Function reference • medfate

Forest definition Forest definition and manipulation functions
`exampleforestMED` `exampleforestMED2`	Example forest stands
`emptyforest()` `summary(<forest>)` `print(<summary.forest>)`	Forest description
`forest_mergeTrees()` `forest_mergeShrubs()`	Forest merge functions
Species parameters Species parameter data and utility functions.
`SpParamsDefinition` `SpParamsMED`	Data tables with species parameter definition and values for Mediterranean and US
`modifySpParams()` `modifyCohortParams()` `modifyInputParams()`	Modify parameters
`trait_family_means`	Parameter average values
Forest structure Plant, species and forest attributes
`stand_basalArea()` `stand_foliarBiomass()` `stand_fuelLoading()` `stand_LAI()` `stand_dominantTreeDiameter()` `stand_dominantTreeHeight()` `stand_hartBeckingIndex()` `stand_quadraticMeanTreeDiameter()` `stand_dominantTreeSpecies()`	Stand values
`moisture_sapwoodWaterCapacity()` `moisture_leafWaterCapacity()` `moisture_turgorLossPoint()` `moisture_symplasticRWC()` `moisture_symplasticPsi()` `moisture_apoplasticRWC()` `moisture_apoplasticPsi()` `moisture_tissueRWC()` `plant_water()` `moisture_pressureVolumeCurvePlot()`	Tissue moisture functions
`plant_ID()` `plant_basalArea()` `plant_largerTreeBasalArea()` `plant_cover()` `plant_species()` `plant_speciesName()` `plant_density()` `plant_height()` `plant_individualArea()` `plant_crownRatio()` `plant_crownBaseHeight()` `plant_crownLength()` `plant_foliarBiomass()` `plant_fuelLoading()` `plant_equilibriumLeafLitter()` `plant_equilibriumSmallBranchLitter()` `plant_phytovolume()` `plant_LAI()` `plant_characterParameter()` `plant_parameter()`	Woody plant cohort description functions
`herb_foliarBiomass()` `herb_fuelLoading()` `herb_LAI()`	Herbaceous description functions
`species_basalArea()` `species_cover()` `species_density()` `species_foliarBiomass()` `species_fuelLoading()` `species_LAI()` `species_characterParameter()` `species_parameter()`	Species description functions
`vprofile_leafAreaDensity()` `vprofile_rootDistribution()` `vprofile_fuelBulkDensity()` `vprofile_PARExtinction()` `vprofile_SWRExtinction()` `vprofile_windExtinction()`	Vertical profiles
`plot(<forest>)` `shinyplot(<forest>)`	Plot forest attributes
Roots Belowground structure
`root_conicDistribution()` `root_ldrDistribution()` `root_individualRootedGroundArea()` `root_specificRootSurfaceArea()` `root_fineRootRadius()` `root_fineRootHalfDistance()` `root_fineRootAreaIndex()` `root_fineRootBiomass()` `root_rhizosphereMaximumConductance()` `root_fineRootSoilVolume()` `root_coarseRootSoilVolumeFromConductance()` `root_coarseRootLengthsFromVolume()` `root_coarseRootLengths()` `root_coarseRootSoilVolume()` `root_horizontalProportions()`	Root functions
Meteorology and physics Forest meteorology and environmental physics
`examplemeteo`	Example daily meteorology data
`biophysics_radiationDiurnalPattern()` `biophysics_temperatureDiurnalPattern()` `biophysics_leafTemperature()` `biophysics_leafTemperature2()` `biophysics_leafVapourPressure()` `biophysics_irradianceToPhotonFlux()` `biophysics_waterDynamicViscosity()`	Physical and biophysical utility functions
`wind_canopyTurbulenceModel()` `wind_canopyTurbulence()`	Models for canopy turbulence
Soil Soil-related functions
`defaultSoilParams()`	Default soil parameters
`soil()` `print(<soil>)`	Soil initialization
`soil_saturatedConductivitySX()` `soil_unsaturatedConductivitySX()` `soil_thetaSATSX()` `soil_theta2psiSX()` `soil_psi2thetaSX()` `soil_psi2thetaVG()` `soil_theta2psiVG()` `soil_USDAType()` `soil_thetaFC()` `soil_thetaWP()` `soil_thetaSAT()` `soil_waterFC()` `soil_waterSAT()` `soil_waterWP()` `soil_waterExtractable()` `soil_theta()` `soil_water()` `soil_rockWeight2Volume()` `soil_psi()` `soil_conductivity()` `soil_waterTableDepth()` `soil_vanGenuchtenParamsCarsel()` `soil_vanGenuchtenParamsToth()` `soil_retentionCurvePlot()`	Soil texture and hydraulics
`soil_thermalCapacity()` `soil_thermalConductivity()` `soil_temperatureGradient()` `soil_temperatureChange()`	Soil thermodynamic functions
Simulation inputs Simulation control and input objects
`forest2aboveground()` `forest2belowground()` `forest2spwbInput()` `forest2growthInput()`	Input for simulation models
`defaultControl()`	Control parameters for simulation models
`defaultManagementFunction()` `defaultManagementArguments()`	Default forest management actions
`resetInputs()`	Reset simulation inputs
Simulation Simulation model functions
`spwb()` `pwb()`	Soil-plant water balance
`growth_day()` `spwb_day()`	Single-day simulation
`growth()`	Forest growth
`fordyn()`	Forest dynamics
`initCochardNetworks()` `semi_implicit_integration()`	Sureau-ECOS inner functions for testing only
Plots and summaries Summaries and plots of simulation results
`plot(<spwb>)` `plot(<pwb>)` `plot(<growth>)` `plot(<fordyn>)`	Plots simulation results
`plot(<spwb_day>)` `plot(<growth_day>)` `plot(<pwb_day>)`	Plots simulation results for one day
`summary(<spwb>)` `summary(<pwb>)` `summary(<growth>)` `summary(<fordyn>)`	Summarize simulation results
`extractSubdaily()`	Extracts subdaily output
`shinyplot()`	Shiny app with interactive plots
Post-processing Other post-processing functions
`resistances()`	Soil-plant resistances
`droughtStress()`	Drought stress indicators
`waterUseEfficiency()`	Water use efficiency
`fireHazard()`	Fire hazard
Model analysis Evaluation and optimization
`exampleobs`	Example observed data
`evaluation_table()` `evaluation_stats()` `evaluation_plot()` `evaluation_metric()`	Evaluation of simulations results
`multiple_runs()` `optimization_function()` `optimization_evaluation_function()` `optimization_multicohort_function()` `optimization_evaluation_multicohort_function()`	Multiple model runs and function factories for optimization routines
Phenology Leaf phenology processes
`pheno_leafDevelopmentStatus()` `pheno_leafSenescenceStatus()` `pheno_updatePhenology()` `pheno_updateLeaves()`	Leaf phenology
Hydraulics Plant hydraulic processes
`hydraulics_psi2K()` `hydraulics_K2Psi()` `hydraulics_averagePsi()` `hydraulics_xylemConductance()` `hydraulics_xylemPsi()` `hydraulics_psiCrit()` `hydraulics_vanGenuchtenConductance()` `hydraulics_correctConductanceForViscosity()` `hydraulics_psi2Weibull()` `hydraulics_vulnerabilityCurvePlot()`	Hydraulic confuctance functions
`hydraulics_maximumSoilPlantConductance()` `hydraulics_soilPlantResistances()` `hydraulics_averageRhizosphereResistancePercent()` `hydraulics_findRhizosphereMaximumConductance()` `hydraulics_taperFactorSavage()` `hydraulics_terminalConduitRadius()` `hydraulics_referenceConductivityHeightFactor()` `hydraulics_maximumStemHydraulicConductance()` `hydraulics_rootxylemConductanceProportions()`	Scaling from conductivity to conductance
`hydraulics_EXylem()` `hydraulics_E2psiXylem()` `hydraulics_E2psiXylemUp()` `hydraulics_EVanGenuchten()` `hydraulics_ECrit()` `hydraulics_ECapacitance()` `hydraulics_E2psiVanGenuchten()` `hydraulics_E2psiTwoElements()` `hydraulics_E2psiBelowground()` `hydraulics_E2psiAboveground()` `hydraulics_E2psiFineRootLeaf()` `hydraulics_E2psiNetworkStem1()` `hydraulics_E2psiNetwork()` `hydraulics_supplyFunctionOneXylem()` `hydraulics_supplyFunctionTwoElements()` `hydraulics_supplyFunctionThreeElements()` `hydraulics_supplyFunctionBelowground()` `hydraulics_supplyFunctionAboveground()` `hydraulics_supplyFunctionFineRootLeaf()` `hydraulics_supplyFunctionNetworkStem1()` `hydraulics_supplyFunctionNetwork()` `hydraulics_regulatedPsiXylem()` `hydraulics_regulatedPsiTwoElements()` `hydraulics_supplyFunctionPlot()`	Hydraulic supply functions
Hydrology Forest hydrology processes
`hydrology_erFactor()` `hydrology_rainInterception()` `hydrology_interceptionPlot()`	Rainfall interception
`hydrology_soilEvaporationAmount()` `hydrology_soilEvaporation()` `hydrology_herbaceousTranspiration()` `hydrology_infiltrationRepartition()` `hydrology_snowMelt()` `hydrology_infiltrationAmount()`	Soil infiltration, percolation and bare soil evaporation
`hydrology_soilWaterInputs()` `hydrology_soilInfiltrationPercolation()`	Soil vertical inputs
Light and photosynthesis Light extinction and photosynthesis processes
`light_PARcohort()` `light_PARground()` `light_SWRground()` `light_cohortAbsorbedSWRFraction()` `light_layerIrradianceFraction()` `light_layerIrradianceFractionBottomUp()` `light_cohortSunlitShadeAbsorbedRadiation()` `light_layerSunlitFraction()` `light_instantaneousLightExtinctionAbsortion()` `light_longwaveRadiationSHAW()`	Radiation transfer functions
`photo_GammaTemp()` `photo_KmTemp()` `photo_VmaxTemp()` `photo_JmaxTemp()` `photo_electronLimitedPhotosynthesis()` `photo_rubiscoLimitedPhotosynthesis()` `photo_photosynthesis()` `photo_leafPhotosynthesisFunction()` `photo_leafPhotosynthesisFunction2()` `photo_sunshadePhotosynthesisFunction()` `photo_multilayerPhotosynthesisFunction()`	Photosynthesis submodel functions
Plant transpiration Plant transpiration processes
`transp_maximumTranspirationModel()`	Maximum transpiration vs. LAI
`transp_transpirationSperry()` `transp_transpirationCochard()` `transp_transpirationGranier()`	Transpiration modes
`transp_profitMaximization()` `transp_stomatalRegulationPlot()`	Stomatal regulation
Carbon balance Carbon balance processes
`carbon_sugarStarchDynamicsLeaf()` `carbon_sugarStarchDynamicsStem()` `carbon_osmoticWaterPotential()` `carbon_sugarConcentration()` `carbon_relativeSapViscosity()` `carbon_leafStructuralBiomass()` `carbon_leafStarchCapacity()` `carbon_sapwoodStructuralBiomass()` `carbon_sapwoodStructuralLivingBiomass()` `carbon_sapwoodStarchCapacity()` `carbon_carbonCompartments()`	Carbon-related functions
Secondary growth, mortality and regeneration Wood formation, mortality, recruitment and resprouting processes
`woodformation_initRing()` `woodformation_temperatureEffect()` `woodformation_relativeExpansionRate()` `woodformation_growRing()` `woodformation_relativeGrowthRate()`	Wood formation
`mortality_dailyProbability()`	Mortality
`recruitment()` `resprouting()`	Plant regeneration
Water content Plant/tissue water contents
`moisture_sapwoodWaterCapacity()` `moisture_leafWaterCapacity()` `moisture_turgorLossPoint()` `moisture_symplasticRWC()` `moisture_symplasticPsi()` `moisture_apoplasticRWC()` `moisture_apoplasticPsi()` `moisture_tissueRWC()` `plant_water()` `moisture_pressureVolumeCurvePlot()`	Tissue moisture functions
Wildfire Fuel characteristics, fire behaviour and fire severity
`fire_FCCS()` `fire_Rothermel()`	Fire behaviour functions
`fire_plumeTemperature()` `fire_barkThermalDiffusivity()` `fire_radialBoleNecrosis()` `fire_leafThermalFactor()` `fire_necrosisCriticalTemperature()` `fire_necrosisHeight()`	Fire severity functions
`fuel_stratification()` `fuel_FCCS()` `fuel_windAdjustmentFactor()`	Fuel stratification and fuel characteristics
`SFM_metric`	Standard fuel models (Albini 1976, Scott & Burgan 2005)

Reference

Forest definition

Species parameters

Forest structure

Roots

Meteorology and physics

Soil

Simulation inputs

Simulation

Plots and summaries

Post-processing

Model analysis

Phenology

Hydraulics

Hydrology

Light and photosynthesis

Plant transpiration

Carbon balance

Secondary growth, mortality and regeneration

Water content

Wildfire