# Mediterranean Forest Simulation

## Documentation for package ‘medfate’ version 0.7.4

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

## Help Pages

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

## -- B --

biophysics.leafTemperature | Physical and biophysical utility functions
biophysics.radiationDiurnalPattern | Physical and biophysical utility functions
biophysics.temperatureDiurnalPattern | Physical and biophysical utility functions

## -- D --

defaultControl | Default control parameters for models
defaultSoilParams | Default soil parameters

## -- E --

emptyforest | Forest description
exampleforest | Example forest stand
examplemeteo | Example daily meteorology data
exampleSGL | Example of spatial grid with forest data
exampleSPL | Example of spatial points with forest data
extractSFIforest | Extract forest from SFI data

## -- F --

fire.FCCS | Fire behaviour functions
fire.Rothermel | Fire behaviour functions
forest | Forest description
forest.BasalArea | Forest description functions
forest2aboveground | Input for simulation models
forest2belowground | Input for simulation models
forest2growthInput | Input for simulation models
forest2spwbInput | Input for simulation models
fuel.cohortFineFMC | Fuel stratification and fuel characteristics
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
growthpoints | Model simulations for spatially-distributed forest stands

## -- H --

head-method | Class '"SpatialPointsLandscape"'
hydraulics.averagePsi | Hydraulic confuctance functions
hydraulics.averageRhizosphereResistancePercent | Scaling from conductivity to conductance
hydraulics.E2psiAboveground | Hydraulic supply functions
hydraulics.E2psiAbovegroundCapacitance | Hydraulic supply functions
hydraulics.E2psiAbovegroundCapacitanceDisconnected | Hydraulic supply functions
hydraulics.E2psiBelowground | Hydraulic supply functions
hydraulics.E2psiNetwork | Hydraulic supply functions
hydraulics.E2psiNetworkCapacitance | Hydraulic supply functions
hydraulics.E2psiTwoElements | Hydraulic supply functions
hydraulics.E2psiVanGenuchten | Hydraulic supply functions
hydraulics.E2psiXylem | 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.maximumRootHydraulicConductance | 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.soilPlantResistances | Scaling from conductivity to conductance
hydraulics.stemWaterCapacity | Scaling from conductivity to conductance
hydraulics.supplyFunctionAboveground | Hydraulic supply functions
hydraulics.supplyFunctionAbovegroundCapacitance | Hydraulic supply functions
hydraulics.supplyFunctionBelowground | Hydraulic supply functions
hydraulics.supplyFunctionNetwork | Hydraulic supply functions
hydraulics.supplyFunctionNetworkCapacitance | 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.infiltrationRepartition | Soil infiltration and bare soil evaporation
hydrology.rainInterception | Rainfall interception
hydrology.soilEvaporation | Soil infiltration and bare soil evaporation
hydrology.soilInfiltration | Soil infiltration and bare soil evaporation

## -- L --

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 --

moisture.apoplasticPsi | Tissue moisture functions
moisture.apoplasticRWC | 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

## -- P --

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.Species | Plant description functions
plant.SpeciesName | Plant description functions
plot.growth | Displays simulation results
plot.spwb | Displays simulation results
plot.spwb.day | Displays simulation results for one day
plot.spwbgrid | Soil-plant water balance and lateral water discharge
print-method | Class '"SpatialPointsLandscape"'
print.soil | Soil initialization
print.summary.forest | Forest description

## -- R --

root.conicDistribution | Distribution of fine roots
root.ldrDistribution | Distribution of fine roots
root.rootLengths | Distribution of fine roots
root.xylemConductanceProportions | Distribution of fine roots

## -- S --

SFI2SGL | Create Landscape Classes from SFI
SFI2SPL | Create Landscape Classes from SFI
SFM_metric | Standard fuel models (Albini 1976, Scott & Burgan 2005)
show-method | Class '"SpatialPointsLandscape"'
soil | Soil initialization
soil.psi | Soil texture and hydraulics
soil.psi2thetaSX | Soil texture and hydraulics
soil.psi2thetaVG | 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.waterFC | Soil texture and hydraulics
soil.waterSAT | Soil texture and hydraulics
soil.waterTableDepth | Soil texture and hydraulics
soil.waterWP | Soil texture and hydraulics
soilgridsParams | SoilGrids soil description fetcher
spatialForestSummary | Forest and soil summaries over space
spatialForestSummary-method | Forest and soil summaries over space
spatialForestSummary-methods | Forest and soil summaries over space
SpatialGridLandscape | Creates Spatial Landscape Classes
SpatialGridLandscape-class | Class '"SpatialGridLandscape"'
SpatialPixelsLandscape | Creates Spatial Landscape Classes
SpatialPixelsLandscape-class | Class '"SpatialPixelsLandscape"'
SpatialPointsLandscape | Creates Spatial Landscape Classes
SpatialPointsLandscape-class | Class '"SpatialPointsLandscape"'
spatialSoilSummary | Forest and soil summaries over space
spatialSoilSummary-method | Forest and soil summaries over space
spatialSoilSummary-methods | Forest and soil summaries over space
species.BasalArea | Species description functions
SpParamsMED | Parameter values for Mediterranean species
spwb | Soil-plant water balance
spwb.day | Soil-plant water balance for a single day
spwb.ldrCalibration | Calibration of root distribution
spwb.ldrOptimization | Optimization of root distribution
spwb.resetInputs | Soil-plant water balance
spwb.resistances | Soil-plant resistances
spwb.stress | Drought stress indices
spwbgrid | Soil-plant water balance and lateral water discharge
spwbInput | Input for simulation models
spwbpoints | Model simulations for spatially-distributed forest stands
summary.forest | Forest description
summary.growth | Displays simulation results
summary.spwb | Displays simulation results

## -- T --

tail-method | Class '"SpatialPointsLandscape"'
translateSpeciesCodes | Extract forest from SFI data
transp.profitMaximization | Transpiration submodel functions
transp.stomatalRegulation | Transpiration submodel functions
transp.stomatalRegulationPlot | 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

## -- misc --

[-method | Class '"SpatialPointsLandscape"'