
| stand_hartBeckingIndex | Stand values |
| stand_LAI | Stand values |
| stand_phytovolume | Stand values |
| stand_quadraticMeanTreeDiameter | Stand values |
| stand_values | Stand values |
| summary.fordyn | Summarize simulation results |
| summary.forest | Forest description |
| summary.growth | Summarize simulation results |
| summary.pwb | Summarize simulation results |
| summary.spwb | Summarize simulation results |
-- T --
| trait_family_means | Parameter average values |
| transp_maximumTranspirationModel | Maximum transpiration vs. LAI |
| transp_modes | Transpiration modes |
| transp_profitMaximization | Stomatal regulation |
| transp_stomatalregulation | Stomatal regulation |
| transp_stomatalRegulationPlot | Stomatal regulation |
| transp_transpirationGranier | Transpiration modes |
| transp_transpirationSperry | Transpiration modes |
-- V --
| vprofile_fuelBulkDensity | Vertical profiles |
| vprofile_leafAreaDensity | Vertical profiles |
| vprofile_PARExtinction | Vertical profiles |
| vprofile_rootDistribution | Vertical profiles |
| vprofile_SWRExtinction | Vertical profiles |
| vprofile_windExtinction | Vertical profiles |
-- W --
| waterUseEfficiency | Water use efficiency |
| wind | Models for canopy turbulence |
| wind_canopyTurbulence | Models for canopy turbulence |
| wind_canopyTurbulenceModel | Models for canopy turbulence |
| woodformation | Wood formation |
| woodformation_growRing | Wood formation |
| woodformation_initRing | Wood formation |
| woodformation_relativeExpansionRate | Wood formation |
| woodformation_relativeGrowthRate | Wood formation |
| woodformation_temperatureEffect | Wood formation |