# Mediterranean Forest Simulation

## Documentation for package ‘medfate’ version 1.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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

## -- B --

biophysics_leafTemperature | 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 control parameters for models
defaultSoilParams | Default soil parameters

## -- E --

emptyforest | Forest description
exampleforestMED | Example forest stands
exampleforestUS | Example forest stands
examplemeteo | Example daily meteorology data
extractSubdaily | Extracts subdaily output

## -- F --

fire_FCCS | Fire behaviour functions
fire_Rothermel | Fire behaviour functions
forest | Forest description
forest2aboveground | Input for simulation models
forest2belowground | Input for simulation models
forest2growthInput | Input for simulation models
forest2spwbInput | Input for simulation models
forest_mapShrubTable | Map forest plot data
forest_mapTreeTable | Map forest plot data
forest_mapWoodyTables | Map forest plot data
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 | Light extinction and absortion functions
light_cohortSunlitShadeAbsorbedRadiation | Light extinction and absortion functions
light_instantaneousLightExtinctionAbsortion | Light extinction and absortion functions
light_layerIrradianceFraction | Light extinction and absortion functions
light_layerIrradianceFractionBottomUp | Light extinction and absortion functions
light_layerSunlitFraction | Light extinction and absortion functions

## -- M --

modifyCohortParams | Modify species/cohort parameters
modifySpParams | Modify species/cohort parameters
moisture_apoplasticPsi | Tissue moisture functions
moisture_apoplasticRWC | Tissue moisture functions
moisture_cohortFMC | 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

## -- 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_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.growth | Displays simulation results
plot.growth_day | Plots simulation results for one day
plot.pwb | Displays simulation results
plot.pwb_day | Plots simulation results for one day
plot.spwb | Displays 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)
soil | Soil initialization
soilgridsParams | SoilGrids soil description fetcher
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_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_phytovolume | Species description functions
SpParamsMED | Data tables with species parameter values for Mediterranean and US
SpParamsUS | Data tables with species parameter 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_maximumTranspirationRatioPlot | Maximum transpiration vs. LAI
spwb_resistances | Soil-plant resistances
spwb_sensitivity | Sensitivity analysis for soil plant water balance simulations
spwb_stress | Drought stress indices
spwb_validation | Validation of soil-plant water balance simulations
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 | Displays simulation results
summary.pwb | Displays simulation results
summary.spwb | Displays simulation results

## -- T --

transp_profitMaximization | Transpiration submodel functions
transp_stomatalRegulationPlot | Transpiration submodel functions
transp_transpirationGranier | Transpiration submodel functions
transp_transpirationSperry | Transpiration submodel functions

## -- 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