# Mediterranean Forest Simulation

## Documentation for package ‘medfate’ version 3.1.4

- DESCRIPTION file.

## Help Pages

B C D E F G H I 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
exampleforestMED2 | Example forest stands
examplemeteo | Example daily meteorology data
exampleobs | Example observed data
extractSubdaily | Extracts subdaily output

## -- F --

fireHazard | Fire hazard
fire_barkThermalDiffusivity | Fire severity functions
fire_behaviour | Fire behaviour functions
fire_FCCS | Fire behaviour functions
fire_leafThermalFactor | Fire severity functions
fire_necrosisCriticalTemperature | Fire severity functions
fire_necrosisHeight | Fire severity functions
fire_plumeTemperature | Fire severity functions
fire_radialBoleNecrosis | Fire severity functions
fire_Rothermel | Fire behaviour functions
fire_severity | Fire severity 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 --

herb_foliarBiomass | Herbaceous description functions
herb_fuelLoading | Herbaceous description functions
herb_LAI | Herbaceous description functions
herb_values | Herbaceous description functions
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_herbaceousTranspiration | Soil infiltration, percolation and bare soil evaporation
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

## -- I --

initCochardNetworks | Sureau-ECOS inner functions for testing only

## -- 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 | Woody plant cohort description functions
plant_characterParameter | Woody plant cohort description functions
plant_cover | Woody plant cohort description functions
plant_crownBaseHeight | Woody plant cohort description functions
plant_crownLength | Woody plant cohort description functions
plant_crownRatio | Woody plant cohort description functions
plant_density | Woody plant cohort description functions
plant_equilibriumLeafLitter | Woody plant cohort description functions
plant_equilibriumSmallBranchLitter | Woody plant cohort description functions
plant_foliarBiomass | Woody plant cohort description functions
plant_fuelLoading | Woody plant cohort description functions
plant_height | Woody plant cohort description functions
plant_ID | Woody plant cohort description functions
plant_individualArea | Woody plant cohort description functions
plant_LAI | Woody plant cohort description functions
plant_largerTreeBasalArea | Woody plant cohort description functions
plant_parameter | Woody plant cohort description functions
plant_phytovolume | Woody plant cohort description functions
plant_species | Woody plant cohort description functions
plant_speciesName | Woody plant cohort description functions
plant_values | Woody plant cohort description functions
plant_water | Tissue moisture 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 regeneration
regeneration | Plant regeneration
resetInputs | Reset simulation inputs
resistances | Soil-plant resistances
resprouting | Plant regeneration
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 --

semi_implicit_integration | Sureau-ECOS inner functions for testing only
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_fuelLoading | Species description functions
species_LAI | Species description functions
species_parameter | 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
spwb | Soil-plant water balance
spwbInput | Input for simulation models
spwb_day | Single-day simulation
stand_basalArea | Stand values
stand_dominantTreeDiameter | Stand values
stand_dominantTreeHeight | Stand values
stand_dominantTreeSpecies | Stand values
stand_foliarBiomass | Stand values
stand_fuelLoading | Stand values
stand_hartBeckingIndex | Stand values
stand_LAI | 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
sureau_ecos | Sureau-ECOS inner functions for testing only

## -- 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_transpirationCochard | Transpiration modes
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