Mediterranean Forest Simulation


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Documentation for package ‘medfate’ version 2.3.7

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B C D E F G H L M O P R S T V W

-- B --

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_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 Default simulation control parameters for models
defaultSoilParams Default soil parameters

-- 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 --

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 utility functions
forest_mergeTrees Forest utility functions
fuel_FCCS 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_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_leafWaterCapacity Scaling from conductivity to conductance
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_soilPlantResistances Scaling from conductivity to conductance
hydraulics_stemWaterCapacity 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_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 and bare soil evaporation
hydrology_infiltrationRepartition Soil infiltration and bare soil evaporation
hydrology_interceptionPlot Rainfall interception
hydrology_rainInterception Rainfall interception
hydrology_snowMelt Soil infiltration and bare soil evaporation
hydrology_soilEvaporation Soil infiltration and bare soil evaporation
hydrology_soilEvaporationAmount Soil infiltration and bare soil evaporation
hydrology_soilInfiltrationPercolation Soil water processes
hydrology_soilWaterInputs Soil water processes

-- L --

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

-- M --

modifyCohortParams Modify parameters
modifyInputParams Modify parameters
modifySpParams Modify parameters
moisture_apoplasticPsi Tissue moisture functions
moisture_apoplasticRWC Tissue moisture functions
moisture_cohortFMC Tissue moisture functions
moisture_cohortFMCDay Tissue moisture functions
moisture_pressureVolumeCurvePlot Tissue moisture functions
moisture_symplasticPsi Tissue moisture functions
moisture_symplasticRWC Tissue moisture functions
moisture_tissueFMC 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_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_LAI Plant description functions
plant_largerTreeBasalArea Plant description functions
plant_parameter Plant description functions
plant_phytovolume Plant description functions
plant_shrubIndividualArea Plant description functions
plant_species Plant description functions
plant_speciesName Plant description functions
plot.fordyn Plots simulation results
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 --

redefineSoilLayers Soil initialization
resetInputs Reset simulation inputs
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
soil Soil initialization
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_thermalCapacity Soil thermodynamic functions
soil_thermalConductivity 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_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
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_resistances Soil-plant resistances
spwb_sensitivity Sensitivity analysis for soil plant water balance simulations
spwb_stress Drought stress indices
spwb_waterUseEfficiency Water use efficiency
stand_basalArea Stand values
stand_foliarBiomass Stand values
stand_fuel Stand values
stand_LAI Stand values
stand_phytovolume Stand values
summary.forest Forest description
summary.growth Summarises simulation results
summary.pwb Summarises simulation results
summary.spwb Summarises simulation results

-- T --

trait_family_means Parameter average values
transp_maximumTranspirationModel Maximum transpiration vs. LAI
transp_profitMaximization 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 --

wind_canopyTurbulence Models for canopy turbulence
wind_canopyTurbulenceModel Models for canopy turbulence
woodformation_growRing Wood formation
woodformation_initRing Wood formation
woodformation_relativeExpansionRate Wood formation