B C D E F G H I L M O P R S T V W
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 |
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 |
defaultControl | Control parameters for simulation models |
defaultManagementArguments | Default forest management actions |
defaultManagementFunction | Default forest management actions |
defaultSoilParams | Default soil parameters |
droughtStress | Drought stress indicators |
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 |
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 |
growth | Forest growth |
growthInput | Input for simulation models |
growth_day | Single-day simulation |
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_initSperryNetworks | Hydraulic supply functions |
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 |
initCochardNetworks | Sureau-ECOS inner functions for testing only |
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 |
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 |
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 |
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 |
regeneration | Plant regeneration |
regeneration_recruitment | Plant regeneration |
regeneration_resprouting | Plant regeneration |
regeneration_seedmortality | Plant regeneration |
regeneration_seedproduction | Plant regeneration |
regeneration_seedrefill | Plant regeneration |
resetInputs | Reset simulation inputs |
resistances | Soil-plant resistances |
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 |
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 |
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 |
vprofile_fuelBulkDensity | Vertical profiles |
vprofile_leafAreaDensity | Vertical profiles |
vprofile_PARExtinction | Vertical profiles |
vprofile_rootDistribution | Vertical profiles |
vprofile_SWRExtinction | Vertical profiles |
vprofile_windExtinction | Vertical profiles |
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 |