Forest definition

Forest definition and manipulation functions

exampleforestMED exampleforestUS

Example forest stands

summary(<forest>) print(<summary.forest>) emptyforest()

Forest description

forest_mergeTrees() forest_mergeShrubs()

Forest utility functions

Species parameters

Species parameter data and utility functions.

SpParamsDefinition SpParamsMED SpParamsUS

Data tables with species parameter definition and values for Mediterranean and US

modifySpParams() modifyCohortParams() modifyInputParams()

Modify parameters

Parameter means

Parameter average values

Forest structure

Plant, species and forest attributes

stand_basalArea() stand_dominantTreeHeight() stand_dominantTreeDiameter() stand_quadraticMeanTreeDiameter() stand_hartBeckingIndex() stand_foliarBiomass() stand_fuel() stand_LAI() stand_phytovolume()

Stand values

plant_basalArea() plant_largerTreeBasalArea() plant_characterParameter() plant_cover() plant_crownBaseHeight() plant_crownLength() plant_crownRatio() plant_density() plant_equilibriumLeafLitter() plant_equilibriumSmallBranchLitter() plant_foliarBiomass() plant_fuel() plant_height() plant_ID() plant_LAI() plant_individualArea() plant_parameter() plant_phytovolume() plant_species() plant_speciesName()

Plant description functions

species_basalArea() species_cover() species_density() species_foliarBiomass() species_fuel() species_LAI() species_phytovolume() species_parameter() species_characterParameter()

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_coarseRootLengths() root_coarseRootLengthsFromVolume() root_coarseRootSoilVolume() root_coarseRootSoilVolumeFromConductance() root_fineRootRadius() root_fineRootHalfDistance() root_fineRootAreaIndex() root_fineRootBiomass() root_rhizosphereMaximumConductance() root_fineRootSoilVolume() root_specificRootSurfaceArea() root_individualRootedGroundArea() root_horizontalProportions()

Root functions

Meteorology and physics

Forest meteorology and environmental physics

examplemeteo

Example daily meteorology data

biophysics_irradianceToPhotonFlux() biophysics_leafTemperature() biophysics_leafTemperature2() biophysics_leafVapourPressure() biophysics_radiationDiurnalPattern() biophysics_temperatureDiurnalPattern() 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>) redefineSoilLayers()

Soil initialization

soil_psi2thetaSX() soil_psi2thetaVG() soil_theta2psiSX() soil_theta2psiVG() soil_saturatedConductivitySX() soil_unsaturatedConductivitySX() soil_USDAType() soil_vanGenuchtenParamsCarsel() soil_vanGenuchtenParamsToth() soil_psi() soil_theta() soil_conductivity() soil_water() soil_waterFC() soil_waterWP() soil_waterSAT() soil_waterExtractable() soil_thetaFC() soil_thetaWP() soil_thetaSAT() soil_thetaSATSX() soil_waterTableDepth() soil_rockWeight2Volume() soil_retentionCurvePlot()

Soil texture and hydraulics

soil_thermalConductivity() soil_thermalCapacity() soil_temperatureChange() soil_temperatureGradient()

Soil thermodynamic functions

Simulation inputs

Simulation control and input objects

forest2aboveground() forest2belowground() forest2growthInput() forest2spwbInput() growthInput() spwbInput()

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

spwb_day() growth_day()

Single day simulation

growth()

Forest growth

fordyn()

Forest dynamics

Plots and summaries

Summaries and plots of simulation results

plot(<spwb>) plot(<pwb>) plot(<growth>) plot(<fordyn>)

Plots simulation results

plot(<growth_day>) plot(<spwb_day>) plot(<pwb_day>)

Plots simulation results for one day

summary(<pwb>) summary(<spwb>) summary(<growth>) summary(<fordyn>)

Summarises simulation results

extractSubdaily()

Extracts subdaily output

shinyplot(<spwb>) shinyplot(<pwb>) shinyplot(<growth>) shinyplot(<fordyn>) shinyplot(<spwb_day>) shinyplot(<pwb_day>) shinyplot(<growth_day>)

Shiny app with interactive plots

Post-processing

Other post-processing functions

resistances()

Soil-plant resistances

droughtStress()

Drought stress indices

waterUseEfficiency()

Water use efficiency

fireHazard()

Fire hazard

Model analysis

Evaluation and optimization

exampleobs

Example observed data

spwb_ldrCalibration()

Calibration of root distribution

spwb_ldrExploration() spwb_ldrOptimization()

Optimization of root distribution

spwb_sensitivity()

Sensitivity analysis for soil plant water balance simulations

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_vulnerabilityCurvePlot() hydraulics_psiCrit() hydraulics_vanGenuchtenConductance() hydraulics_xylemConductance() hydraulics_xylemPsi() hydraulics_correctConductanceForViscosity() hydraulics_psi2Weibull()

Hydraulic confuctance functions

hydraulics_maximumSoilPlantConductance() hydraulics_soilPlantResistances() hydraulics_averageRhizosphereResistancePercent() hydraulics_findRhizosphereMaximumConductance() hydraulics_maximumStemHydraulicConductance() hydraulics_rootxylemConductanceProportions() hydraulics_referenceConductivityHeightFactor() hydraulics_terminalConduitRadius() hydraulics_taperFactorSavage()

Scaling from conductivity to conductance

hydraulics_EXylem() hydraulics_EVanGenuchten() hydraulics_ECapacitance() hydraulics_ECrit() hydraulics_E2psiXylem() hydraulics_E2psiXylemUp() hydraulics_E2psiVanGenuchten() hydraulics_E2psiTwoElements() hydraulics_E2psiFineRootLeaf() hydraulics_E2psiBelowground() hydraulics_E2psiAboveground() hydraulics_E2psiNetwork() hydraulics_E2psiNetworkStem1() hydraulics_supplyFunctionOneXylem() hydraulics_supplyFunctionTwoElements() hydraulics_supplyFunctionThreeElements() hydraulics_supplyFunctionBelowground() hydraulics_supplyFunctionAboveground() hydraulics_supplyFunctionFineRootLeaf() hydraulics_supplyFunctionNetworkStem1() hydraulics_supplyFunctionNetwork() hydraulics_supplyFunctionPlot() hydraulics_regulatedPsiXylem() hydraulics_regulatedPsiTwoElements()

Hydraulic supply functions

Hydrology

Forest hydrology processes

hydrology_rainInterception() hydrology_erFactor() hydrology_interceptionPlot()

Rainfall interception

hydrology_infiltrationAmount() hydrology_infiltrationRepartition() hydrology_soilEvaporationAmount() hydrology_soilEvaporation() hydrology_snowMelt()

Soil infiltration and bare soil evaporation

hydrology_soilWaterInputs() hydrology_soilInfiltrationPercolation()

Soil water processes

Light and photosynthesis

Light extinction and photosynthesis processes

light_layerIrradianceFraction() light_layerIrradianceFractionBottomUp() light_layerSunlitFraction() light_cohortSunlitShadeAbsorbedRadiation() light_instantaneousLightExtinctionAbsortion() light_longwaveRadiationSHAW() light_cohortAbsorbedSWRFraction() light_PARground() light_SWRground() light_PARcohort()

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_transpirationGranier() transp_transpirationSperry()

Transpiration modes

transp_profitMaximization() transp_stomatalRegulationPlot()

Stomatal regulation

Carbon balance

Carbon balance processes

carbon_leafStarchCapacity() carbon_leafStructuralBiomass() carbon_sapwoodStarchCapacity() carbon_sapwoodStructuralBiomass() carbon_sapwoodStructuralLivingBiomass() carbon_sugarConcentration() carbon_osmoticWaterPotential() carbon_relativeSapViscosity() carbon_sugarStarchDynamicsLeaf() carbon_sugarStarchDynamicsStem() carbon_carbonCompartments()

Carbon-related functions

Secondary growth, mortality and recruitment

Wood formation, mortality and recruitment processes

woodformation_initRing() woodformation_growRing() woodformation_relativeExpansionRate() woodformation_temperatureEffect() woodformation_relativeGrowthRate()

Wood formation

mortality_dailyProbability()

Mortality

recruitment()

Plant recruitment

Water content

Plant/tissue water contents

moisture_symplasticRWC() moisture_symplasticPsi() moisture_apoplasticRWC() moisture_apoplasticPsi() moisture_turgorLossPoint() moisture_tissueRWC() moisture_pressureVolumeCurvePlot() moisture_sapwoodWaterCapacity() moisture_leafWaterCapacity()

Tissue moisture functions

Fuels and fire behaviour

Fuel characteristics and fire behaviour

fire_FCCS() fire_Rothermel()

Fire behaviour functions

fuel_stratification() fuel_FCCS() fuel_windAdjustmentFactor()

Fuel stratification and fuel characteristics

SFM_metric

Standard fuel models (Albini 1976, Scott & Burgan 2005)