Forest definition and manipulation functions
exampleforestMED exampleforestMED2
exampleforestMED
exampleforestMED2
Example forest stands
emptyforest() summary(<forest>) print(<summary.forest>)
emptyforest()
summary(<forest>)
print(<summary.forest>)
Forest description
forest_mergeTrees() forest_mergeShrubs()
forest_mergeTrees()
forest_mergeShrubs()
Forest merge functions
Species parameter data and utility functions.
SpParamsDefinition SpParamsMED
SpParamsDefinition
SpParamsMED
Data tables with species parameter definition and values for Mediterranean and US
modifySpParams() modifyCohortParams() modifyInputParams()
modifySpParams()
modifyCohortParams()
modifyInputParams()
Modify parameters
trait_family_means
Parameter average values
Plant, species and forest attributes
stand_basalArea() stand_foliarBiomass() stand_fuelLoading() stand_LAI() stand_dominantTreeDiameter() stand_dominantTreeHeight() stand_hartBeckingIndex() stand_quadraticMeanTreeDiameter() stand_dominantTreeSpecies()
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()
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()
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()
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_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()
vprofile_leafAreaDensity()
vprofile_rootDistribution()
vprofile_fuelBulkDensity()
vprofile_PARExtinction()
vprofile_SWRExtinction()
vprofile_windExtinction()
Vertical profiles
plot(<forest>) shinyplot(<forest>)
plot(<forest>)
shinyplot(<forest>)
Plot forest attributes
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_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
Forest meteorology and environmental physics
examplemeteo
Example daily meteorology data
biophysics_radiationDiurnalPattern() biophysics_temperatureDiurnalPattern() biophysics_leafTemperature() biophysics_leafTemperature2() biophysics_leafVapourPressure() biophysics_irradianceToPhotonFlux() biophysics_waterDynamicViscosity()
biophysics_radiationDiurnalPattern()
biophysics_temperatureDiurnalPattern()
biophysics_leafTemperature()
biophysics_leafTemperature2()
biophysics_leafVapourPressure()
biophysics_irradianceToPhotonFlux()
biophysics_waterDynamicViscosity()
Physical and biophysical utility functions
wind_canopyTurbulenceModel() wind_canopyTurbulence()
wind_canopyTurbulenceModel()
wind_canopyTurbulence()
Models for canopy turbulence
Soil-related functions
defaultSoilParams()
Default soil parameters
soil() print(<soil>)
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_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_thermalCapacity()
soil_thermalConductivity()
soil_temperatureGradient()
soil_temperatureChange()
Soil thermodynamic functions
Simulation control and input objects
forest2aboveground() forest2belowground() forest2spwbInput() forest2growthInput()
forest2aboveground()
forest2belowground()
forest2spwbInput()
forest2growthInput()
Input for simulation models
defaultControl()
Control parameters for simulation models
defaultManagementFunction() defaultManagementArguments()
defaultManagementFunction()
defaultManagementArguments()
Default forest management actions
resetInputs()
Reset simulation inputs
Simulation model functions
spwb() pwb()
spwb()
pwb()
Soil-plant water balance
growth_day() spwb_day()
growth_day()
spwb_day()
Single-day simulation
growth()
Forest growth
fordyn()
Forest dynamics
initCochardNetworks() semi_implicit_integration()
initCochardNetworks()
semi_implicit_integration()
Sureau-ECOS inner functions for testing only
Summaries and plots of simulation results
plot(<spwb>) plot(<pwb>) plot(<growth>) plot(<fordyn>)
plot(<spwb>)
plot(<pwb>)
plot(<growth>)
plot(<fordyn>)
Plots simulation results
plot(<spwb_day>) plot(<growth_day>) plot(<pwb_day>)
plot(<spwb_day>)
plot(<growth_day>)
plot(<pwb_day>)
Plots simulation results for one day
summary(<spwb>) summary(<pwb>) summary(<growth>) summary(<fordyn>)
summary(<spwb>)
summary(<pwb>)
summary(<growth>)
summary(<fordyn>)
Summarize simulation results
extractSubdaily()
Extracts subdaily output
shinyplot()
Shiny app with interactive plots
Other post-processing functions
resistances()
Soil-plant resistances
droughtStress()
Drought stress indicators
waterUseEfficiency()
Water use efficiency
fireHazard()
Fire hazard
Evaluation and optimization
exampleobs
Example observed data
evaluation_table() evaluation_stats() evaluation_plot() evaluation_metric()
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_runs()
optimization_function()
optimization_evaluation_function()
optimization_multicohort_function()
optimization_evaluation_multicohort_function()
Multiple model runs and function factories for optimization routines
Leaf phenology processes
pheno_leafDevelopmentStatus() pheno_leafSenescenceStatus() pheno_updatePhenology() pheno_updateLeaves()
pheno_leafDevelopmentStatus()
pheno_leafSenescenceStatus()
pheno_updatePhenology()
pheno_updateLeaves()
Leaf phenology
Plant hydraulic processes
hydraulics_psi2K() hydraulics_K2Psi() hydraulics_averagePsi() hydraulics_xylemConductance() hydraulics_xylemPsi() hydraulics_psiCrit() hydraulics_vanGenuchtenConductance() hydraulics_correctConductanceForViscosity() hydraulics_psi2Weibull() hydraulics_vulnerabilityCurvePlot()
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()
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()
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
Forest hydrology processes
hydrology_erFactor() hydrology_rainInterception() hydrology_interceptionPlot()
hydrology_erFactor()
hydrology_rainInterception()
hydrology_interceptionPlot()
Rainfall interception
hydrology_soilEvaporationAmount() hydrology_soilEvaporation() hydrology_herbaceousTranspiration() hydrology_infiltrationRepartition() hydrology_snowMelt() hydrology_infiltrationAmount()
hydrology_soilEvaporationAmount()
hydrology_soilEvaporation()
hydrology_herbaceousTranspiration()
hydrology_infiltrationRepartition()
hydrology_snowMelt()
hydrology_infiltrationAmount()
Soil infiltration, percolation and bare soil evaporation
hydrology_soilWaterInputs() hydrology_soilInfiltrationPercolation()
hydrology_soilWaterInputs()
hydrology_soilInfiltrationPercolation()
Soil vertical inputs
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()
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()
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 processes
transp_maximumTranspirationModel()
Maximum transpiration vs. LAI
transp_transpirationSperry() transp_transpirationCochard() transp_transpirationGranier()
transp_transpirationSperry()
transp_transpirationCochard()
transp_transpirationGranier()
Transpiration modes
transp_profitMaximization() transp_stomatalRegulationPlot()
transp_profitMaximization()
transp_stomatalRegulationPlot()
Stomatal regulation
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_sugarStarchDynamicsLeaf()
carbon_sugarStarchDynamicsStem()
carbon_osmoticWaterPotential()
carbon_sugarConcentration()
carbon_relativeSapViscosity()
carbon_leafStructuralBiomass()
carbon_leafStarchCapacity()
carbon_sapwoodStructuralBiomass()
carbon_sapwoodStructuralLivingBiomass()
carbon_sapwoodStarchCapacity()
carbon_carbonCompartments()
Carbon-related functions
Wood formation, mortality, recruitment and resprouting processes
woodformation_initRing() woodformation_temperatureEffect() woodformation_relativeExpansionRate() woodformation_growRing() woodformation_relativeGrowthRate()
woodformation_initRing()
woodformation_temperatureEffect()
woodformation_relativeExpansionRate()
woodformation_growRing()
woodformation_relativeGrowthRate()
Wood formation
mortality_dailyProbability()
Mortality
recruitment() resprouting()
recruitment()
resprouting()
Plant regeneration
Plant/tissue water contents
Fuel characteristics, fire behaviour and fire severity
fire_FCCS() fire_Rothermel()
fire_FCCS()
fire_Rothermel()
Fire behaviour functions
fire_plumeTemperature() fire_barkThermalDiffusivity() fire_radialBoleNecrosis() fire_leafThermalFactor() fire_necrosisCriticalTemperature() fire_necrosisHeight()
fire_plumeTemperature()
fire_barkThermalDiffusivity()
fire_radialBoleNecrosis()
fire_leafThermalFactor()
fire_necrosisCriticalTemperature()
fire_necrosisHeight()
Fire severity functions
fuel_stratification() fuel_FCCS() fuel_windAdjustmentFactor()
fuel_stratification()
fuel_FCCS()
fuel_windAdjustmentFactor()
Fuel stratification and fuel characteristics
SFM_metric
Standard fuel models (Albini 1976, Scott & Burgan 2005)