Functions spwbInput() and growthInput() take an object of class forest
and a soil data input to create input objects for simulation functions spwb (or pwb) and growth, respectively.
Arguments
- x
An object of class
forest.- soil
An object of class
data.frameorsoil, containing soil parameters per soil layer.- SpParams
A data frame with species parameters (see
SpParamsDefinitionandSpParamsMED).- control
A list with default control parameters (see
defaultControl).
Value
Function spwbInput() returns a list of class spwbInput with the following elements (rows of data frames are identified as specified by function plant_ID):
control: List with control parameters (seedefaultControl).soil: A data frame with initialized soil parameters (seesoil).snowpack: The amount of snow (in mm) in the snow pack over the soil.canopy: A list of stand-level state variables.cohorts: A data frame with cohort information, with columnsSPandName.above: A data frame with columnsH,CRandLAI(see functionforest2aboveground).below: A data frame with columnsZ50,Z95. Ifcontrol$transpirationMode = "Sperry"additional columns arefineRootBiomassandcoarseRootSoilVolume.belowLayers: A list. Ifcontrol$transpirationMode = "Granier"it contains elements:V: A matrix with the proportion of fine roots of each cohort (in rows) in each soil layer (in columns).L: A matrix with the length of coarse roots of each cohort (in rows) in each soil layer (in columns).Wpool: A matrix with the soil moisture relative to field capacity around the rhizosphere of each cohort (in rows) in each soil layer (in columns).
control$transpirationMode = "Sperry"orcontrol$transpirationMode = "Sureau"there are the following additional elements:VGrhizo_kmax: A matrix with maximum rhizosphere conductance values of each cohort (in rows) in each soil layer (in columns).VGroot_kmax: A matrix with maximum root xylem conductance values of each cohort (in rows) in each soil layer (in columns).RhizoPsi: A matrix with the water potential around the rhizosphere of each cohort (in rows) in each soil layer (in columns).
paramsPhenology: A data frame with leaf phenology parameters:PhenologyType: Leaf phenology type.LeafDuration: Leaf duration (in years).Sgdd: Degree days needed for leaf budburst (for winter decideous species).Tbgdd: Base temperature for the calculation of degree days to leaf budburst.Ssen: Degree days corresponding to leaf senescence.Phsen: Photoperiod corresponding to start counting senescence degree-days.Tbsen: Base temperature for the calculation of degree days to leaf senescence.
paramsAnatomy: A data frame with plant anatomy parameters for each cohort:Hmax: Maximum plant height (cm).Hmed: Median plant height (cm).Al2As: Leaf area to sapwood area ratio (in m2·m-2).Ar2Al: Fine root area to leaf area ratio (in m2·m-2).SLA: Specific leaf area (mm2/mg = m2/kg).LeafWidth: Leaf width (in cm).LeafDensity: Density of leaf tissue (dry weight over volume).WoodDensity: Density of wood tissue (dry weight over volume).FineRootDensity: Density of fine root tissue (dry weight over volume).SRL: Specific Root length (cm·g-1).RLD: Root length density (cm·cm-3).r635: Ratio between the weight of leaves plus branches and the weight of leaves alone for branches of 6.35 mm.
paramsInterception: A data frame with rain interception and light extinction parameters for each cohort:kPAR: PAR extinction coefficient.g: Canopy water retention capacity per LAI unit (mm/LAI).
control$transpirationMode = "Sperry"orcontrol$transpirationMode = "Sureau"additional columns are:gammaSWR: Reflectance (albedo) coefficient for SWR .alphaSWR: Absorbance coefficient for SWR .
paramsTranspiration: A data frame with parameters for transpiration and photosynthesis. Ifcontrol$transpirationMode = "Granier", columns are:Gswmin: Minimum stomatal conductance to water vapor (in mol H2O·m-2·s-1).Tmax_LAI: Coefficient relating LAI with the ratio of maximum transpiration over potential evapotranspiration.Tmax_LAIsq: Coefficient relating squared LAI with the ratio of maximum transpiration over potential evapotranspiration.Psi_Extract: Water potential corresponding to 50% relative transpiration (in MPa).Exp_Extract: Parameter of the Weibull function regulating transpiration reduction.VCstem_c,VCstem_d: Parameters of the stem xylem vulnerability curve (Weibull).WUE: Daily water use efficiency (gross photosynthesis over transpiration) under no light, water or CO2 limitations and VPD = 1kPa (g C/mm water).WUE_par: Coefficient regulating the influence of % PAR on gross photosynthesis.WUE_co2: Coefficient regulating the influence of atmospheric CO2 concentration on gross photosynthesis.WUE_vpd: Coefficient regulating the influence of vapor pressure deficit (VPD) on gross photosynthesis.
control$transpirationMode = "Sperry"columns are:Gswmin: Minimum stomatal conductance to water vapor (in mol H2O·m-2·s-1).Gswmax: Maximum stomatal conductance to water vapor (in mol H2O·m-2·s-1).Vmax298: Maximum Rubisco carboxilation rate at 25ºC (in micromol CO2·s-1·m-2).Jmax298: Maximum rate of electron transport at 25ºC (in micromol photons·s-1·m-2).Kmax_stemxylem: Sapwood-specific hydraulic conductivity of stem xylem (in kg H2O·s-1·m-1·MPa-1).Kmax_rootxylem: Sapwood-specific hydraulic conductivity of root xylem (in kg H2O·s-1·m-1·MPa-1).VCleaf_kmax: Maximum leaf hydraulic conductance (in mmol H2O·s-1·m-2·MPa-1).VCleaf_c,VCleaf_d: Parameters of the leaf vulnerability curve (Weibull).VCstem_kmax: Maximum stem xylem conductance (in mmol H2O·s-1·m-2·MPa-1).VCstem_c,VCstem_d: Parameters of the stem xylem vulnerability curve (Weibull).VCroot_c,VCroot_d: Parameters of the root xylem vulnerability curve (Weibull).Plant_kmax: Maximum whole-plant conductance (in mmol H2O·s-1·m-2·MPa-1).FR_leaf,FR_stem,FR_root: Fraction of whole-plant resistance corresponding to each segment.
control$transpirationMode = "Sureau"columns are:Gswmin: Minimum stomatal conductance to water vapor (in mol H2O·m-2·s-1).Gswmax: Maximum stomatal conductance to water vapor (in mol H2O·m-2·s-1).Gsw_AC_slope: Slope of the Gsw vs Ac/Cs relationship (seephoto_photosynthesisBaldocchi).Gs_P50,Gs_slope: Parameters of the curve describing the decrease in stomatal conductance as a function of leaf water potential (sigmoid).Vmax298: Maximum Rubisco carboxylation rate at 25ºC (in micromol CO2·s-1·m-2).Jmax298: Maximum rate of electron transport at 25ºC (in micromol photons·s-1·m-2).Kmax_stemxylem: Sapwood-specific hydraulic conductivity of stem xylem (in kg H2O·s-1·m-1·MPa-1).Kmax_rootxylem: Sapwood-specific hydraulic conductivity of root xylem (in kg H2O·s-1·m-1·MPa-1).VCleaf_kmax: Maximum leaf hydraulic conductance (in mmol H2O·s-1·m-2·MPa-1).VCleaf_c,VCleaf_d: Parameters of the leaf vulnerability curve (Weibull).VCleaf_P50,VCleaf_slope: Parameters of the leaf vulnerability curve (sigmoid).VCstem_kmax: Maximum stem xylem conductance (in mmol H2O·s-1·m-2·MPa-1).VCstem_c,VCstem_d: Parameters of the stem xylem vulnerability curve (Weibull).VCstem_P50,VCstem_slope: Parameters of the stem xylem vulnerability curve (sigmoid).VCroot_c,VCroot_d: Parameters of the root xylem vulnerability curve (Weibull).VCroot_P50,VCroot_slope: Parameters of the root xylem vulnerability curve (sigmoid).Plant_kmax: Maximum whole-plant conductance (in mmol H2O·s-1·m-2·MPa-1).FR_leaf,FR_stem,FR_root: Fraction of whole-plant resistance corresponding to each segment.
paramsWaterStorage: A data frame with plant water storage parameters for each cohort:LeafPI0: Osmotic potential at full turgor of leaves (MPa).LeafEPS: Modulus of elasticity (capacity of the cell wall to resist changes in volume in response to changes in turgor) of leaves (MPa).LeafAF: Apoplastic fraction (proportion of water outside the living cells) in leaves.Vleaf: Storage water capacity in leaves, per leaf area (L/m2).StemPI0: Osmotic potential at full turgor of symplastic xylem tissue (MPa).StemEPS: Modulus of elasticity (capacity of the cell wall to resist changes in volume in response to changes in turgor) of symplastic xylem tissue (Mpa).StemAF: Apoplastic fraction (proportion of water outside the living cells) in stem xylem.Vstem: Storage water capacity in sapwood, per leaf area (L/m2).
internalPhenologyandinternalWater: data frames to store internal state variables.internalFCCS: A data frame with fuel characteristics, according tofuel_FCCS(only iffireHazardResults = TRUE, in the control list).
Function growthInput() returns a list of class growthInput with the same elements as spwbInput, but with additional information.
Element
aboveincludes the following additional columns:LA_live: Live leaf area per individual (m2/ind).LA_dead: Dead leaf area per individual (m2/ind).SA: Live sapwood area per individual (cm2/ind).
paramsGrowth: A data frame with growth parameters for each cohort:RERleaf: Maintenance respiration rates (at 20ºC) for leaves (in g gluc·g dry-1·day-1).RERsapwood: Maintenance respiration rates (at 20ºC) for sapwood (in g gluc·g dry-1·day-1).RERfineroot: Maintenance respiration rates (at 20ºC) for fine roots (in g gluc·g dry-1·day-1).CCleaf: Leaf construction costs (in g gluc·g dry-1).CCsapwood: Sapwood construction costs (in g gluc·g dry-1).CCfineroot: Fine root construction costs (in g gluc·g dry-1).RGRleafmax: Maximum leaf relative growth rate (in m2·cm-2·day-1).RGRsapwoodmax: Maximum sapwood relative growth rate (in cm2·cm-2·day-1).RGRfinerootmax: Maximum fine root relative growth rate (in g dry·g dry-1·day-1).SRsapwood: Sapwood daily senescence rate (in day-1).SRfineroot: Fine root daily senescence rate (in day-1).RSSG: Minimum relative starch for sapwood growth (proportion).fHDmin: Minimum value of the height-to-diameter ratio (dimensionless).fHDmax: Maximum value of the height-to-diameter ratio (dimensionless).WoodC: Wood carbon content per dry weight (g C /g dry).
paramsMortalityRegeneration: A data frame with mortality/regeneration parameters for each cohort:MortalityBaselineRate: Deterministic proportion or probability specifying the baseline reduction of cohort's density occurring in a year.SurvivalModelStep: Time step in years of the empirical survival model depending on stand basal area (e.g. 10).SurvivalB0: Intercept of the logistic baseline survival model depending on stand basal area.SurvivalB1: Slope of the logistic baseline survival model depending on stand basal area.RecrTreeDensity: Density of tree recruits from seeds.IngrowthTreeDensity: Density of trees reaching ingrowth DBH.RecrTreeDBH: DBH for tree recruits from seeds or resprouting (e.g. 1 cm).IngrowthTreeDBH: Ingrowth DBH for trees (e.g. 7.5 cm).
paramsAllometry: A data frame with allometric parameters for each cohort:Aash: Regression coefficient relating the square of shrub height with shrub area.Absh,Bbsh: Allometric coefficients relating phytovolume with dry weight of shrub individuals.Acr,B1cr,B2cr,B3cr,C1cr,C2cr: Regression coefficients used to calculate crown ratio of trees.Acw,Bcw: Regression coefficients used to calculated crown width of trees.
internalAllocation: A data frame with internal allocation variables for each cohort:allocationTarget: Value of the allocation target variable.leafAreaTarget: Target leaf area (m2) per individual.sapwoodAreaTarget: Target sapwood area (cm2) per individual.fineRootBiomassTarget: Target fine root biomass (g dry) per individual.crownBudPercent: Percentage of the crown with buds.
internalCarbon: A data frame with the concentration (mol·gluc·l-1) of metabolic and storage carbon compartments for leaves and sapwood.internalMortality: A data frame to store the cumulative mortality (density for trees and cover for shrubs) predicted during the simulation, also distinguishing mortality due to starvation or dessication.
Details
Functions spwbInput() and growthInput() initialize inputs differently depending on control parameters.
IMPORTANT NOTE: Older function names forest2spwbInput and forest2growthInput are now deprecated, but
they can still be used for back-compatibility.
Examples
#Load example plot plant data
data(exampleforest)
# Example of aboveground parameters taken from a forest
# described using LAI and crown ratio
data(exampleforest2)
#Default species parameterization
data(SpParamsMED)
# Define soil with default soil params (4 layers)
examplesoil <- defaultSoilParams(4)
# Initialize control parameters using 'Granier' transpiration mode
control <- defaultControl("Granier")
# Prepare spwb input
spwbInput(exampleforest, examplesoil, SpParamsMED, control)
#> $control
#> $control$fillMissingRootParams
#> [1] TRUE
#>
#> $control$fillMissingSpParams
#> [1] TRUE
#>
#> $control$fillMissingWithGenusParams
#> [1] TRUE
#>
#> $control$verbose
#> [1] TRUE
#>
#> $control$subdailyResults
#> [1] FALSE
#>
#> $control$standResults
#> [1] TRUE
#>
#> $control$soilResults
#> [1] TRUE
#>
#> $control$snowResults
#> [1] TRUE
#>
#> $control$plantResults
#> [1] TRUE
#>
#> $control$plantWaterBalanceResults
#> [1] TRUE
#>
#> $control$labileCarbonBalanceResults
#> [1] TRUE
#>
#> $control$plantStructureResults
#> [1] TRUE
#>
#> $control$growthMortalityResults
#> [1] TRUE
#>
#> $control$leafResults
#> [1] TRUE
#>
#> $control$temperatureResults
#> [1] TRUE
#>
#> $control$fireHazardResults
#> [1] FALSE
#>
#> $control$fireHazardStandardWind
#> [1] NA
#>
#> $control$fireHazardStandardDFMC
#> [1] NA
#>
#> $control$transpirationMode
#> [1] "Granier"
#>
#> $control$soilFunctions
#> [1] "VG"
#>
#> $control$VG_PTF
#> [1] "Toth"
#>
#> $control$ndailysteps
#> [1] 24
#>
#> $control$max_nsubsteps_soil
#> [1] 300
#>
#> $control$defaultWindSpeed
#> [1] 2.5
#>
#> $control$defaultCO2
#> [1] 386
#>
#> $control$defaultRainfallIntensityPerMonth
#> [1] 1.5 1.5 1.5 1.5 1.5 1.5 5.6 5.6 5.6 5.6 5.6 1.5
#>
#> $control$leafPhenology
#> [1] TRUE
#>
#> $control$bareSoilEvaporation
#> [1] TRUE
#>
#> $control$unlimitedSoilWater
#> [1] FALSE
#>
#> $control$interceptionMode
#> [1] "Gash1995"
#>
#> $control$infiltrationMode
#> [1] "GreenAmpt1911"
#>
#> $control$infiltrationCorrection
#> [1] 5
#>
#> $control$soilDomains
#> [1] "buckets"
#>
#> $control$rhizosphereOverlap
#> [1] "total"
#>
#> $control$unfoldingDD
#> [1] 300
#>
#> $control$verticalLayerSize
#> [1] 100
#>
#> $control$windMeasurementHeight
#> [1] 200
#>
#> $control$segmentedXylemVulnerability
#> [1] TRUE
#>
#> $control$stemCavitationRecovery
#> [1] "annual"
#>
#> $control$leafCavitationRecovery
#> [1] "annual"
#>
#> $control$lfmcComponent
#> [1] "fine"
#>
#> $control$hydraulicRedistributionFraction
#> [1] 0.1
#>
#> $control$nsubsteps_canopy
#> [1] 3600
#>
#> $control$taper
#> [1] TRUE
#>
#> $control$multiLayerBalance
#> [1] FALSE
#>
#> $control$sapFluidityVariation
#> [1] TRUE
#>
#> $control$TPhase_gmin
#> [1] 37.5
#>
#> $control$Q10_1_gmin
#> [1] 1.2
#>
#> $control$Q10_2_gmin
#> [1] 4.8
#>
#> $control$rootRadialConductance
#> [1] 4
#>
#> $control$averageFracRhizosphereResistance
#> [1] 0.15
#>
#> $control$thermalCapacityLAI
#> [1] 1e+06
#>
#> $control$boundaryLayerSize
#> [1] 2000
#>
#> $control$cavitationRecoveryMaximumRate
#> [1] 0.05
#>
#> $control$sunlitShade
#> [1] TRUE
#>
#> $control$numericParams
#> $control$numericParams$maxNsteps
#> [1] 400
#>
#> $control$numericParams$ntrial
#> [1] 200
#>
#> $control$numericParams$psiTol
#> [1] 1e-04
#>
#> $control$numericParams$ETol
#> [1] 1e-07
#>
#>
#> $control$leafCavitationEffects
#> [1] FALSE
#>
#> $control$stemCavitationEffects
#> [1] TRUE
#>
#> $control$stomatalSubmodel
#> [1] "Baldocchi"
#>
#> $control$plantCapacitance
#> [1] TRUE
#>
#> $control$cavitationFlux
#> [1] TRUE
#>
#> $control$soilDisconnection
#> [1] FALSE
#>
#> $control$leafCuticularTranspiration
#> [1] TRUE
#>
#> $control$stemCuticularTranspiration
#> [1] FALSE
#>
#> $control$C_SApoInit
#> [1] 2e-05
#>
#> $control$C_LApoInit
#> [1] 1e-05
#>
#> $control$k_SSym
#> [1] 0.26
#>
#> $control$fractionLeafSymplasm
#> [1] 0.5
#>
#> $control$gs_NightFrac
#> [1] 0.05
#>
#> $control$JarvisPAR
#> [1] 0.003
#>
#> $control$fTRBToLeaf
#> [1] 0.8
#>
#> $control$subdailyCarbonBalance
#> [1] FALSE
#>
#> $control$allowDessication
#> [1] TRUE
#>
#> $control$allowStarvation
#> [1] TRUE
#>
#> $control$sinkLimitation
#> [1] TRUE
#>
#> $control$shrubDynamics
#> [1] TRUE
#>
#> $control$herbDynamics
#> [1] TRUE
#>
#> $control$allocationStrategy
#> [1] "Al2As"
#>
#> $control$phloemConductanceFactor
#> [1] 0.2
#>
#> $control$nonSugarConcentration
#> [1] 0.25
#>
#> $control$equilibriumOsmoticConcentration
#> $control$equilibriumOsmoticConcentration$leaf
#> [1] 0.8
#>
#> $control$equilibriumOsmoticConcentration$sapwood
#> [1] 0.6
#>
#>
#> $control$minimumRelativeStarchForGrowth
#> [1] 0.5
#>
#> $control$constructionCosts
#> $control$constructionCosts$leaf
#> [1] 1.5
#>
#> $control$constructionCosts$sapwood
#> [1] 1.47
#>
#> $control$constructionCosts$fineroot
#> [1] 1.3
#>
#>
#> $control$senescenceRates
#> $control$senescenceRates$sapwood
#> [1] 0.000135
#>
#> $control$senescenceRates$fineroot
#> [1] 0.001897231
#>
#>
#> $control$maximumRelativeGrowthRates
#> $control$maximumRelativeGrowthRates$leaf
#> [1] 0.09
#>
#> $control$maximumRelativeGrowthRates$cambium
#> [1] 0.0025
#>
#> $control$maximumRelativeGrowthRates$sapwood
#> [1] 0.002
#>
#> $control$maximumRelativeGrowthRates$fineroot
#> [1] 0.1
#>
#>
#> $control$mortalityMode
#> [1] "density/deterministic"
#>
#> $control$mortalityBaselineRate
#> [1] 0.0015
#>
#> $control$mortalityRelativeSugarThreshold
#> [1] 0.4
#>
#> $control$mortalityRWCThreshold
#> [1] 0.4
#>
#> $control$recrTreeDBH
#> [1] 1
#>
#> $control$recrTreeDensity
#> [1] 3000
#>
#> $control$ingrowthTreeDBH
#> [1] 7.5
#>
#> $control$ingrowthTreeDensity
#> [1] 127
#>
#> $control$allowSeedBankDynamics
#> [1] TRUE
#>
#> $control$allowRecruitment
#> [1] TRUE
#>
#> $control$allowResprouting
#> [1] TRUE
#>
#> $control$recruitmentMode
#> [1] "stochastic"
#>
#> $control$removeEmptyCohorts
#> [1] TRUE
#>
#> $control$minimumTreeCohortDensity
#> [1] 1
#>
#> $control$minimumShrubCohortCover
#> [1] 0.01
#>
#> $control$dynamicallyMergeCohorts
#> [1] TRUE
#>
#> $control$keepCohortsWithObsID
#> [1] FALSE
#>
#> $control$seedRain
#> NULL
#>
#> $control$seedProductionTreeHeight
#> [1] 300
#>
#> $control$seedProductionShrubHeight
#> [1] 30
#>
#> $control$probRecr
#> [1] 0.05
#>
#> $control$minTempRecr
#> [1] 0
#>
#> $control$minMoistureRecr
#> [1] 0.3
#>
#> $control$minFPARRecr
#> [1] 10
#>
#> $control$recrTreeHeight
#> [1] 620
#>
#> $control$recrShrubCover
#> [1] 1
#>
#> $control$recrShrubHeight
#> [1] 25
#>
#> $control$recrTreeZ50
#> [1] 100
#>
#> $control$recrShrubZ50
#> [1] 50
#>
#> $control$recrTreeZ95
#> [1] 1000
#>
#> $control$recrShrubZ95
#> [1] 500
#>
#>
#> $soil
#> widths sand clay usda om nitrogen bd rfc macro Ksat VG_alpha
#> 1 300 25 25 Silt loam NA NA 1.5 25 0.0485 5401.471 89.16112
#> 2 700 25 25 Silt loam NA NA 1.5 45 0.0485 5401.471 89.16112
#> 3 1000 25 25 Silt loam NA NA 1.5 75 0.0485 5401.471 89.16112
#> 4 2000 25 25 Silt loam NA NA 1.5 95 0.0485 5401.471 89.16112
#> VG_n VG_theta_res VG_theta_sat W Temp
#> 1 1.303861 0.041 0.423715 1 NA
#> 2 1.303861 0.041 0.423715 1 NA
#> 3 1.303861 0.041 0.423715 1 NA
#> 4 1.303861 0.041 0.423715 1 NA
#>
#> $snowpack
#> [1] 0
#>
#> $canopy
#> zlow zmid zup LAIlive LAIexpanded LAIdead Tair Cair VPair
#> 1 0 50 100 NA NA NA NA NA NA
#> 2 100 150 200 NA NA NA NA NA NA
#> 3 200 250 300 NA NA NA NA NA NA
#> 4 300 350 400 NA NA NA NA NA NA
#> 5 400 450 500 NA NA NA NA NA NA
#> 6 500 550 600 NA NA NA NA NA NA
#> 7 600 650 700 NA NA NA NA NA NA
#> 8 700 750 800 NA NA NA NA NA NA
#> 9 800 850 900 NA NA NA NA NA NA
#> 10 900 950 1000 NA NA NA NA NA NA
#> 11 1000 1050 1100 NA NA NA NA NA NA
#> 12 1100 1150 1200 NA NA NA NA NA NA
#> 13 1200 1250 1300 NA NA NA NA NA NA
#> 14 1300 1350 1400 NA NA NA NA NA NA
#> 15 1400 1450 1500 NA NA NA NA NA NA
#> 16 1500 1550 1600 NA NA NA NA NA NA
#> 17 1600 1650 1700 NA NA NA NA NA NA
#> 18 1700 1750 1800 NA NA NA NA NA NA
#> 19 1800 1850 1900 NA NA NA NA NA NA
#> 20 1900 1950 2000 NA NA NA NA NA NA
#> 21 2000 2050 2100 NA NA NA NA NA NA
#> 22 2100 2150 2200 NA NA NA NA NA NA
#> 23 2200 2250 2300 NA NA NA NA NA NA
#> 24 2300 2350 2400 NA NA NA NA NA NA
#> 25 2400 2450 2500 NA NA NA NA NA NA
#> 26 2500 2550 2600 NA NA NA NA NA NA
#> 27 2600 2650 2700 NA NA NA NA NA NA
#> 28 2700 2750 2800 NA NA NA NA NA NA
#>
#> $herbLAI
#> [1] 0.1736369
#>
#> $herbLAImax
#> [1] 0.252
#>
#> $cohorts
#> SP Name
#> T1_148 148 Pinus halepensis
#> T2_168 168 Quercus ilex
#> S1_165 165 Quercus coccifera
#>
#> $above
#> H CR LAI_live LAI_expanded LAI_dead ObsID
#> T1_148 800 0.6605196 0.84874773 0.84874773 0 <NA>
#> T2_168 660 0.6055642 0.70557382 0.70557382 0 <NA>
#> S1_165 80 0.8032817 0.03062604 0.03062604 0 <NA>
#>
#> $below
#> Z50 Z95 Z100
#> T1_148 100 600 NA
#> T2_168 300 1000 NA
#> S1_165 200 1000 NA
#>
#> $belowLayers
#> $belowLayers$V
#> 1 2 3 4
#> T1_148 0.8604899 0.1194556 0.01511005 0.004944476
#> T2_168 0.5008953 0.4505941 0.04064831 0.007862284
#> S1_165 0.6799879 0.2737911 0.03567632 0.010544678
#>
#> $belowLayers$L
#> 1 2 3 4
#> T1_148 150 650 1500 3000
#> T2_168 150 650 1500 3000
#> S1_165 150 650 1500 3000
#>
#> $belowLayers$Wpool
#> 1 2 3 4
#> T1_148 1 1 1 1
#> T2_168 1 1 1 1
#> S1_165 1 1 1 1
#>
#>
#> $paramsPhenology
#> PhenologyType LeafDuration t0gdd Sgdd Tbgdd Ssen Phsen Tbsen xsen
#> T1_148 oneflush-evergreen 2.536875 50.0 200.0 0.00 8268 12.5 28.5 2
#> T2_168 oneflush-evergreen 2.183837 54.5 240.7 4.34 10178 12.5 28.5 2
#> S1_165 oneflush-evergreen 1.250000 54.5 240.7 4.34 10178 12.5 28.5 2
#> ysen
#> T1_148 2
#> T2_168 2
#> S1_165 2
#>
#> $paramsAnatomy
#> Al2As Ar2Al SLA LeafDensity WoodDensity FineRootDensity SRL
#> T1_148 1317.523 1 5.140523 0.2982842 0.6077016 0.2982842 3172.572
#> T2_168 3908.823 1 6.340000 0.4893392 0.9008264 0.4893392 4398.812
#> S1_165 4189.325 1 4.980084 0.3709679 0.4389106 0.3709679 4398.812
#> RLD r635
#> T1_148 10 1.964226
#> T2_168 10 1.805872
#> S1_165 10 2.289452
#>
#> $paramsInterception
#> kPAR kSWR g
#> T1_148 0.50 0.3703704 1.0
#> T2_168 0.55 0.4074074 0.5
#> S1_165 0.55 0.4074074 0.5
#>
#> $paramsTranspiration
#> Gswmin Tmax_LAI Tmax_LAIsq Psi_Extract Exp_Extract VCleaf_c
#> T1_148 0.003086667 0.1869849 -0.008372458 -0.9218219 1.504542 11.137050
#> T2_168 0.004473333 0.1251027 -0.005601615 -1.9726871 1.149052 1.339370
#> S1_165 0.010455247 0.1340000 -0.006000000 -2.1210726 1.300000 2.254991
#> VCleaf_d VCstem_c VCstem_d WUE WUE_par WUE_co2 WUE_vpd
#> T1_148 -2.380849 12.709999 -5.290000 8.525550 0.5239136 0.002586327 -0.2647169
#> T2_168 -2.582279 3.560000 -7.720000 8.968208 0.1412266 0.002413091 -0.5664879
#> S1_165 -3.133381 3.095442 -7.857378 7.900000 0.3643000 0.002757000 -0.4636000
#>
#> $paramsWaterStorage
#> maxFMC LeafPI0 LeafEPS LeafAF Vleaf StemPI0 StemEPS
#> T1_148 126.03063 -1.591429 8.918571 0.3525 0.5258525 -2.008039 13.256355
#> T2_168 93.15304 -1.483333 19.260000 0.1700 0.2199087 -3.227438 46.420610
#> S1_165 96.53441 -2.370000 17.230000 0.2400 0.4108968 -1.305868 6.297155
#> StemAF Vsapwood
#> T1_148 0.9236406 4.1638559
#> T2_168 0.6238125 0.8135590
#> S1_165 0.6238125 0.3177724
#>
#> $internalPhenology
#> gdd sen budFormation leafUnfolding leafSenescence leafDormancy phi
#> T1_148 0 0 FALSE FALSE FALSE FALSE 0
#> T2_168 0 0 FALSE FALSE FALSE FALSE 0
#> S1_165 0 0 FALSE FALSE FALSE FALSE 0
#>
#> $internalWater
#> PlantPsi LeafPLC StemPLC
#> T1_148 -0.033 0 0
#> T2_168 -0.033 0 0
#> S1_165 -0.033 0 0
#>
#> $internalLAIDistribution
#> $internalLAIDistribution$PrevLAIexpanded
#> [1] 0 0 0
#>
#> $internalLAIDistribution$PrevLAIdead
#> [1] 0 0 0
#>
#> $internalLAIDistribution$PARcohort
#> [1] 0 0 0
#>
#> $internalLAIDistribution$live
#> T1_148 T2_168 S1_165
#> 1 0 0 0
#> 2 0 0 0
#> 3 0 0 0
#> 4 0 0 0
#> 5 0 0 0
#> 6 0 0 0
#> 7 0 0 0
#> 8 0 0 0
#> 9 0 0 0
#> 10 0 0 0
#> 11 0 0 0
#> 12 0 0 0
#> 13 0 0 0
#> 14 0 0 0
#> 15 0 0 0
#> 16 0 0 0
#> 17 0 0 0
#> 18 0 0 0
#> 19 0 0 0
#> 20 0 0 0
#> 21 0 0 0
#> 22 0 0 0
#> 23 0 0 0
#> 24 0 0 0
#> 25 0 0 0
#> 26 0 0 0
#> 27 0 0 0
#> 28 0 0 0
#>
#> $internalLAIDistribution$expanded
#> T1_148 T2_168 S1_165
#> 1 0 0 0
#> 2 0 0 0
#> 3 0 0 0
#> 4 0 0 0
#> 5 0 0 0
#> 6 0 0 0
#> 7 0 0 0
#> 8 0 0 0
#> 9 0 0 0
#> 10 0 0 0
#> 11 0 0 0
#> 12 0 0 0
#> 13 0 0 0
#> 14 0 0 0
#> 15 0 0 0
#> 16 0 0 0
#> 17 0 0 0
#> 18 0 0 0
#> 19 0 0 0
#> 20 0 0 0
#> 21 0 0 0
#> 22 0 0 0
#> 23 0 0 0
#> 24 0 0 0
#> 25 0 0 0
#> 26 0 0 0
#> 27 0 0 0
#> 28 0 0 0
#>
#> $internalLAIDistribution$dead
#> T1_148 T2_168 S1_165
#> 1 0 0 0
#> 2 0 0 0
#> 3 0 0 0
#> 4 0 0 0
#> 5 0 0 0
#> 6 0 0 0
#> 7 0 0 0
#> 8 0 0 0
#> 9 0 0 0
#> 10 0 0 0
#> 11 0 0 0
#> 12 0 0 0
#> 13 0 0 0
#> 14 0 0 0
#> 15 0 0 0
#> 16 0 0 0
#> 17 0 0 0
#> 18 0 0 0
#> 19 0 0 0
#> 20 0 0 0
#> 21 0 0 0
#> 22 0 0 0
#> 23 0 0 0
#> 24 0 0 0
#> 25 0 0 0
#> 26 0 0 0
#> 27 0 0 0
#> 28 0 0 0
#>
#>
#> $internalFCCS
#> data frame with 0 columns and 0 rows
#>
#> attr(,"class")
#> [1] "spwbInput" "list"
# Prepare input for 'Sperry' transpiration mode
control <- defaultControl("Sperry")
spwbInput(exampleforest,examplesoil,SpParamsMED, control)
#> $control
#> $control$fillMissingRootParams
#> [1] TRUE
#>
#> $control$fillMissingSpParams
#> [1] TRUE
#>
#> $control$fillMissingWithGenusParams
#> [1] TRUE
#>
#> $control$verbose
#> [1] TRUE
#>
#> $control$subdailyResults
#> [1] FALSE
#>
#> $control$standResults
#> [1] TRUE
#>
#> $control$soilResults
#> [1] TRUE
#>
#> $control$snowResults
#> [1] TRUE
#>
#> $control$plantResults
#> [1] TRUE
#>
#> $control$plantWaterBalanceResults
#> [1] TRUE
#>
#> $control$labileCarbonBalanceResults
#> [1] TRUE
#>
#> $control$plantStructureResults
#> [1] TRUE
#>
#> $control$growthMortalityResults
#> [1] TRUE
#>
#> $control$leafResults
#> [1] TRUE
#>
#> $control$temperatureResults
#> [1] TRUE
#>
#> $control$fireHazardResults
#> [1] FALSE
#>
#> $control$fireHazardStandardWind
#> [1] NA
#>
#> $control$fireHazardStandardDFMC
#> [1] NA
#>
#> $control$transpirationMode
#> [1] "Sperry"
#>
#> $control$soilFunctions
#> [1] "VG"
#>
#> $control$VG_PTF
#> [1] "Toth"
#>
#> $control$ndailysteps
#> [1] 24
#>
#> $control$max_nsubsteps_soil
#> [1] 300
#>
#> $control$defaultWindSpeed
#> [1] 2.5
#>
#> $control$defaultCO2
#> [1] 386
#>
#> $control$defaultRainfallIntensityPerMonth
#> [1] 1.5 1.5 1.5 1.5 1.5 1.5 5.6 5.6 5.6 5.6 5.6 1.5
#>
#> $control$leafPhenology
#> [1] TRUE
#>
#> $control$bareSoilEvaporation
#> [1] TRUE
#>
#> $control$unlimitedSoilWater
#> [1] FALSE
#>
#> $control$interceptionMode
#> [1] "Gash1995"
#>
#> $control$infiltrationMode
#> [1] "GreenAmpt1911"
#>
#> $control$infiltrationCorrection
#> [1] 5
#>
#> $control$soilDomains
#> [1] "buckets"
#>
#> $control$rhizosphereOverlap
#> [1] "total"
#>
#> $control$unfoldingDD
#> [1] 300
#>
#> $control$verticalLayerSize
#> [1] 100
#>
#> $control$windMeasurementHeight
#> [1] 200
#>
#> $control$segmentedXylemVulnerability
#> [1] TRUE
#>
#> $control$stemCavitationRecovery
#> [1] "annual"
#>
#> $control$leafCavitationRecovery
#> [1] "annual"
#>
#> $control$lfmcComponent
#> [1] "fine"
#>
#> $control$hydraulicRedistributionFraction
#> [1] 0.1
#>
#> $control$nsubsteps_canopy
#> [1] 3600
#>
#> $control$taper
#> [1] TRUE
#>
#> $control$multiLayerBalance
#> [1] FALSE
#>
#> $control$sapFluidityVariation
#> [1] TRUE
#>
#> $control$TPhase_gmin
#> [1] 37.5
#>
#> $control$Q10_1_gmin
#> [1] 1.2
#>
#> $control$Q10_2_gmin
#> [1] 4.8
#>
#> $control$rootRadialConductance
#> [1] 4
#>
#> $control$averageFracRhizosphereResistance
#> [1] 0.15
#>
#> $control$thermalCapacityLAI
#> [1] 1e+06
#>
#> $control$boundaryLayerSize
#> [1] 2000
#>
#> $control$cavitationRecoveryMaximumRate
#> [1] 0.05
#>
#> $control$sunlitShade
#> [1] TRUE
#>
#> $control$numericParams
#> $control$numericParams$maxNsteps
#> [1] 400
#>
#> $control$numericParams$ntrial
#> [1] 200
#>
#> $control$numericParams$psiTol
#> [1] 1e-04
#>
#> $control$numericParams$ETol
#> [1] 1e-07
#>
#>
#> $control$leafCavitationEffects
#> [1] FALSE
#>
#> $control$stemCavitationEffects
#> [1] TRUE
#>
#> $control$stomatalSubmodel
#> [1] "Baldocchi"
#>
#> $control$plantCapacitance
#> [1] TRUE
#>
#> $control$cavitationFlux
#> [1] TRUE
#>
#> $control$soilDisconnection
#> [1] FALSE
#>
#> $control$leafCuticularTranspiration
#> [1] TRUE
#>
#> $control$stemCuticularTranspiration
#> [1] FALSE
#>
#> $control$C_SApoInit
#> [1] 2e-05
#>
#> $control$C_LApoInit
#> [1] 1e-05
#>
#> $control$k_SSym
#> [1] 0.26
#>
#> $control$fractionLeafSymplasm
#> [1] 0.5
#>
#> $control$gs_NightFrac
#> [1] 0.05
#>
#> $control$JarvisPAR
#> [1] 0.003
#>
#> $control$fTRBToLeaf
#> [1] 0.8
#>
#> $control$subdailyCarbonBalance
#> [1] FALSE
#>
#> $control$allowDessication
#> [1] TRUE
#>
#> $control$allowStarvation
#> [1] TRUE
#>
#> $control$sinkLimitation
#> [1] TRUE
#>
#> $control$shrubDynamics
#> [1] TRUE
#>
#> $control$herbDynamics
#> [1] TRUE
#>
#> $control$allocationStrategy
#> [1] "Al2As"
#>
#> $control$phloemConductanceFactor
#> [1] 0.2
#>
#> $control$nonSugarConcentration
#> [1] 0.25
#>
#> $control$equilibriumOsmoticConcentration
#> $control$equilibriumOsmoticConcentration$leaf
#> [1] 0.8
#>
#> $control$equilibriumOsmoticConcentration$sapwood
#> [1] 0.6
#>
#>
#> $control$minimumRelativeStarchForGrowth
#> [1] 0.5
#>
#> $control$constructionCosts
#> $control$constructionCosts$leaf
#> [1] 1.5
#>
#> $control$constructionCosts$sapwood
#> [1] 1.47
#>
#> $control$constructionCosts$fineroot
#> [1] 1.3
#>
#>
#> $control$senescenceRates
#> $control$senescenceRates$sapwood
#> [1] 0.000135
#>
#> $control$senescenceRates$fineroot
#> [1] 0.001897231
#>
#>
#> $control$maximumRelativeGrowthRates
#> $control$maximumRelativeGrowthRates$leaf
#> [1] 0.09
#>
#> $control$maximumRelativeGrowthRates$cambium
#> [1] 0.0025
#>
#> $control$maximumRelativeGrowthRates$sapwood
#> [1] 0.002
#>
#> $control$maximumRelativeGrowthRates$fineroot
#> [1] 0.1
#>
#>
#> $control$mortalityMode
#> [1] "density/deterministic"
#>
#> $control$mortalityBaselineRate
#> [1] 0.0015
#>
#> $control$mortalityRelativeSugarThreshold
#> [1] 0.4
#>
#> $control$mortalityRWCThreshold
#> [1] 0.4
#>
#> $control$recrTreeDBH
#> [1] 1
#>
#> $control$recrTreeDensity
#> [1] 3000
#>
#> $control$ingrowthTreeDBH
#> [1] 7.5
#>
#> $control$ingrowthTreeDensity
#> [1] 127
#>
#> $control$allowSeedBankDynamics
#> [1] TRUE
#>
#> $control$allowRecruitment
#> [1] TRUE
#>
#> $control$allowResprouting
#> [1] TRUE
#>
#> $control$recruitmentMode
#> [1] "stochastic"
#>
#> $control$removeEmptyCohorts
#> [1] TRUE
#>
#> $control$minimumTreeCohortDensity
#> [1] 1
#>
#> $control$minimumShrubCohortCover
#> [1] 0.01
#>
#> $control$dynamicallyMergeCohorts
#> [1] TRUE
#>
#> $control$keepCohortsWithObsID
#> [1] FALSE
#>
#> $control$seedRain
#> NULL
#>
#> $control$seedProductionTreeHeight
#> [1] 300
#>
#> $control$seedProductionShrubHeight
#> [1] 30
#>
#> $control$probRecr
#> [1] 0.05
#>
#> $control$minTempRecr
#> [1] 0
#>
#> $control$minMoistureRecr
#> [1] 0.3
#>
#> $control$minFPARRecr
#> [1] 10
#>
#> $control$recrTreeHeight
#> [1] 620
#>
#> $control$recrShrubCover
#> [1] 1
#>
#> $control$recrShrubHeight
#> [1] 25
#>
#> $control$recrTreeZ50
#> [1] 100
#>
#> $control$recrShrubZ50
#> [1] 50
#>
#> $control$recrTreeZ95
#> [1] 1000
#>
#> $control$recrShrubZ95
#> [1] 500
#>
#>
#> $soil
#> widths sand clay usda om nitrogen bd rfc macro Ksat VG_alpha
#> 1 300 25 25 Silt loam NA NA 1.5 25 0.0485 5401.471 89.16112
#> 2 700 25 25 Silt loam NA NA 1.5 45 0.0485 5401.471 89.16112
#> 3 1000 25 25 Silt loam NA NA 1.5 75 0.0485 5401.471 89.16112
#> 4 2000 25 25 Silt loam NA NA 1.5 95 0.0485 5401.471 89.16112
#> VG_n VG_theta_res VG_theta_sat W Temp
#> 1 1.303861 0.041 0.423715 1 NA
#> 2 1.303861 0.041 0.423715 1 NA
#> 3 1.303861 0.041 0.423715 1 NA
#> 4 1.303861 0.041 0.423715 1 NA
#>
#> $snowpack
#> [1] 0
#>
#> $canopy
#> zlow zmid zup LAIlive LAIexpanded LAIdead Tair Cair VPair
#> 1 0 50 100 NA NA NA NA NA NA
#> 2 100 150 200 NA NA NA NA NA NA
#> 3 200 250 300 NA NA NA NA NA NA
#> 4 300 350 400 NA NA NA NA NA NA
#> 5 400 450 500 NA NA NA NA NA NA
#> 6 500 550 600 NA NA NA NA NA NA
#> 7 600 650 700 NA NA NA NA NA NA
#> 8 700 750 800 NA NA NA NA NA NA
#> 9 800 850 900 NA NA NA NA NA NA
#> 10 900 950 1000 NA NA NA NA NA NA
#> 11 1000 1050 1100 NA NA NA NA NA NA
#> 12 1100 1150 1200 NA NA NA NA NA NA
#> 13 1200 1250 1300 NA NA NA NA NA NA
#> 14 1300 1350 1400 NA NA NA NA NA NA
#> 15 1400 1450 1500 NA NA NA NA NA NA
#> 16 1500 1550 1600 NA NA NA NA NA NA
#> 17 1600 1650 1700 NA NA NA NA NA NA
#> 18 1700 1750 1800 NA NA NA NA NA NA
#> 19 1800 1850 1900 NA NA NA NA NA NA
#> 20 1900 1950 2000 NA NA NA NA NA NA
#> 21 2000 2050 2100 NA NA NA NA NA NA
#> 22 2100 2150 2200 NA NA NA NA NA NA
#> 23 2200 2250 2300 NA NA NA NA NA NA
#> 24 2300 2350 2400 NA NA NA NA NA NA
#> 25 2400 2450 2500 NA NA NA NA NA NA
#> 26 2500 2550 2600 NA NA NA NA NA NA
#> 27 2600 2650 2700 NA NA NA NA NA NA
#> 28 2700 2750 2800 NA NA NA NA NA NA
#>
#> $herbLAI
#> [1] 0.1736369
#>
#> $herbLAImax
#> [1] 0.252
#>
#> $cohorts
#> SP Name
#> T1_148 148 Pinus halepensis
#> T2_168 168 Quercus ilex
#> S1_165 165 Quercus coccifera
#>
#> $above
#> H CR LAI_live LAI_expanded LAI_dead ObsID
#> T1_148 800 0.6605196 0.84874773 0.84874773 0 <NA>
#> T2_168 660 0.6055642 0.70557382 0.70557382 0 <NA>
#> S1_165 80 0.8032817 0.03062604 0.03062604 0 <NA>
#>
#> $below
#> Z50 Z95 Z100
#> T1_148 100 600 NA
#> T2_168 300 1000 NA
#> S1_165 200 1000 NA
#>
#> $belowLayers
#> $belowLayers$V
#> 1 2 3 4
#> T1_148 0.8604899 0.1194556 0.01511005 0.004944476
#> T2_168 0.5008953 0.4505941 0.04064831 0.007862284
#> S1_165 0.6799879 0.2737911 0.03567632 0.010544678
#>
#> $belowLayers$L
#> 1 2 3 4
#> T1_148 2289.062 1566.552 2250.052 4226.166
#> T2_168 1817.571 2100.346 2410.127 4285.194
#> S1_165 1085.030 1380.808 2170.587 4146.637
#>
#> $belowLayers$VGrhizo_kmax
#> 1 2 3 4
#> T1_148 11478618 1593494 201562.5 65957.49
#> T2_168 36121247 32493859 2931286.8 566975.78
#> S1_165 10941459 4405482 574055.7 169670.90
#>
#> $belowLayers$VCroot_kmax
#> 1 2 3 4
#> T1_148 2.382795 0.4833484 0.04256689 0.007416044
#> T2_168 1.568929 1.2213562 0.09601747 0.010445417
#> S1_165 2.407779 0.7618041 0.06314806 0.009770000
#>
#> $belowLayers$Wpool
#> 1 2 3 4
#> T1_148 1 1 1 1
#> T2_168 1 1 1 1
#> S1_165 1 1 1 1
#>
#> $belowLayers$RhizoPsi
#> 1 2 3 4
#> T1_148 -0.033 -0.033 -0.033 -0.033
#> T2_168 -0.033 -0.033 -0.033 -0.033
#> S1_165 -0.033 -0.033 -0.033 -0.033
#>
#>
#> $paramsPhenology
#> PhenologyType LeafDuration t0gdd Sgdd Tbgdd Ssen Phsen Tbsen xsen
#> T1_148 oneflush-evergreen 2.536875 50.0 200.0 0.00 8268 12.5 28.5 2
#> T2_168 oneflush-evergreen 2.183837 54.5 240.7 4.34 10178 12.5 28.5 2
#> S1_165 oneflush-evergreen 1.250000 54.5 240.7 4.34 10178 12.5 28.5 2
#> ysen
#> T1_148 2
#> T2_168 2
#> S1_165 2
#>
#> $paramsAnatomy
#> Hmed Al2As SLA LeafWidth LeafDensity WoodDensity FineRootDensity
#> T1_148 850 1317.523 5.140523 0.1384772 0.2982842 0.6077016 0.2982842
#> T2_168 500 3908.823 6.340000 1.7674359 0.4893392 0.9008264 0.4893392
#> S1_165 80 4189.325 4.980084 1.3761085 0.3709679 0.4389106 0.3709679
#> conduit2sapwood SRL RLD r635
#> T1_148 0.9236406 3172.572 10 1.964226
#> T2_168 0.6238125 4398.812 10 1.805872
#> S1_165 0.6238125 4398.812 10 2.289452
#>
#> $paramsInterception
#> LeafAngle LeafAngleSD Beta_p Beta_q ClumpingIndex kPAR alphaSWR
#> T1_148 53.7 21.55 1.907817 1.289641 0.75 0.50 0.7
#> T2_168 53.7 21.55 1.907817 1.289641 0.75 0.55 0.7
#> S1_165 53.7 21.55 1.907817 1.289641 0.75 0.55 0.7
#> gammaSWR g
#> T1_148 0.14 1.0
#> T2_168 0.18 0.5
#> S1_165 0.18 0.5
#>
#> $paramsTranspiration
#> Gswmin Gswmax Vmax298 Jmax298 Kmax_stemxylem Kmax_rootxylem
#> T1_148 0.003086667 0.2850000 72.19617 124.1687 0.15 0.60
#> T2_168 0.004473333 0.2007222 68.51600 118.7863 0.40 1.60
#> S1_165 0.010455247 0.2830167 62.78100 118.4486 0.29 1.16
#> VCleaf_kmax VCleafapo_kmax VCleaf_c VCleaf_d kleaf_symp VCstem_kmax
#> T1_148 4.000000 8.00000 11.137050 -2.380849 8.00000 1.339563
#> T2_168 4.000000 8.00000 1.339370 -2.582279 8.00000 1.620936
#> S1_165 9.579077 19.15815 2.254991 -3.133381 19.15815 4.599269
#> VCstem_c VCstem_d VCroot_kmax VCroot_c VCroot_d VGrhizo_kmax
#> T1_148 12.709999 -5.290000 2.916127 11.137050 -3.065569 13339632
#> T2_168 3.560000 -7.720000 2.896748 1.339370 -2.214081 72113368
#> S1_165 3.095442 -7.857378 3.242501 1.402489 -1.523324 16090667
#> Plant_kmax FR_leaf FR_stem FR_root
#> T1_148 0.7465846 0.1866462 0.5573346 0.2560193
#> T2_168 0.8249857 0.2062464 0.5089563 0.2847972
#> S1_165 1.5867376 0.1656462 0.3449978 0.4893561
#>
#> $paramsWaterStorage
#> maxFMC LeafPI0 LeafEPS LeafAF Vleaf StemPI0 StemEPS
#> T1_148 126.03063 -1.591429 8.918571 0.3525 0.5258525 -2.008039 13.256355
#> T2_168 93.15304 -1.483333 19.260000 0.1700 0.2199087 -3.227438 46.420610
#> S1_165 96.53441 -2.370000 17.230000 0.2400 0.4108968 -1.305868 6.297155
#> StemAF Vsapwood
#> T1_148 0.9236406 6.174277
#> T2_168 0.6238125 1.278142
#> S1_165 0.6238125 1.064511
#>
#> $internalPhenology
#> gdd sen budFormation leafUnfolding leafSenescence leafDormancy phi
#> T1_148 0 0 FALSE FALSE FALSE FALSE 0
#> T2_168 0 0 FALSE FALSE FALSE FALSE 0
#> S1_165 0 0 FALSE FALSE FALSE FALSE 0
#>
#> $internalWater
#> Einst RootCrownPsi LeafPsi StemPsi LeafSympPsi StemSympPsi LeafPLC
#> T1_148 0 -0.033 -0.033 -0.033 -0.033 -0.033 0
#> T2_168 0 -0.033 -0.033 -0.033 -0.033 -0.033 0
#> S1_165 0 -0.033 -0.033 -0.033 -0.033 -0.033 0
#> StemPLC
#> T1_148 0
#> T2_168 0
#> S1_165 0
#>
#> $internalLAIDistribution
#> $internalLAIDistribution$PrevLAIexpanded
#> [1] 0 0 0
#>
#> $internalLAIDistribution$PrevLAIdead
#> [1] 0 0 0
#>
#> $internalLAIDistribution$PARcohort
#> [1] 0 0 0
#>
#> $internalLAIDistribution$live
#> T1_148 T2_168 S1_165
#> 1 0 0 0
#> 2 0 0 0
#> 3 0 0 0
#> 4 0 0 0
#> 5 0 0 0
#> 6 0 0 0
#> 7 0 0 0
#> 8 0 0 0
#> 9 0 0 0
#> 10 0 0 0
#> 11 0 0 0
#> 12 0 0 0
#> 13 0 0 0
#> 14 0 0 0
#> 15 0 0 0
#> 16 0 0 0
#> 17 0 0 0
#> 18 0 0 0
#> 19 0 0 0
#> 20 0 0 0
#> 21 0 0 0
#> 22 0 0 0
#> 23 0 0 0
#> 24 0 0 0
#> 25 0 0 0
#> 26 0 0 0
#> 27 0 0 0
#> 28 0 0 0
#>
#> $internalLAIDistribution$expanded
#> T1_148 T2_168 S1_165
#> 1 0 0 0
#> 2 0 0 0
#> 3 0 0 0
#> 4 0 0 0
#> 5 0 0 0
#> 6 0 0 0
#> 7 0 0 0
#> 8 0 0 0
#> 9 0 0 0
#> 10 0 0 0
#> 11 0 0 0
#> 12 0 0 0
#> 13 0 0 0
#> 14 0 0 0
#> 15 0 0 0
#> 16 0 0 0
#> 17 0 0 0
#> 18 0 0 0
#> 19 0 0 0
#> 20 0 0 0
#> 21 0 0 0
#> 22 0 0 0
#> 23 0 0 0
#> 24 0 0 0
#> 25 0 0 0
#> 26 0 0 0
#> 27 0 0 0
#> 28 0 0 0
#>
#> $internalLAIDistribution$dead
#> T1_148 T2_168 S1_165
#> 1 0 0 0
#> 2 0 0 0
#> 3 0 0 0
#> 4 0 0 0
#> 5 0 0 0
#> 6 0 0 0
#> 7 0 0 0
#> 8 0 0 0
#> 9 0 0 0
#> 10 0 0 0
#> 11 0 0 0
#> 12 0 0 0
#> 13 0 0 0
#> 14 0 0 0
#> 15 0 0 0
#> 16 0 0 0
#> 17 0 0 0
#> 18 0 0 0
#> 19 0 0 0
#> 20 0 0 0
#> 21 0 0 0
#> 22 0 0 0
#> 23 0 0 0
#> 24 0 0 0
#> 25 0 0 0
#> 26 0 0 0
#> 27 0 0 0
#> 28 0 0 0
#>
#>
#> $internalFCCS
#> data frame with 0 columns and 0 rows
#>
#> attr(,"class")
#> [1] "spwbInput" "list"
# Prepare input for 'Sureau' transpiration mode
control <- defaultControl("Sureau")
spwbInput(exampleforest,examplesoil,SpParamsMED, control)
#> $control
#> $control$fillMissingRootParams
#> [1] TRUE
#>
#> $control$fillMissingSpParams
#> [1] TRUE
#>
#> $control$fillMissingWithGenusParams
#> [1] TRUE
#>
#> $control$verbose
#> [1] TRUE
#>
#> $control$subdailyResults
#> [1] FALSE
#>
#> $control$standResults
#> [1] TRUE
#>
#> $control$soilResults
#> [1] TRUE
#>
#> $control$snowResults
#> [1] TRUE
#>
#> $control$plantResults
#> [1] TRUE
#>
#> $control$plantWaterBalanceResults
#> [1] TRUE
#>
#> $control$labileCarbonBalanceResults
#> [1] TRUE
#>
#> $control$plantStructureResults
#> [1] TRUE
#>
#> $control$growthMortalityResults
#> [1] TRUE
#>
#> $control$leafResults
#> [1] TRUE
#>
#> $control$temperatureResults
#> [1] TRUE
#>
#> $control$fireHazardResults
#> [1] FALSE
#>
#> $control$fireHazardStandardWind
#> [1] NA
#>
#> $control$fireHazardStandardDFMC
#> [1] NA
#>
#> $control$transpirationMode
#> [1] "Sureau"
#>
#> $control$soilFunctions
#> [1] "VG"
#>
#> $control$VG_PTF
#> [1] "Toth"
#>
#> $control$ndailysteps
#> [1] 24
#>
#> $control$max_nsubsteps_soil
#> [1] 300
#>
#> $control$defaultWindSpeed
#> [1] 2.5
#>
#> $control$defaultCO2
#> [1] 386
#>
#> $control$defaultRainfallIntensityPerMonth
#> [1] 1.5 1.5 1.5 1.5 1.5 1.5 5.6 5.6 5.6 5.6 5.6 1.5
#>
#> $control$leafPhenology
#> [1] TRUE
#>
#> $control$bareSoilEvaporation
#> [1] TRUE
#>
#> $control$unlimitedSoilWater
#> [1] FALSE
#>
#> $control$interceptionMode
#> [1] "Gash1995"
#>
#> $control$infiltrationMode
#> [1] "GreenAmpt1911"
#>
#> $control$infiltrationCorrection
#> [1] 5
#>
#> $control$soilDomains
#> [1] "buckets"
#>
#> $control$rhizosphereOverlap
#> [1] "total"
#>
#> $control$unfoldingDD
#> [1] 300
#>
#> $control$verticalLayerSize
#> [1] 100
#>
#> $control$windMeasurementHeight
#> [1] 200
#>
#> $control$segmentedXylemVulnerability
#> [1] FALSE
#>
#> $control$stemCavitationRecovery
#> [1] "annual"
#>
#> $control$leafCavitationRecovery
#> [1] "annual"
#>
#> $control$lfmcComponent
#> [1] "fine"
#>
#> $control$hydraulicRedistributionFraction
#> [1] 0.1
#>
#> $control$nsubsteps_canopy
#> [1] 3600
#>
#> $control$taper
#> [1] TRUE
#>
#> $control$multiLayerBalance
#> [1] FALSE
#>
#> $control$sapFluidityVariation
#> [1] TRUE
#>
#> $control$TPhase_gmin
#> [1] 37.5
#>
#> $control$Q10_1_gmin
#> [1] 1.2
#>
#> $control$Q10_2_gmin
#> [1] 4.8
#>
#> $control$rootRadialConductance
#> [1] 4
#>
#> $control$averageFracRhizosphereResistance
#> [1] 0.15
#>
#> $control$thermalCapacityLAI
#> [1] 1e+06
#>
#> $control$boundaryLayerSize
#> [1] 2000
#>
#> $control$cavitationRecoveryMaximumRate
#> [1] 0.05
#>
#> $control$sunlitShade
#> [1] TRUE
#>
#> $control$numericParams
#> $control$numericParams$maxNsteps
#> [1] 400
#>
#> $control$numericParams$ntrial
#> [1] 200
#>
#> $control$numericParams$psiTol
#> [1] 1e-04
#>
#> $control$numericParams$ETol
#> [1] 1e-07
#>
#>
#> $control$leafCavitationEffects
#> [1] FALSE
#>
#> $control$stemCavitationEffects
#> [1] TRUE
#>
#> $control$stomatalSubmodel
#> [1] "Baldocchi"
#>
#> $control$plantCapacitance
#> [1] TRUE
#>
#> $control$cavitationFlux
#> [1] TRUE
#>
#> $control$soilDisconnection
#> [1] FALSE
#>
#> $control$leafCuticularTranspiration
#> [1] TRUE
#>
#> $control$stemCuticularTranspiration
#> [1] FALSE
#>
#> $control$C_SApoInit
#> [1] 2e-05
#>
#> $control$C_LApoInit
#> [1] 1e-05
#>
#> $control$k_SSym
#> [1] 0.26
#>
#> $control$fractionLeafSymplasm
#> [1] 0.5
#>
#> $control$gs_NightFrac
#> [1] 0.05
#>
#> $control$JarvisPAR
#> [1] 0.003
#>
#> $control$fTRBToLeaf
#> [1] 0.8
#>
#> $control$subdailyCarbonBalance
#> [1] FALSE
#>
#> $control$allowDessication
#> [1] TRUE
#>
#> $control$allowStarvation
#> [1] TRUE
#>
#> $control$sinkLimitation
#> [1] TRUE
#>
#> $control$shrubDynamics
#> [1] TRUE
#>
#> $control$herbDynamics
#> [1] TRUE
#>
#> $control$allocationStrategy
#> [1] "Al2As"
#>
#> $control$phloemConductanceFactor
#> [1] 0.2
#>
#> $control$nonSugarConcentration
#> [1] 0.25
#>
#> $control$equilibriumOsmoticConcentration
#> $control$equilibriumOsmoticConcentration$leaf
#> [1] 0.8
#>
#> $control$equilibriumOsmoticConcentration$sapwood
#> [1] 0.6
#>
#>
#> $control$minimumRelativeStarchForGrowth
#> [1] 0.5
#>
#> $control$constructionCosts
#> $control$constructionCosts$leaf
#> [1] 1.5
#>
#> $control$constructionCosts$sapwood
#> [1] 1.47
#>
#> $control$constructionCosts$fineroot
#> [1] 1.3
#>
#>
#> $control$senescenceRates
#> $control$senescenceRates$sapwood
#> [1] 0.000135
#>
#> $control$senescenceRates$fineroot
#> [1] 0.001897231
#>
#>
#> $control$maximumRelativeGrowthRates
#> $control$maximumRelativeGrowthRates$leaf
#> [1] 0.09
#>
#> $control$maximumRelativeGrowthRates$cambium
#> [1] 0.0025
#>
#> $control$maximumRelativeGrowthRates$sapwood
#> [1] 0.002
#>
#> $control$maximumRelativeGrowthRates$fineroot
#> [1] 0.1
#>
#>
#> $control$mortalityMode
#> [1] "density/deterministic"
#>
#> $control$mortalityBaselineRate
#> [1] 0.0015
#>
#> $control$mortalityRelativeSugarThreshold
#> [1] 0.4
#>
#> $control$mortalityRWCThreshold
#> [1] 0.4
#>
#> $control$recrTreeDBH
#> [1] 1
#>
#> $control$recrTreeDensity
#> [1] 3000
#>
#> $control$ingrowthTreeDBH
#> [1] 7.5
#>
#> $control$ingrowthTreeDensity
#> [1] 127
#>
#> $control$allowSeedBankDynamics
#> [1] TRUE
#>
#> $control$allowRecruitment
#> [1] TRUE
#>
#> $control$allowResprouting
#> [1] TRUE
#>
#> $control$recruitmentMode
#> [1] "stochastic"
#>
#> $control$removeEmptyCohorts
#> [1] TRUE
#>
#> $control$minimumTreeCohortDensity
#> [1] 1
#>
#> $control$minimumShrubCohortCover
#> [1] 0.01
#>
#> $control$dynamicallyMergeCohorts
#> [1] TRUE
#>
#> $control$keepCohortsWithObsID
#> [1] FALSE
#>
#> $control$seedRain
#> NULL
#>
#> $control$seedProductionTreeHeight
#> [1] 300
#>
#> $control$seedProductionShrubHeight
#> [1] 30
#>
#> $control$probRecr
#> [1] 0.05
#>
#> $control$minTempRecr
#> [1] 0
#>
#> $control$minMoistureRecr
#> [1] 0.3
#>
#> $control$minFPARRecr
#> [1] 10
#>
#> $control$recrTreeHeight
#> [1] 620
#>
#> $control$recrShrubCover
#> [1] 1
#>
#> $control$recrShrubHeight
#> [1] 25
#>
#> $control$recrTreeZ50
#> [1] 100
#>
#> $control$recrShrubZ50
#> [1] 50
#>
#> $control$recrTreeZ95
#> [1] 1000
#>
#> $control$recrShrubZ95
#> [1] 500
#>
#>
#> $soil
#> widths sand clay usda om nitrogen bd rfc macro Ksat VG_alpha
#> 1 300 25 25 Silt loam NA NA 1.5 25 0.0485 5401.471 89.16112
#> 2 700 25 25 Silt loam NA NA 1.5 45 0.0485 5401.471 89.16112
#> 3 1000 25 25 Silt loam NA NA 1.5 75 0.0485 5401.471 89.16112
#> 4 2000 25 25 Silt loam NA NA 1.5 95 0.0485 5401.471 89.16112
#> VG_n VG_theta_res VG_theta_sat W Temp
#> 1 1.303861 0.041 0.423715 1 NA
#> 2 1.303861 0.041 0.423715 1 NA
#> 3 1.303861 0.041 0.423715 1 NA
#> 4 1.303861 0.041 0.423715 1 NA
#>
#> $snowpack
#> [1] 0
#>
#> $canopy
#> zlow zmid zup LAIlive LAIexpanded LAIdead Tair Cair VPair
#> 1 0 50 100 NA NA NA NA NA NA
#> 2 100 150 200 NA NA NA NA NA NA
#> 3 200 250 300 NA NA NA NA NA NA
#> 4 300 350 400 NA NA NA NA NA NA
#> 5 400 450 500 NA NA NA NA NA NA
#> 6 500 550 600 NA NA NA NA NA NA
#> 7 600 650 700 NA NA NA NA NA NA
#> 8 700 750 800 NA NA NA NA NA NA
#> 9 800 850 900 NA NA NA NA NA NA
#> 10 900 950 1000 NA NA NA NA NA NA
#> 11 1000 1050 1100 NA NA NA NA NA NA
#> 12 1100 1150 1200 NA NA NA NA NA NA
#> 13 1200 1250 1300 NA NA NA NA NA NA
#> 14 1300 1350 1400 NA NA NA NA NA NA
#> 15 1400 1450 1500 NA NA NA NA NA NA
#> 16 1500 1550 1600 NA NA NA NA NA NA
#> 17 1600 1650 1700 NA NA NA NA NA NA
#> 18 1700 1750 1800 NA NA NA NA NA NA
#> 19 1800 1850 1900 NA NA NA NA NA NA
#> 20 1900 1950 2000 NA NA NA NA NA NA
#> 21 2000 2050 2100 NA NA NA NA NA NA
#> 22 2100 2150 2200 NA NA NA NA NA NA
#> 23 2200 2250 2300 NA NA NA NA NA NA
#> 24 2300 2350 2400 NA NA NA NA NA NA
#> 25 2400 2450 2500 NA NA NA NA NA NA
#> 26 2500 2550 2600 NA NA NA NA NA NA
#> 27 2600 2650 2700 NA NA NA NA NA NA
#> 28 2700 2750 2800 NA NA NA NA NA NA
#>
#> $herbLAI
#> [1] 0.1736369
#>
#> $herbLAImax
#> [1] 0.252
#>
#> $cohorts
#> SP Name
#> T1_148 148 Pinus halepensis
#> T2_168 168 Quercus ilex
#> S1_165 165 Quercus coccifera
#>
#> $above
#> H CR LAI_live LAI_expanded LAI_dead ObsID
#> T1_148 800 0.6605196 0.84874773 0.84874773 0 <NA>
#> T2_168 660 0.6055642 0.70557382 0.70557382 0 <NA>
#> S1_165 80 0.8032817 0.03062604 0.03062604 0 <NA>
#>
#> $below
#> Z50 Z95 Z100
#> T1_148 100 600 NA
#> T2_168 300 1000 NA
#> S1_165 200 1000 NA
#>
#> $belowLayers
#> $belowLayers$V
#> 1 2 3 4
#> T1_148 0.8604899 0.1194556 0.01511005 0.004944476
#> T2_168 0.5008953 0.4505941 0.04064831 0.007862284
#> S1_165 0.6799879 0.2737911 0.03567632 0.010544678
#>
#> $belowLayers$L
#> 1 2 3 4
#> T1_148 2289.062 1566.552 2250.052 4226.166
#> T2_168 1817.571 2100.346 2410.127 4285.194
#> S1_165 1085.030 1380.808 2170.587 4146.637
#>
#> $belowLayers$VGrhizo_kmax
#> 1 2 3 4
#> T1_148 278101462 38606817 4883412 1598004
#> T2_168 406976825 366107176 33026706 6388096
#> S1_165 1116059122 449371399 58555276 17306902
#>
#> $belowLayers$VCroot_kmax
#> 1 2 3 4
#> T1_148 2.382795 0.4833484 0.04256689 0.007416044
#> T2_168 1.568929 1.2213562 0.09601747 0.010445417
#> S1_165 2.407779 0.7618041 0.06314806 0.009770000
#>
#> $belowLayers$Wpool
#> 1 2 3 4
#> T1_148 1 1 1 1
#> T2_168 1 1 1 1
#> S1_165 1 1 1 1
#>
#> $belowLayers$RhizoPsi
#> 1 2 3 4
#> T1_148 -0.033 -0.033 -0.033 -0.033
#> T2_168 -0.033 -0.033 -0.033 -0.033
#> S1_165 -0.033 -0.033 -0.033 -0.033
#>
#>
#> $paramsPhenology
#> PhenologyType LeafDuration t0gdd Sgdd Tbgdd Ssen Phsen Tbsen xsen
#> T1_148 oneflush-evergreen 2.536875 50.0 200.0 0.00 8268 12.5 28.5 2
#> T2_168 oneflush-evergreen 2.183837 54.5 240.7 4.34 10178 12.5 28.5 2
#> S1_165 oneflush-evergreen 1.250000 54.5 240.7 4.34 10178 12.5 28.5 2
#> ysen
#> T1_148 2
#> T2_168 2
#> S1_165 2
#>
#> $paramsAnatomy
#> Hmed Al2As SLA LeafWidth LeafDensity WoodDensity FineRootDensity
#> T1_148 850 1317.523 5.140523 0.1384772 0.2982842 0.6077016 0.2982842
#> T2_168 500 3908.823 6.340000 1.7674359 0.4893392 0.9008264 0.4893392
#> S1_165 80 4189.325 4.980084 1.3761085 0.3709679 0.4389106 0.3709679
#> conduit2sapwood SRL RLD r635
#> T1_148 0.9236406 3172.572 10 1.964226
#> T2_168 0.6238125 4398.812 10 1.805872
#> S1_165 0.6238125 4398.812 10 2.289452
#>
#> $paramsInterception
#> LeafAngle LeafAngleSD Beta_p Beta_q ClumpingIndex kPAR alphaSWR
#> T1_148 53.7 21.55 1.907817 1.289641 0.75 0.50 0.7
#> T2_168 53.7 21.55 1.907817 1.289641 0.75 0.55 0.7
#> S1_165 53.7 21.55 1.907817 1.289641 0.75 0.55 0.7
#> gammaSWR g
#> T1_148 0.14 1.0
#> T2_168 0.18 0.5
#> S1_165 0.18 0.5
#>
#> $paramsTranspiration
#> Gswmin Gswmax Gsw_AC_slope Gs_P50 Gs_slope Vmax298 Jmax298
#> T1_148 0.003086667 0.2850000 6.238912 -2.303772 30 72.19617 124.1687
#> T2_168 0.004473333 0.2007222 4.957957 -1.964085 30 68.51600 118.7863
#> S1_165 0.010455247 0.2830167 6.590920 -2.663333 30 62.78100 118.4486
#> Kmax_stemxylem Kmax_rootxylem VCleaf_kmax VCleafapo_kmax VCleaf_slope
#> T1_148 0.15 0.60 4.000000 8.00000 68.30291
#> T2_168 0.40 1.60 4.000000 8.00000 14.60786
#> S1_165 0.29 1.16 9.579077 19.15815 12.52202
#> VCleaf_P50 VCleaf_c VCleaf_d kleaf_symp VCstem_kmax VCstem_slope
#> T1_148 -5.139633 12.709999 -5.290000 8.00000 1.339563 68.30291
#> T2_168 -6.964747 3.560000 -7.720000 8.00000 1.620936 14.60786
#> S1_165 -6.980000 3.095442 -7.857378 19.15815 4.599269 12.52202
#> VCstem_P50 VCstem_c VCstem_d kstem_symp VCroot_kmax VCroot_slope
#> T1_148 -5.139633 12.709999 -5.290000 0.26 2.916127 68.30291
#> T2_168 -6.964747 3.560000 -7.720000 0.26 2.896748 14.60786
#> S1_165 -6.980000 3.095442 -7.857378 0.26 3.242501 12.52202
#> VCroot_P50 VCroot_c VCroot_d VGrhizo_kmax Plant_kmax FR_leaf
#> T1_148 -5.139633 12.709999 -5.290000 323189695 0.7465846 0.1866462
#> T2_168 -6.964747 3.560000 -7.720000 812498804 0.8249857 0.2062464
#> S1_165 -6.980000 3.095442 -7.857378 1641292700 1.5867376 0.1656462
#> FR_stem FR_root
#> T1_148 0.5573346 0.2560193
#> T2_168 0.5089563 0.2847972
#> S1_165 0.3449978 0.4893561
#>
#> $paramsWaterStorage
#> maxFMC LeafPI0 LeafEPS LeafAF Vleaf StemPI0 StemEPS
#> T1_148 126.03063 -1.591429 8.918571 0.3525 0.5258525 -2.008039 13.256355
#> T2_168 93.15304 -1.483333 19.260000 0.1700 0.2199087 -3.227438 46.420610
#> S1_165 96.53441 -2.370000 17.230000 0.2400 0.4108968 -1.305868 6.297155
#> StemAF Vsapwood
#> T1_148 0.9236406 6.174277
#> T2_168 0.6238125 1.278142
#> S1_165 0.6238125 1.064511
#>
#> $internalPhenology
#> gdd sen budFormation leafUnfolding leafSenescence leafDormancy phi
#> T1_148 0 0 FALSE FALSE FALSE FALSE 0
#> T2_168 0 0 FALSE FALSE FALSE FALSE 0
#> S1_165 0 0 FALSE FALSE FALSE FALSE 0
#>
#> $internalWater
#> Einst Elim Emin_L Emin_S RootCrownPsi LeafPsi StemPsi LeafSympPsi
#> T1_148 0 0 0 0 -0.033 -0.033 -0.033 -0.033
#> T2_168 0 0 0 0 -0.033 -0.033 -0.033 -0.033
#> S1_165 0 0 0 0 -0.033 -0.033 -0.033 -0.033
#> StemSympPsi LeafPLC StemPLC
#> T1_148 -0.033 0 0
#> T2_168 -0.033 0 0
#> S1_165 -0.033 0 0
#>
#> $internalLAIDistribution
#> $internalLAIDistribution$PrevLAIexpanded
#> [1] 0 0 0
#>
#> $internalLAIDistribution$PrevLAIdead
#> [1] 0 0 0
#>
#> $internalLAIDistribution$PARcohort
#> [1] 0 0 0
#>
#> $internalLAIDistribution$live
#> T1_148 T2_168 S1_165
#> 1 0 0 0
#> 2 0 0 0
#> 3 0 0 0
#> 4 0 0 0
#> 5 0 0 0
#> 6 0 0 0
#> 7 0 0 0
#> 8 0 0 0
#> 9 0 0 0
#> 10 0 0 0
#> 11 0 0 0
#> 12 0 0 0
#> 13 0 0 0
#> 14 0 0 0
#> 15 0 0 0
#> 16 0 0 0
#> 17 0 0 0
#> 18 0 0 0
#> 19 0 0 0
#> 20 0 0 0
#> 21 0 0 0
#> 22 0 0 0
#> 23 0 0 0
#> 24 0 0 0
#> 25 0 0 0
#> 26 0 0 0
#> 27 0 0 0
#> 28 0 0 0
#>
#> $internalLAIDistribution$expanded
#> T1_148 T2_168 S1_165
#> 1 0 0 0
#> 2 0 0 0
#> 3 0 0 0
#> 4 0 0 0
#> 5 0 0 0
#> 6 0 0 0
#> 7 0 0 0
#> 8 0 0 0
#> 9 0 0 0
#> 10 0 0 0
#> 11 0 0 0
#> 12 0 0 0
#> 13 0 0 0
#> 14 0 0 0
#> 15 0 0 0
#> 16 0 0 0
#> 17 0 0 0
#> 18 0 0 0
#> 19 0 0 0
#> 20 0 0 0
#> 21 0 0 0
#> 22 0 0 0
#> 23 0 0 0
#> 24 0 0 0
#> 25 0 0 0
#> 26 0 0 0
#> 27 0 0 0
#> 28 0 0 0
#>
#> $internalLAIDistribution$dead
#> T1_148 T2_168 S1_165
#> 1 0 0 0
#> 2 0 0 0
#> 3 0 0 0
#> 4 0 0 0
#> 5 0 0 0
#> 6 0 0 0
#> 7 0 0 0
#> 8 0 0 0
#> 9 0 0 0
#> 10 0 0 0
#> 11 0 0 0
#> 12 0 0 0
#> 13 0 0 0
#> 14 0 0 0
#> 15 0 0 0
#> 16 0 0 0
#> 17 0 0 0
#> 18 0 0 0
#> 19 0 0 0
#> 20 0 0 0
#> 21 0 0 0
#> 22 0 0 0
#> 23 0 0 0
#> 24 0 0 0
#> 25 0 0 0
#> 26 0 0 0
#> 27 0 0 0
#> 28 0 0 0
#>
#>
#> $internalFCCS
#> data frame with 0 columns and 0 rows
#>
#> attr(,"class")
#> [1] "spwbInput" "list"
# Example of initialization from a forest
# described using LAI and crown ratio
control <- defaultControl("Granier")
spwbInput(exampleforest2, examplesoil, SpParamsMED, control)
#> $control
#> $control$fillMissingRootParams
#> [1] TRUE
#>
#> $control$fillMissingSpParams
#> [1] TRUE
#>
#> $control$fillMissingWithGenusParams
#> [1] TRUE
#>
#> $control$verbose
#> [1] TRUE
#>
#> $control$subdailyResults
#> [1] FALSE
#>
#> $control$standResults
#> [1] TRUE
#>
#> $control$soilResults
#> [1] TRUE
#>
#> $control$snowResults
#> [1] TRUE
#>
#> $control$plantResults
#> [1] TRUE
#>
#> $control$plantWaterBalanceResults
#> [1] TRUE
#>
#> $control$labileCarbonBalanceResults
#> [1] TRUE
#>
#> $control$plantStructureResults
#> [1] TRUE
#>
#> $control$growthMortalityResults
#> [1] TRUE
#>
#> $control$leafResults
#> [1] TRUE
#>
#> $control$temperatureResults
#> [1] TRUE
#>
#> $control$fireHazardResults
#> [1] FALSE
#>
#> $control$fireHazardStandardWind
#> [1] NA
#>
#> $control$fireHazardStandardDFMC
#> [1] NA
#>
#> $control$transpirationMode
#> [1] "Granier"
#>
#> $control$soilFunctions
#> [1] "VG"
#>
#> $control$VG_PTF
#> [1] "Toth"
#>
#> $control$ndailysteps
#> [1] 24
#>
#> $control$max_nsubsteps_soil
#> [1] 300
#>
#> $control$defaultWindSpeed
#> [1] 2.5
#>
#> $control$defaultCO2
#> [1] 386
#>
#> $control$defaultRainfallIntensityPerMonth
#> [1] 1.5 1.5 1.5 1.5 1.5 1.5 5.6 5.6 5.6 5.6 5.6 1.5
#>
#> $control$leafPhenology
#> [1] TRUE
#>
#> $control$bareSoilEvaporation
#> [1] TRUE
#>
#> $control$unlimitedSoilWater
#> [1] FALSE
#>
#> $control$interceptionMode
#> [1] "Gash1995"
#>
#> $control$infiltrationMode
#> [1] "GreenAmpt1911"
#>
#> $control$infiltrationCorrection
#> [1] 5
#>
#> $control$soilDomains
#> [1] "buckets"
#>
#> $control$rhizosphereOverlap
#> [1] "total"
#>
#> $control$unfoldingDD
#> [1] 300
#>
#> $control$verticalLayerSize
#> [1] 100
#>
#> $control$windMeasurementHeight
#> [1] 200
#>
#> $control$segmentedXylemVulnerability
#> [1] TRUE
#>
#> $control$stemCavitationRecovery
#> [1] "annual"
#>
#> $control$leafCavitationRecovery
#> [1] "annual"
#>
#> $control$lfmcComponent
#> [1] "fine"
#>
#> $control$hydraulicRedistributionFraction
#> [1] 0.1
#>
#> $control$nsubsteps_canopy
#> [1] 3600
#>
#> $control$taper
#> [1] TRUE
#>
#> $control$multiLayerBalance
#> [1] FALSE
#>
#> $control$sapFluidityVariation
#> [1] TRUE
#>
#> $control$TPhase_gmin
#> [1] 37.5
#>
#> $control$Q10_1_gmin
#> [1] 1.2
#>
#> $control$Q10_2_gmin
#> [1] 4.8
#>
#> $control$rootRadialConductance
#> [1] 4
#>
#> $control$averageFracRhizosphereResistance
#> [1] 0.15
#>
#> $control$thermalCapacityLAI
#> [1] 1e+06
#>
#> $control$boundaryLayerSize
#> [1] 2000
#>
#> $control$cavitationRecoveryMaximumRate
#> [1] 0.05
#>
#> $control$sunlitShade
#> [1] TRUE
#>
#> $control$numericParams
#> $control$numericParams$maxNsteps
#> [1] 400
#>
#> $control$numericParams$ntrial
#> [1] 200
#>
#> $control$numericParams$psiTol
#> [1] 1e-04
#>
#> $control$numericParams$ETol
#> [1] 1e-07
#>
#>
#> $control$leafCavitationEffects
#> [1] FALSE
#>
#> $control$stemCavitationEffects
#> [1] TRUE
#>
#> $control$stomatalSubmodel
#> [1] "Baldocchi"
#>
#> $control$plantCapacitance
#> [1] TRUE
#>
#> $control$cavitationFlux
#> [1] TRUE
#>
#> $control$soilDisconnection
#> [1] FALSE
#>
#> $control$leafCuticularTranspiration
#> [1] TRUE
#>
#> $control$stemCuticularTranspiration
#> [1] FALSE
#>
#> $control$C_SApoInit
#> [1] 2e-05
#>
#> $control$C_LApoInit
#> [1] 1e-05
#>
#> $control$k_SSym
#> [1] 0.26
#>
#> $control$fractionLeafSymplasm
#> [1] 0.5
#>
#> $control$gs_NightFrac
#> [1] 0.05
#>
#> $control$JarvisPAR
#> [1] 0.003
#>
#> $control$fTRBToLeaf
#> [1] 0.8
#>
#> $control$subdailyCarbonBalance
#> [1] FALSE
#>
#> $control$allowDessication
#> [1] TRUE
#>
#> $control$allowStarvation
#> [1] TRUE
#>
#> $control$sinkLimitation
#> [1] TRUE
#>
#> $control$shrubDynamics
#> [1] TRUE
#>
#> $control$herbDynamics
#> [1] TRUE
#>
#> $control$allocationStrategy
#> [1] "Al2As"
#>
#> $control$phloemConductanceFactor
#> [1] 0.2
#>
#> $control$nonSugarConcentration
#> [1] 0.25
#>
#> $control$equilibriumOsmoticConcentration
#> $control$equilibriumOsmoticConcentration$leaf
#> [1] 0.8
#>
#> $control$equilibriumOsmoticConcentration$sapwood
#> [1] 0.6
#>
#>
#> $control$minimumRelativeStarchForGrowth
#> [1] 0.5
#>
#> $control$constructionCosts
#> $control$constructionCosts$leaf
#> [1] 1.5
#>
#> $control$constructionCosts$sapwood
#> [1] 1.47
#>
#> $control$constructionCosts$fineroot
#> [1] 1.3
#>
#>
#> $control$senescenceRates
#> $control$senescenceRates$sapwood
#> [1] 0.000135
#>
#> $control$senescenceRates$fineroot
#> [1] 0.001897231
#>
#>
#> $control$maximumRelativeGrowthRates
#> $control$maximumRelativeGrowthRates$leaf
#> [1] 0.09
#>
#> $control$maximumRelativeGrowthRates$cambium
#> [1] 0.0025
#>
#> $control$maximumRelativeGrowthRates$sapwood
#> [1] 0.002
#>
#> $control$maximumRelativeGrowthRates$fineroot
#> [1] 0.1
#>
#>
#> $control$mortalityMode
#> [1] "density/deterministic"
#>
#> $control$mortalityBaselineRate
#> [1] 0.0015
#>
#> $control$mortalityRelativeSugarThreshold
#> [1] 0.4
#>
#> $control$mortalityRWCThreshold
#> [1] 0.4
#>
#> $control$recrTreeDBH
#> [1] 1
#>
#> $control$recrTreeDensity
#> [1] 3000
#>
#> $control$ingrowthTreeDBH
#> [1] 7.5
#>
#> $control$ingrowthTreeDensity
#> [1] 127
#>
#> $control$allowSeedBankDynamics
#> [1] TRUE
#>
#> $control$allowRecruitment
#> [1] TRUE
#>
#> $control$allowResprouting
#> [1] TRUE
#>
#> $control$recruitmentMode
#> [1] "stochastic"
#>
#> $control$removeEmptyCohorts
#> [1] TRUE
#>
#> $control$minimumTreeCohortDensity
#> [1] 1
#>
#> $control$minimumShrubCohortCover
#> [1] 0.01
#>
#> $control$dynamicallyMergeCohorts
#> [1] TRUE
#>
#> $control$keepCohortsWithObsID
#> [1] FALSE
#>
#> $control$seedRain
#> NULL
#>
#> $control$seedProductionTreeHeight
#> [1] 300
#>
#> $control$seedProductionShrubHeight
#> [1] 30
#>
#> $control$probRecr
#> [1] 0.05
#>
#> $control$minTempRecr
#> [1] 0
#>
#> $control$minMoistureRecr
#> [1] 0.3
#>
#> $control$minFPARRecr
#> [1] 10
#>
#> $control$recrTreeHeight
#> [1] 620
#>
#> $control$recrShrubCover
#> [1] 1
#>
#> $control$recrShrubHeight
#> [1] 25
#>
#> $control$recrTreeZ50
#> [1] 100
#>
#> $control$recrShrubZ50
#> [1] 50
#>
#> $control$recrTreeZ95
#> [1] 1000
#>
#> $control$recrShrubZ95
#> [1] 500
#>
#>
#> $soil
#> widths sand clay usda om nitrogen bd rfc macro Ksat VG_alpha
#> 1 300 25 25 Silt loam NA NA 1.5 25 0.0485 5401.471 89.16112
#> 2 700 25 25 Silt loam NA NA 1.5 45 0.0485 5401.471 89.16112
#> 3 1000 25 25 Silt loam NA NA 1.5 75 0.0485 5401.471 89.16112
#> 4 2000 25 25 Silt loam NA NA 1.5 95 0.0485 5401.471 89.16112
#> VG_n VG_theta_res VG_theta_sat W Temp
#> 1 1.303861 0.041 0.423715 1 NA
#> 2 1.303861 0.041 0.423715 1 NA
#> 3 1.303861 0.041 0.423715 1 NA
#> 4 1.303861 0.041 0.423715 1 NA
#>
#> $snowpack
#> [1] 0
#>
#> $canopy
#> zlow zmid zup LAIlive LAIexpanded LAIdead Tair Cair VPair
#> 1 0 50 100 NA NA NA NA NA NA
#> 2 100 150 200 NA NA NA NA NA NA
#> 3 200 250 300 NA NA NA NA NA NA
#> 4 300 350 400 NA NA NA NA NA NA
#> 5 400 450 500 NA NA NA NA NA NA
#> 6 500 550 600 NA NA NA NA NA NA
#> 7 600 650 700 NA NA NA NA NA NA
#> 8 700 750 800 NA NA NA NA NA NA
#> 9 800 850 900 NA NA NA NA NA NA
#> 10 900 950 1000 NA NA NA NA NA NA
#> 11 1000 1050 1100 NA NA NA NA NA NA
#> 12 1100 1150 1200 NA NA NA NA NA NA
#> 13 1200 1250 1300 NA NA NA NA NA NA
#> 14 1300 1350 1400 NA NA NA NA NA NA
#> 15 1400 1450 1500 NA NA NA NA NA NA
#> 16 1500 1550 1600 NA NA NA NA NA NA
#> 17 1600 1650 1700 NA NA NA NA NA NA
#> 18 1700 1750 1800 NA NA NA NA NA NA
#> 19 1800 1850 1900 NA NA NA NA NA NA
#> 20 1900 1950 2000 NA NA NA NA NA NA
#> 21 2000 2050 2100 NA NA NA NA NA NA
#> 22 2100 2150 2200 NA NA NA NA NA NA
#> 23 2200 2250 2300 NA NA NA NA NA NA
#> 24 2300 2350 2400 NA NA NA NA NA NA
#> 25 2400 2450 2500 NA NA NA NA NA NA
#> 26 2500 2550 2600 NA NA NA NA NA NA
#> 27 2600 2650 2700 NA NA NA NA NA NA
#> 28 2700 2750 2800 NA NA NA NA NA NA
#>
#> $herbLAI
#> [1] 0
#>
#> $herbLAImax
#> [1] 0
#>
#> $cohorts
#> SP Name
#> T1_148 148 Pinus halepensis
#> T2_168 168 Quercus ilex
#> S1_165 165 Quercus coccifera
#>
#> $above
#> H CR LAI_live LAI_expanded LAI_dead ObsID
#> T1_148 800 0.66 0.80 0.80 0 <NA>
#> T2_168 660 0.60 0.50 0.50 0 <NA>
#> S1_165 80 0.80 0.03 0.03 0 <NA>
#>
#> $below
#> Z50 Z95 Z100
#> T1_148 100 600 NA
#> T2_168 300 1000 NA
#> S1_165 200 1000 NA
#>
#> $belowLayers
#> $belowLayers$V
#> 1 2 3 4
#> T1_148 0.8604899 0.1194556 0.01511005 0.004944476
#> T2_168 0.5008953 0.4505941 0.04064831 0.007862284
#> S1_165 0.6799879 0.2737911 0.03567632 0.010544678
#>
#> $belowLayers$L
#> 1 2 3 4
#> T1_148 150 650 1500 3000
#> T2_168 150 650 1500 3000
#> S1_165 150 650 1500 3000
#>
#> $belowLayers$Wpool
#> 1 2 3 4
#> T1_148 1 1 1 1
#> T2_168 1 1 1 1
#> S1_165 1 1 1 1
#>
#>
#> $paramsPhenology
#> PhenologyType LeafDuration t0gdd Sgdd Tbgdd Ssen Phsen Tbsen xsen
#> T1_148 oneflush-evergreen 2.536875 50.0 200.0 0.00 8268 12.5 28.5 2
#> T2_168 oneflush-evergreen 2.183837 54.5 240.7 4.34 10178 12.5 28.5 2
#> S1_165 oneflush-evergreen 1.250000 54.5 240.7 4.34 10178 12.5 28.5 2
#> ysen
#> T1_148 2
#> T2_168 2
#> S1_165 2
#>
#> $paramsAnatomy
#> Al2As Ar2Al SLA LeafDensity WoodDensity FineRootDensity SRL
#> T1_148 1317.523 1 5.140523 0.2982842 0.6077016 0.2982842 3172.572
#> T2_168 3908.823 1 6.340000 0.4893392 0.9008264 0.4893392 4398.812
#> S1_165 4189.325 1 4.980084 0.3709679 0.4389106 0.3709679 4398.812
#> RLD r635
#> T1_148 10 1.964226
#> T2_168 10 1.805872
#> S1_165 10 2.289452
#>
#> $paramsInterception
#> kPAR kSWR g
#> T1_148 0.50 0.3703704 1.0
#> T2_168 0.55 0.4074074 0.5
#> S1_165 0.55 0.4074074 0.5
#>
#> $paramsTranspiration
#> Gswmin Tmax_LAI Tmax_LAIsq Psi_Extract Exp_Extract VCleaf_c
#> T1_148 0.003086667 0.1869849 -0.008372458 -0.9218219 1.504542 11.137050
#> T2_168 0.004473333 0.1251027 -0.005601615 -1.9726871 1.149052 1.339370
#> S1_165 0.010455247 0.1340000 -0.006000000 -2.1210726 1.300000 2.254991
#> VCleaf_d VCstem_c VCstem_d WUE WUE_par WUE_co2 WUE_vpd
#> T1_148 -2.380849 12.709999 -5.290000 8.525550 0.5239136 0.002586327 -0.2647169
#> T2_168 -2.582279 3.560000 -7.720000 8.968208 0.1412266 0.002413091 -0.5664879
#> S1_165 -3.133381 3.095442 -7.857378 7.900000 0.3643000 0.002757000 -0.4636000
#>
#> $paramsWaterStorage
#> maxFMC LeafPI0 LeafEPS LeafAF Vleaf StemPI0 StemEPS
#> T1_148 126.03063 -1.591429 8.918571 0.3525 0.5258525 -2.008039 13.256355
#> T2_168 93.15304 -1.483333 19.260000 0.1700 0.2199087 -3.227438 46.420610
#> S1_165 96.53441 -2.370000 17.230000 0.2400 0.4108968 -1.305868 6.297155
#> StemAF Vsapwood
#> T1_148 0.9236406 4.1638559
#> T2_168 0.6238125 0.8135590
#> S1_165 0.6238125 0.3177724
#>
#> $internalPhenology
#> gdd sen budFormation leafUnfolding leafSenescence leafDormancy phi
#> T1_148 0 0 FALSE FALSE FALSE FALSE 0
#> T2_168 0 0 FALSE FALSE FALSE FALSE 0
#> S1_165 0 0 FALSE FALSE FALSE FALSE 0
#>
#> $internalWater
#> PlantPsi LeafPLC StemPLC
#> T1_148 -0.033 0 0
#> T2_168 -0.033 0 0
#> S1_165 -0.033 0 0
#>
#> $internalLAIDistribution
#> $internalLAIDistribution$PrevLAIexpanded
#> [1] 0 0 0
#>
#> $internalLAIDistribution$PrevLAIdead
#> [1] 0 0 0
#>
#> $internalLAIDistribution$PARcohort
#> [1] 0 0 0
#>
#> $internalLAIDistribution$live
#> T1_148 T2_168 S1_165
#> 1 0 0 0
#> 2 0 0 0
#> 3 0 0 0
#> 4 0 0 0
#> 5 0 0 0
#> 6 0 0 0
#> 7 0 0 0
#> 8 0 0 0
#> 9 0 0 0
#> 10 0 0 0
#> 11 0 0 0
#> 12 0 0 0
#> 13 0 0 0
#> 14 0 0 0
#> 15 0 0 0
#> 16 0 0 0
#> 17 0 0 0
#> 18 0 0 0
#> 19 0 0 0
#> 20 0 0 0
#> 21 0 0 0
#> 22 0 0 0
#> 23 0 0 0
#> 24 0 0 0
#> 25 0 0 0
#> 26 0 0 0
#> 27 0 0 0
#> 28 0 0 0
#>
#> $internalLAIDistribution$expanded
#> T1_148 T2_168 S1_165
#> 1 0 0 0
#> 2 0 0 0
#> 3 0 0 0
#> 4 0 0 0
#> 5 0 0 0
#> 6 0 0 0
#> 7 0 0 0
#> 8 0 0 0
#> 9 0 0 0
#> 10 0 0 0
#> 11 0 0 0
#> 12 0 0 0
#> 13 0 0 0
#> 14 0 0 0
#> 15 0 0 0
#> 16 0 0 0
#> 17 0 0 0
#> 18 0 0 0
#> 19 0 0 0
#> 20 0 0 0
#> 21 0 0 0
#> 22 0 0 0
#> 23 0 0 0
#> 24 0 0 0
#> 25 0 0 0
#> 26 0 0 0
#> 27 0 0 0
#> 28 0 0 0
#>
#> $internalLAIDistribution$dead
#> T1_148 T2_168 S1_165
#> 1 0 0 0
#> 2 0 0 0
#> 3 0 0 0
#> 4 0 0 0
#> 5 0 0 0
#> 6 0 0 0
#> 7 0 0 0
#> 8 0 0 0
#> 9 0 0 0
#> 10 0 0 0
#> 11 0 0 0
#> 12 0 0 0
#> 13 0 0 0
#> 14 0 0 0
#> 15 0 0 0
#> 16 0 0 0
#> 17 0 0 0
#> 18 0 0 0
#> 19 0 0 0
#> 20 0 0 0
#> 21 0 0 0
#> 22 0 0 0
#> 23 0 0 0
#> 24 0 0 0
#> 25 0 0 0
#> 26 0 0 0
#> 27 0 0 0
#> 28 0 0 0
#>
#>
#> $internalFCCS
#> data frame with 0 columns and 0 rows
#>
#> attr(,"class")
#> [1] "spwbInput" "list"