Input for simulation models

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.

Usage

spwbInput(x, soil, SpParams, control)

growthInput(x, soil, SpParams, control)

Arguments

x

An object of class forest.

soil

An object of class data.frame or soil, containing soil parameters per soil layer.

SpParams

A data frame with species parameters (see SpParamsDefinition and SpParamsMED).

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 (see defaultControl).

• soil: A data frame with initialized soil parameters (see soil).

• 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 columns SP and Name.

• above: A data frame with columns such as H, CR and LAI_live (see internal function forest2aboveground).

• below: A data frame with columns Z50, Z95 and Z100.

• belowLayers: A list. If control$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).

  If control$transpirationMode = "Sperry" or control$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).

  If control$transpirationMode = "Sperry" or control$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. If control$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.

  If 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.

  If 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_Baldocchi: Slope of the Gsw vs Ac/Cs relationship (see photo_photosynthesisBaldocchi).

  • Gsw_P50_Baldocchi, Gsw_slope_Baldocchi: 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).

• internalPhenology and internalWater: data frames to store internal state variables.

• internalFCCS: A data frame with fuel characteristics, according to fuel_FCCS (only if fireHazardResults = TRUE, in the control list).

Function growthInput() returns a list of class growthInput with the same elements as spwbInput, but with additional information.

• Element above includes 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).

  • RespFire: Probability of resprouting after a fire disturbance.

  • RespDist: Probability of resprouting after undefined disturbance (typically desiccation).

• 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.

• internalSnags: A data frame with characteristics (species identity, height, diameter, age), small branch mass and large wood mass (both in g C/m2) corresponding to decomposing snag cohorts (see forest).

• internalLitter: A data frame with the aboveground and belowground mass (g C/m2) of different litter components: leaves, twigs, small branches, large wood, coarse roots and fine roots.

• internalSOC: A named numeric vector with surface/soil decomposing carbon pools (g C/m2).

• 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, the number of resprouting elements and the accumulation of aboveground dead wood (branches and large wood).

Details

Functions spwbInput() and growthInput() initialize inputs differently depending on control parameters.

See also

resetInputs, spwb, growth, soil, forest, SpParamsMED, defaultSoilParams, plant_ID

Author

Miquel De Cáceres Ainsa, CREAF

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
#> 
#> $control$soilPoolResults
#> [1] FALSE
#> 
#> $control$snowResults
#> [1] TRUE
#> 
#> $control$plantResults
#> [1] TRUE
#> 
#> $control$labileCarbonBalanceResults
#> [1] TRUE
#> 
#> $control$plantStructureResults
#> [1] TRUE
#> 
#> $control$growthMortalityResults
#> [1] TRUE
#> 
#> $control$decompositionPoolResults
#> [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"
#> 
#> $control$soilDomains
#> [1] "buckets"
#> 
#> $control$rhizosphereOverlap
#> [1] "partial"
#> 
#> $control$truncateRootDistribution
#> [1] FALSE
#> 
#> $control$fullRhizosphereOverlapConductivity
#> [1] 0.01
#> 
#> $control$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
#> 
#> $control$unfoldingDD
#> [1] 300
#> 
#> $control$verticalLayerSize
#> [1] 100
#> 
#> $control$windMeasurementHeight
#> [1] 200
#> 
#> $control$segmentedXylemVulnerability
#> [1] TRUE
#> 
#> $control$stemCavitationRecovery
#> [1] "rate"
#> 
#> $control$leafCavitationRecovery
#> [1] "rate"
#> 
#> $control$lfmcComponent
#> [1] "fine"
#> 
#> $control$mistletoeParams
#> $control$mistletoeParams$kPAR
#> [1] 0.5
#> 
#> $control$mistletoeParams$g
#> [1] 0.8
#> 
#> $control$mistletoeParams$LeafWidth
#> [1] 1
#> 
#> $control$mistletoeParams$Tmax_LAI
#> [1] 0.134
#> 
#> $control$mistletoeParams$Tmax_LAIsq
#> [1] -0.006
#> 
#> $control$mistletoeParams$Gsw_P50_Baldocchi
#> [1] -2.5
#> 
#> $control$mistletoeParams$Gsw_slope_Baldocchi
#> [1] 30
#> 
#> $control$mistletoeParams$Gsw_AC_slope_Baldocchi
#> [1] 8
#> 
#> $control$mistletoeParams$Vmax298
#> [1] 80
#> 
#> $control$mistletoeParams$Jmax298
#> [1] 120
#> 
#> 
#> $control$defoliationParams
#> $control$defoliationParams$cavitationInducedDefoliation
#> [1] TRUE
#> 
#> $control$defoliationParams$criticalLeafPLC
#> [1] 0.88
#> 
#> $control$defoliationParams$cvLeafP50
#> [1] 10
#> 
#> 
#> $control$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
#> 
#> $control$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
#> 
#> $control$decompositionAnnualBaseRates
#>     SurfaceMetabolic BelowgroundMetabolic               Leaves 
#>               8.0000              18.5000               2.0000 
#>            FineRoots                Twigs        SmallBranches 
#>               4.9000               1.8000               1.5000 
#>            LargeWood          CoarseRoots        SurfaceActive 
#>               0.0200               0.1000               6.0000 
#>    BelowgroundActive          SurfaceSlow      BelowgroundSlow 
#>              11.0000               0.0800               0.4000 
#>   BelowgroundPassive 
#>               0.0033 
#> 
#> $control$decompositionAnnualTurnoverRate
#> [1] 0.1
#> 
#> $control$allowSeedBankDynamics
#> [1] TRUE
#> 
#> $control$allowRecruitment
#> [1] TRUE
#> 
#> $control$allowResprouting
#> [1] TRUE
#> 
#> $control$recruitmentMode
#> [1] "annual/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
#> 
#> $control$recrAge
#> [1] 5
#> 
#> $control$recrTreeHeight
#> [1] 620
#> 
#> $control$recrShrubCover
#> [1] 1
#> 
#> $control$recrShrubHeight
#> [1] 25
#> 
#> 
#> $soil
#>   widths sand clay      usda om nitrogen ph  bd rfc  macro     Ksat VG_alpha
#> 1    300   25   25 Silt loam NA       NA NA 1.5  25 0.0485 5401.471 89.16112
#> 2    700   25   25 Silt loam NA       NA NA 1.5  45 0.0485 5401.471 89.16112
#> 3   1000   25   25 Silt loam NA       NA NA 1.5  75 0.0485 5401.471 89.16112
#> 4   2000   25   25 Silt loam NA       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 LAImistletoe Tair Cair VPair
#> 1     0   50  100      NA          NA      NA           NA   NA   NA    NA
#> 2   100  150  200      NA          NA      NA           NA   NA   NA    NA
#> 3   200  250  300      NA          NA      NA           NA   NA   NA    NA
#> 4   300  350  400      NA          NA      NA           NA   NA   NA    NA
#> 5   400  450  500      NA          NA      NA           NA   NA   NA    NA
#> 6   500  550  600      NA          NA      NA           NA   NA   NA    NA
#> 7   600  650  700      NA          NA      NA           NA   NA   NA    NA
#> 8   700  750  800      NA          NA      NA           NA   NA   NA    NA
#> 9   800  850  900      NA          NA      NA           NA   NA   NA    NA
#> 10  900  950 1000      NA          NA      NA           NA   NA   NA    NA
#> 11 1000 1050 1100      NA          NA      NA           NA   NA   NA    NA
#> 12 1100 1150 1200      NA          NA      NA           NA   NA   NA    NA
#> 13 1200 1250 1300      NA          NA      NA           NA   NA   NA    NA
#> 14 1300 1350 1400      NA          NA      NA           NA   NA   NA    NA
#> 15 1400 1450 1500      NA          NA      NA           NA   NA   NA    NA
#> 16 1500 1550 1600      NA          NA      NA           NA   NA   NA    NA
#> 17 1600 1650 1700      NA          NA      NA           NA   NA   NA    NA
#> 18 1700 1750 1800      NA          NA      NA           NA   NA   NA    NA
#> 19 1800 1850 1900      NA          NA      NA           NA   NA   NA    NA
#> 20 1900 1950 2000      NA          NA      NA           NA   NA   NA    NA
#> 21 2000 2050 2100      NA          NA      NA           NA   NA   NA    NA
#> 22 2100 2150 2200      NA          NA      NA           NA   NA   NA    NA
#> 23 2200 2250 2300      NA          NA      NA           NA   NA   NA    NA
#> 24 2300 2350 2400      NA          NA      NA           NA   NA   NA    NA
#> 25 2400 2450 2500      NA          NA      NA           NA   NA   NA    NA
#> 26 2500 2550 2600      NA          NA      NA           NA   NA   NA    NA
#> 27 2600 2650 2700      NA          NA      NA           NA   NA   NA    NA
#> 28 2700 2750 2800      NA          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 LAI_mistletoe Age ObsID
#> T1_148 800 0.6534132 0.75422783   0.75422783        0             0  NA  <NA>
#> T2_168 660 0.6359169 0.64411380   0.64411380        0             0  NA  <NA>
#> S1_165  80 0.8032817 0.05332129   0.05332129        0             0  NA  <NA>
#> 
#> $below
#>        Z50  Z95 Z100 poolProportions
#> T1_148 100  300   NA      0.51956127
#> T2_168 300 1000   NA      0.44370755
#> S1_165 200 1000   NA      0.03673118
#> 
#> $belowLayers
#> $belowLayers$V
#>                1          2           3            4
#> T1_148 0.9498377 0.04811006 0.001774047 0.0002781442
#> T2_168 0.5008953 0.45059411 0.040648313 0.0078622840
#> S1_165 0.6799879 0.27379114 0.035676316 0.0105446776
#> 
#> $belowLayers$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
#> 
#> $belowLayers$RHOP
#> $belowLayers$RHOP$T1_148
#>                 1          2          3          4
#> T1_148 0.51956127 0.51956127 0.51956127 0.51956127
#> T2_168 0.44370755 0.44370755 0.44370755 0.44370755
#> S1_165 0.03673118 0.03673118 0.03673118 0.03673118
#> 
#> $belowLayers$RHOP$T2_168
#>                 1          2          3          4
#> T1_148 0.51956127 0.51956127 0.51956127 0.51956127
#> T2_168 0.44370755 0.44370755 0.44370755 0.44370755
#> S1_165 0.03673118 0.03673118 0.03673118 0.03673118
#> 
#> $belowLayers$RHOP$S1_165
#>                 1          2          3          4
#> T1_148 0.51956127 0.51956127 0.51956127 0.51956127
#> T2_168 0.44370755 0.44370755 0.44370755 0.44370755
#> S1_165 0.03673118 0.03673118 0.03673118 0.03673118
#> 
#> 
#> 
#> $paramsPhenology
#>             PhenologyType LeafDuration t0gdd Sgdd Tbgdd Ssen Phsen Tbsen xsen
#> T1_148 oneflush-evergreen     2.083333    50  200     0 8268  12.5  28.5    2
#> T2_168 oneflush-evergreen     2.000000    50  200     0 8268  12.5  28.5    2
#> S1_165 oneflush-evergreen     1.341667    50  200     0 8268  12.5  28.5    2
#>        ysen
#> T1_148    2
#> T2_168    2
#> S1_165    2
#> 
#> $paramsAnatomy
#>           Al2As Ar2Al      SLA LeafDensity WoodDensity FineRootDensity
#> T1_148 1317.523     1 5.140523   0.2881200        0.60       0.2881200
#> T2_168 3908.823     1 6.340000   0.6650000        0.89       0.6650000
#> S1_165 2436.475     1 7.152702   0.3669009        0.73       0.3669009
#>              SRL RLD     r635
#> T1_148 2115.0874  10 1.964226
#> T2_168  735.7025  10 1.805872
#> S1_165  996.2760  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  -1.0913031    1.300000  4.412593
#>         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 -3.284789  2.132799 -8.312465 7.900000 0.3643000 0.002757000 -0.4636000
#> 
#> $paramsWaterStorage
#>           maxFMC maxMCleaf maxMCstem   LeafPI0  LeafEPS    LeafAF     Vleaf
#> T1_148 122.16441  142.2755 101.30719 -1.236151 10.52923 0.3447917 0.5488595
#> T2_168 109.23042  159.3801  47.00007 -2.070000 18.27000 0.4580000 0.1347648
#> S1_165  98.39177  132.9039  71.62682 -2.370000 17.23000 0.2400000 0.2902653
#>        StemPI0  StemEPS    StemAF  Vsapwood
#> T1_148 -1.9760 12.82234 0.9258273 4.1672242
#> T2_168 -3.1824 44.33022 0.6263370 0.8201071
#> S1_165 -2.5168 22.41056 0.6263370 0.3874813
#> 
#> $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] NA NA NA
#> 
#> $internalLAIDistribution$PrevLAIdead
#> [1] NA NA NA
#> 
#> $internalLAIDistribution$PrevLAImistletoe
#> [1] NA NA NA
#> 
#> $internalLAIDistribution$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
#> 
#> $internalLAIDistribution$mistletoe
#>    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
#> 
#> $version
#> [1] "5.1.0"
#> 
#> 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
#> 
#> $control$soilPoolResults
#> [1] FALSE
#> 
#> $control$snowResults
#> [1] TRUE
#> 
#> $control$plantResults
#> [1] TRUE
#> 
#> $control$labileCarbonBalanceResults
#> [1] TRUE
#> 
#> $control$plantStructureResults
#> [1] TRUE
#> 
#> $control$growthMortalityResults
#> [1] TRUE
#> 
#> $control$decompositionPoolResults
#> [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"
#> 
#> $control$soilDomains
#> [1] "buckets"
#> 
#> $control$rhizosphereOverlap
#> [1] "partial"
#> 
#> $control$truncateRootDistribution
#> [1] FALSE
#> 
#> $control$fullRhizosphereOverlapConductivity
#> [1] 0.01
#> 
#> $control$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
#> 
#> $control$unfoldingDD
#> [1] 300
#> 
#> $control$verticalLayerSize
#> [1] 100
#> 
#> $control$windMeasurementHeight
#> [1] 200
#> 
#> $control$segmentedXylemVulnerability
#> [1] TRUE
#> 
#> $control$stemCavitationRecovery
#> [1] "rate"
#> 
#> $control$leafCavitationRecovery
#> [1] "rate"
#> 
#> $control$lfmcComponent
#> [1] "fine"
#> 
#> $control$mistletoeParams
#> $control$mistletoeParams$kPAR
#> [1] 0.5
#> 
#> $control$mistletoeParams$g
#> [1] 0.8
#> 
#> $control$mistletoeParams$LeafWidth
#> [1] 1
#> 
#> $control$mistletoeParams$Tmax_LAI
#> [1] 0.134
#> 
#> $control$mistletoeParams$Tmax_LAIsq
#> [1] -0.006
#> 
#> $control$mistletoeParams$Gsw_P50_Baldocchi
#> [1] -2.5
#> 
#> $control$mistletoeParams$Gsw_slope_Baldocchi
#> [1] 30
#> 
#> $control$mistletoeParams$Gsw_AC_slope_Baldocchi
#> [1] 8
#> 
#> $control$mistletoeParams$Vmax298
#> [1] 80
#> 
#> $control$mistletoeParams$Jmax298
#> [1] 120
#> 
#> 
#> $control$defoliationParams
#> $control$defoliationParams$cavitationInducedDefoliation
#> [1] TRUE
#> 
#> $control$defoliationParams$criticalLeafPLC
#> [1] 0.88
#> 
#> $control$defoliationParams$cvLeafP50
#> [1] 10
#> 
#> 
#> $control$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
#> 
#> $control$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
#> 
#> $control$decompositionAnnualBaseRates
#>     SurfaceMetabolic BelowgroundMetabolic               Leaves 
#>               8.0000              18.5000               2.0000 
#>            FineRoots                Twigs        SmallBranches 
#>               4.9000               1.8000               1.5000 
#>            LargeWood          CoarseRoots        SurfaceActive 
#>               0.0200               0.1000               6.0000 
#>    BelowgroundActive          SurfaceSlow      BelowgroundSlow 
#>              11.0000               0.0800               0.4000 
#>   BelowgroundPassive 
#>               0.0033 
#> 
#> $control$decompositionAnnualTurnoverRate
#> [1] 0.1
#> 
#> $control$allowSeedBankDynamics
#> [1] TRUE
#> 
#> $control$allowRecruitment
#> [1] TRUE
#> 
#> $control$allowResprouting
#> [1] TRUE
#> 
#> $control$recruitmentMode
#> [1] "annual/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
#> 
#> $control$recrAge
#> [1] 5
#> 
#> $control$recrTreeHeight
#> [1] 620
#> 
#> $control$recrShrubCover
#> [1] 1
#> 
#> $control$recrShrubHeight
#> [1] 25
#> 
#> 
#> $soil
#>   widths sand clay      usda om nitrogen ph  bd rfc  macro     Ksat VG_alpha
#> 1    300   25   25 Silt loam NA       NA NA 1.5  25 0.0485 5401.471 89.16112
#> 2    700   25   25 Silt loam NA       NA NA 1.5  45 0.0485 5401.471 89.16112
#> 3   1000   25   25 Silt loam NA       NA NA 1.5  75 0.0485 5401.471 89.16112
#> 4   2000   25   25 Silt loam NA       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 LAImistletoe Tair Cair VPair
#> 1     0   50  100      NA          NA      NA           NA   NA   NA    NA
#> 2   100  150  200      NA          NA      NA           NA   NA   NA    NA
#> 3   200  250  300      NA          NA      NA           NA   NA   NA    NA
#> 4   300  350  400      NA          NA      NA           NA   NA   NA    NA
#> 5   400  450  500      NA          NA      NA           NA   NA   NA    NA
#> 6   500  550  600      NA          NA      NA           NA   NA   NA    NA
#> 7   600  650  700      NA          NA      NA           NA   NA   NA    NA
#> 8   700  750  800      NA          NA      NA           NA   NA   NA    NA
#> 9   800  850  900      NA          NA      NA           NA   NA   NA    NA
#> 10  900  950 1000      NA          NA      NA           NA   NA   NA    NA
#> 11 1000 1050 1100      NA          NA      NA           NA   NA   NA    NA
#> 12 1100 1150 1200      NA          NA      NA           NA   NA   NA    NA
#> 13 1200 1250 1300      NA          NA      NA           NA   NA   NA    NA
#> 14 1300 1350 1400      NA          NA      NA           NA   NA   NA    NA
#> 15 1400 1450 1500      NA          NA      NA           NA   NA   NA    NA
#> 16 1500 1550 1600      NA          NA      NA           NA   NA   NA    NA
#> 17 1600 1650 1700      NA          NA      NA           NA   NA   NA    NA
#> 18 1700 1750 1800      NA          NA      NA           NA   NA   NA    NA
#> 19 1800 1850 1900      NA          NA      NA           NA   NA   NA    NA
#> 20 1900 1950 2000      NA          NA      NA           NA   NA   NA    NA
#> 21 2000 2050 2100      NA          NA      NA           NA   NA   NA    NA
#> 22 2100 2150 2200      NA          NA      NA           NA   NA   NA    NA
#> 23 2200 2250 2300      NA          NA      NA           NA   NA   NA    NA
#> 24 2300 2350 2400      NA          NA      NA           NA   NA   NA    NA
#> 25 2400 2450 2500      NA          NA      NA           NA   NA   NA    NA
#> 26 2500 2550 2600      NA          NA      NA           NA   NA   NA    NA
#> 27 2600 2650 2700      NA          NA      NA           NA   NA   NA    NA
#> 28 2700 2750 2800      NA          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 LAI_mistletoe Age ObsID
#> T1_148 800 0.6534132 0.75422783   0.75422783        0             0  NA  <NA>
#> T2_168 660 0.6359169 0.64411380   0.64411380        0             0  NA  <NA>
#> S1_165  80 0.8032817 0.05332129   0.05332129        0             0  NA  <NA>
#> 
#> $below
#>        Z50  Z95 Z100 poolProportions
#> T1_148 100  300   NA      0.51956127
#> T2_168 300 1000   NA      0.44370755
#> S1_165 200 1000   NA      0.03673118
#> 
#> $belowLayers
#> $belowLayers$V
#>                1          2           3            4
#> T1_148 0.9498377 0.04811006 0.001774047 0.0002781442
#> T2_168 0.5008953 0.45059411 0.040648313 0.0078622840
#> S1_165 0.6799879 0.27379114 0.035676316 0.0105446776
#> 
#> $belowLayers$L
#>               1        2        3        4
#> T1_148 2086.448 1307.358 2073.244 4045.856
#> T2_168 1413.593 1807.433 2300.951 4209.276
#> S1_165 1907.898 1779.971 2349.397 4300.342
#> 
#> $belowLayers$VGrhizo_kmax
#>                1        2          3          4
#> T1_148  38422773  1946145   71763.65   11251.47
#> T2_168  16281121 14646130 1321234.47  255556.01
#> S1_165 127190265 51212043 6673177.96 1972359.23
#> 
#> $belowLayers$VCroot_kmax
#>               1         2           3            4
#> T1_148 2.889971 0.2336108 0.005432084 0.0004364266
#> T2_168 2.024110 1.4240808 0.100912866 0.0106697119
#> S1_165 2.361274 1.0190767 0.100606036 0.0162454141
#> 
#> $belowLayers$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
#> 
#> $belowLayers$RHOP
#> $belowLayers$RHOP$T1_148
#>                 1          2          3          4
#> T1_148 0.51956127 0.51956127 0.51956127 0.51956127
#> T2_168 0.44370755 0.44370755 0.44370755 0.44370755
#> S1_165 0.03673118 0.03673118 0.03673118 0.03673118
#> 
#> $belowLayers$RHOP$T2_168
#>                 1          2          3          4
#> T1_148 0.51956127 0.51956127 0.51956127 0.51956127
#> T2_168 0.44370755 0.44370755 0.44370755 0.44370755
#> S1_165 0.03673118 0.03673118 0.03673118 0.03673118
#> 
#> $belowLayers$RHOP$S1_165
#>                 1          2          3          4
#> T1_148 0.51956127 0.51956127 0.51956127 0.51956127
#> T2_168 0.44370755 0.44370755 0.44370755 0.44370755
#> S1_165 0.03673118 0.03673118 0.03673118 0.03673118
#> 
#> 
#> 
#> $paramsPhenology
#>             PhenologyType LeafDuration t0gdd Sgdd Tbgdd Ssen Phsen Tbsen xsen
#> T1_148 oneflush-evergreen     2.083333    50  200     0 8268  12.5  28.5    2
#> T2_168 oneflush-evergreen     2.000000    50  200     0 8268  12.5  28.5    2
#> S1_165 oneflush-evergreen     1.341667    50  200     0 8268  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   0.2881200        0.60       0.2881200
#> T2_168   48 3908.823 6.340000 1.7674359   0.6650000        0.89       0.6650000
#> S1_165   90 2436.475 7.152702 1.3200000   0.3669009        0.73       0.3669009
#>        conduit2sapwood       SRL RLD     r635
#> T1_148       0.9258273 2115.0874  10 1.964226
#> T2_168       0.6263370  735.7025  10 1.805872
#> S1_165       0.6263370  996.2760  10 2.289452
#> 
#> $paramsInterception
#>        LeafAngle LeafAngleSD   Beta_p   Beta_q ClumpingIndex kPAR alphaSWR
#> T1_148  53.70000    21.55000 1.907817 1.289641          0.75 0.50      0.7
#> T2_168  36.00819    20.15953 1.513844 2.269906          0.75 0.55      0.7
#> S1_165  53.70000    21.55000 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 0.1800000 58.79590 104.3488           0.29           1.16
#>        VCleaf_kmax VCleafapo_kmax VCleaf_slope VCleaf_P50  VCleaf_c  VCleaf_d
#> T1_148    4.000000        8.00000    133.86620  -2.303772 11.137050 -2.380849
#> T2_168    4.000000        8.00000     19.14428  -1.964085  1.339370 -2.582279
#> S1_165    8.489906       16.97981     47.93469  -3.022976  4.412593 -3.284789
#>        kleaf_symp VCstem_kmax VCstem_slope VCstem_P50  VCstem_c  VCstem_d
#> T1_148    8.00000    1.339563    68.302912  -5.139633 12.709999 -5.290000
#> T2_168    8.00000    4.992013    14.607857  -6.964747  3.560000 -7.720000
#> S1_165   16.97981    7.473393     9.773996  -7.000000  2.132799 -8.312465
#>        VCroot_kmax VCroot_slope VCroot_P50  VCroot_c  VCroot_d VGrhizo_kmax
#> T1_148    3.129450    103.96607  -2.966325 11.137050 -3.065569     40451933
#> T2_168    3.559773     22.32794  -1.684034  1.339370 -2.214081     32504042
#> S1_165    3.497202     16.46463  -4.389000  2.469094 -5.091343    187047845
#>        Plant_kmax   FR_leaf   FR_stem   FR_root
#> T1_148  0.7598454 0.1899614 0.5672339 0.2428047
#> T2_168  1.3675461 0.3418865 0.2739468 0.3841667
#> S1_165  1.8603342 0.2191231 0.2489276 0.5319493
#> 
#> $paramsWaterStorage
#>           maxFMC maxMCleaf maxMCstem   LeafPI0  LeafEPS    LeafAF     Vleaf
#> T1_148 122.16441  142.2755 101.30719 -1.236151 10.52923 0.3447917 0.5488595
#> T2_168 109.23042  159.3801  47.00007 -2.070000 18.27000 0.4580000 0.1347648
#> S1_165  98.39177  132.9039  71.62682 -2.370000 17.23000 0.2400000 0.2902653
#>        StemPI0  StemEPS    StemAF Vsapwood
#> T1_148 -1.9760 12.82234 0.9258273 6.306451
#> T2_168 -3.1824 44.33022 0.6263370 1.318710
#> S1_165 -2.5168 22.41056 0.6263370 1.384287
#> 
#> $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 Emist RootCrownPsi LeafPsi StemPsi LeafSympPsi StemSympPsi LeafPLC
#> T1_148     0     0       -0.033  -0.033  -0.033      -0.033      -0.033       0
#> T2_168     0     0       -0.033  -0.033  -0.033      -0.033      -0.033       0
#> S1_165     0     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] NA NA NA
#> 
#> $internalLAIDistribution$PrevLAIdead
#> [1] NA NA NA
#> 
#> $internalLAIDistribution$PrevLAImistletoe
#> [1] NA NA NA
#> 
#> $internalLAIDistribution$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
#> 
#> $internalLAIDistribution$mistletoe
#>    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
#> 
#> $version
#> [1] "5.1.0"
#> 
#> 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
#> 
#> $control$soilPoolResults
#> [1] FALSE
#> 
#> $control$snowResults
#> [1] TRUE
#> 
#> $control$plantResults
#> [1] TRUE
#> 
#> $control$labileCarbonBalanceResults
#> [1] TRUE
#> 
#> $control$plantStructureResults
#> [1] TRUE
#> 
#> $control$growthMortalityResults
#> [1] TRUE
#> 
#> $control$decompositionPoolResults
#> [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"
#> 
#> $control$soilDomains
#> [1] "buckets"
#> 
#> $control$rhizosphereOverlap
#> [1] "partial"
#> 
#> $control$truncateRootDistribution
#> [1] FALSE
#> 
#> $control$fullRhizosphereOverlapConductivity
#> [1] 0.01
#> 
#> $control$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
#> 
#> $control$unfoldingDD
#> [1] 300
#> 
#> $control$verticalLayerSize
#> [1] 100
#> 
#> $control$windMeasurementHeight
#> [1] 200
#> 
#> $control$segmentedXylemVulnerability
#> [1] FALSE
#> 
#> $control$stemCavitationRecovery
#> [1] "rate"
#> 
#> $control$leafCavitationRecovery
#> [1] "rate"
#> 
#> $control$lfmcComponent
#> [1] "fine"
#> 
#> $control$mistletoeParams
#> $control$mistletoeParams$kPAR
#> [1] 0.5
#> 
#> $control$mistletoeParams$g
#> [1] 0.8
#> 
#> $control$mistletoeParams$LeafWidth
#> [1] 1
#> 
#> $control$mistletoeParams$Tmax_LAI
#> [1] 0.134
#> 
#> $control$mistletoeParams$Tmax_LAIsq
#> [1] -0.006
#> 
#> $control$mistletoeParams$Gsw_P50_Baldocchi
#> [1] -2.5
#> 
#> $control$mistletoeParams$Gsw_slope_Baldocchi
#> [1] 30
#> 
#> $control$mistletoeParams$Gsw_AC_slope_Baldocchi
#> [1] 8
#> 
#> $control$mistletoeParams$Vmax298
#> [1] 80
#> 
#> $control$mistletoeParams$Jmax298
#> [1] 120
#> 
#> 
#> $control$defoliationParams
#> $control$defoliationParams$cavitationInducedDefoliation
#> [1] TRUE
#> 
#> $control$defoliationParams$criticalLeafPLC
#> [1] 0.88
#> 
#> $control$defoliationParams$cvLeafP50
#> [1] 10
#> 
#> 
#> $control$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
#> 
#> $control$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
#> 
#> $control$decompositionAnnualBaseRates
#>     SurfaceMetabolic BelowgroundMetabolic               Leaves 
#>               8.0000              18.5000               2.0000 
#>            FineRoots                Twigs        SmallBranches 
#>               4.9000               1.8000               1.5000 
#>            LargeWood          CoarseRoots        SurfaceActive 
#>               0.0200               0.1000               6.0000 
#>    BelowgroundActive          SurfaceSlow      BelowgroundSlow 
#>              11.0000               0.0800               0.4000 
#>   BelowgroundPassive 
#>               0.0033 
#> 
#> $control$decompositionAnnualTurnoverRate
#> [1] 0.1
#> 
#> $control$allowSeedBankDynamics
#> [1] TRUE
#> 
#> $control$allowRecruitment
#> [1] TRUE
#> 
#> $control$allowResprouting
#> [1] TRUE
#> 
#> $control$recruitmentMode
#> [1] "annual/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
#> 
#> $control$recrAge
#> [1] 5
#> 
#> $control$recrTreeHeight
#> [1] 620
#> 
#> $control$recrShrubCover
#> [1] 1
#> 
#> $control$recrShrubHeight
#> [1] 25
#> 
#> 
#> $soil
#>   widths sand clay      usda om nitrogen ph  bd rfc  macro     Ksat VG_alpha
#> 1    300   25   25 Silt loam NA       NA NA 1.5  25 0.0485 5401.471 89.16112
#> 2    700   25   25 Silt loam NA       NA NA 1.5  45 0.0485 5401.471 89.16112
#> 3   1000   25   25 Silt loam NA       NA NA 1.5  75 0.0485 5401.471 89.16112
#> 4   2000   25   25 Silt loam NA       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 LAImistletoe Tair Cair VPair
#> 1     0   50  100      NA          NA      NA           NA   NA   NA    NA
#> 2   100  150  200      NA          NA      NA           NA   NA   NA    NA
#> 3   200  250  300      NA          NA      NA           NA   NA   NA    NA
#> 4   300  350  400      NA          NA      NA           NA   NA   NA    NA
#> 5   400  450  500      NA          NA      NA           NA   NA   NA    NA
#> 6   500  550  600      NA          NA      NA           NA   NA   NA    NA
#> 7   600  650  700      NA          NA      NA           NA   NA   NA    NA
#> 8   700  750  800      NA          NA      NA           NA   NA   NA    NA
#> 9   800  850  900      NA          NA      NA           NA   NA   NA    NA
#> 10  900  950 1000      NA          NA      NA           NA   NA   NA    NA
#> 11 1000 1050 1100      NA          NA      NA           NA   NA   NA    NA
#> 12 1100 1150 1200      NA          NA      NA           NA   NA   NA    NA
#> 13 1200 1250 1300      NA          NA      NA           NA   NA   NA    NA
#> 14 1300 1350 1400      NA          NA      NA           NA   NA   NA    NA
#> 15 1400 1450 1500      NA          NA      NA           NA   NA   NA    NA
#> 16 1500 1550 1600      NA          NA      NA           NA   NA   NA    NA
#> 17 1600 1650 1700      NA          NA      NA           NA   NA   NA    NA
#> 18 1700 1750 1800      NA          NA      NA           NA   NA   NA    NA
#> 19 1800 1850 1900      NA          NA      NA           NA   NA   NA    NA
#> 20 1900 1950 2000      NA          NA      NA           NA   NA   NA    NA
#> 21 2000 2050 2100      NA          NA      NA           NA   NA   NA    NA
#> 22 2100 2150 2200      NA          NA      NA           NA   NA   NA    NA
#> 23 2200 2250 2300      NA          NA      NA           NA   NA   NA    NA
#> 24 2300 2350 2400      NA          NA      NA           NA   NA   NA    NA
#> 25 2400 2450 2500      NA          NA      NA           NA   NA   NA    NA
#> 26 2500 2550 2600      NA          NA      NA           NA   NA   NA    NA
#> 27 2600 2650 2700      NA          NA      NA           NA   NA   NA    NA
#> 28 2700 2750 2800      NA          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 LAI_mistletoe Age ObsID
#> T1_148 800 0.6534132 0.75422783   0.75422783        0             0  NA  <NA>
#> T2_168 660 0.6359169 0.64411380   0.64411380        0             0  NA  <NA>
#> S1_165  80 0.8032817 0.05332129   0.05332129        0             0  NA  <NA>
#> 
#> $below
#>        Z50  Z95 Z100 poolProportions
#> T1_148 100  300   NA      0.51956127
#> T2_168 300 1000   NA      0.44370755
#> S1_165 200 1000   NA      0.03673118
#> 
#> $belowLayers
#> $belowLayers$V
#>                1          2           3            4
#> T1_148 0.9498377 0.04811006 0.001774047 0.0002781442
#> T2_168 0.5008953 0.45059411 0.040648313 0.0078622840
#> S1_165 0.6799879 0.27379114 0.035676316 0.0105446776
#> 
#> $belowLayers$L
#>               1        2        3        4
#> T1_148 2086.448 1307.358 2073.244 4045.856
#> T2_168 1413.593 1807.433 2300.951 4209.276
#> S1_165 1907.898 1779.971 2349.397 4300.342
#> 
#> $belowLayers$VGrhizo_kmax
#>                1        2          3          4
#> T1_148  34984333  1771985   65341.55   10244.58
#> T2_168  24061938 21645577 1952657.97  377687.29
#> S1_165 137525468 55373421 7215425.77 2132628.82
#> 
#> $belowLayers$VCroot_kmax
#>               1         2           3            4
#> T1_148 2.889971 0.2336108 0.005432084 0.0004364266
#> T2_168 2.024110 1.4240808 0.100912866 0.0106697119
#> S1_165 2.361274 1.0190767 0.100606036 0.0162454141
#> 
#> $belowLayers$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
#> 
#> $belowLayers$RHOP
#> $belowLayers$RHOP$T1_148
#>                 1          2          3          4
#> T1_148 0.51956127 0.51956127 0.51956127 0.51956127
#> T2_168 0.44370755 0.44370755 0.44370755 0.44370755
#> S1_165 0.03673118 0.03673118 0.03673118 0.03673118
#> 
#> $belowLayers$RHOP$T2_168
#>                 1          2          3          4
#> T1_148 0.51956127 0.51956127 0.51956127 0.51956127
#> T2_168 0.44370755 0.44370755 0.44370755 0.44370755
#> S1_165 0.03673118 0.03673118 0.03673118 0.03673118
#> 
#> $belowLayers$RHOP$S1_165
#>                 1          2          3          4
#> T1_148 0.51956127 0.51956127 0.51956127 0.51956127
#> T2_168 0.44370755 0.44370755 0.44370755 0.44370755
#> S1_165 0.03673118 0.03673118 0.03673118 0.03673118
#> 
#> 
#> 
#> $paramsPhenology
#>             PhenologyType LeafDuration t0gdd Sgdd Tbgdd Ssen Phsen Tbsen xsen
#> T1_148 oneflush-evergreen     2.083333    50  200     0 8268  12.5  28.5    2
#> T2_168 oneflush-evergreen     2.000000    50  200     0 8268  12.5  28.5    2
#> S1_165 oneflush-evergreen     1.341667    50  200     0 8268  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   0.2881200        0.60       0.2881200
#> T2_168   48 3908.823 6.340000 1.7674359   0.6650000        0.89       0.6650000
#> S1_165   90 2436.475 7.152702 1.3200000   0.3669009        0.73       0.3669009
#>        conduit2sapwood       SRL RLD     r635
#> T1_148       0.9258273 2115.0874  10 1.964226
#> T2_168       0.6263370  735.7025  10 1.805872
#> S1_165       0.6263370  996.2760  10 2.289452
#> 
#> $paramsInterception
#>        LeafAngle LeafAngleSD   Beta_p   Beta_q ClumpingIndex kPAR alphaSWR
#> T1_148  53.70000    21.55000 1.907817 1.289641          0.75 0.50      0.7
#> T2_168  36.00819    20.15953 1.513844 2.269906          0.75 0.55      0.7
#> S1_165  53.70000    21.55000 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_Baldocchi Gsw_P50_Baldocchi
#> T1_148 0.003086667 0.2850000               6.238912         -2.200000
#> T2_168 0.004473333 0.2007222               4.957957         -1.964085
#> S1_165 0.010455247 0.1800000               4.898507         -3.022976
#>        Gsw_slope_Baldocchi  Vmax298  Jmax298 Kmax_stemxylem Kmax_rootxylem
#> T1_148            59.78537 72.19617 124.1687           0.15           0.60
#> T2_168            64.81348 68.51600 118.7863           0.40           1.60
#> S1_165            47.03891 58.79590 104.3488           0.29           1.16
#>        VCleaf_kmax VCleafapo_kmax VCleaf_slope VCleaf_P50  VCleaf_c  VCleaf_d
#> T1_148    4.000000        8.00000    68.302912  -5.139633 12.709999 -5.290000
#> T2_168    4.000000        8.00000    14.607857  -6.964747  3.560000 -7.720000
#> S1_165    8.489906       16.97981     9.773996  -7.000000  2.132799 -8.312465
#>        kleaf_symp VCstem_kmax VCstem_slope VCstem_P50  VCstem_c  VCstem_d
#> T1_148    8.00000    1.339563    68.302912  -5.139633 12.709999 -5.290000
#> T2_168    8.00000    4.992013    14.607857  -6.964747  3.560000 -7.720000
#> S1_165   16.97981    7.473393     9.773996  -7.000000  2.132799 -8.312465
#>        kstem_symp VCroot_kmax VCroot_slope VCroot_P50  VCroot_c  VCroot_d
#> T1_148       0.26    3.129450    68.302912  -5.139633 12.709999 -5.290000
#> T2_168       0.26    3.559773    14.607857  -6.964747  3.560000 -7.720000
#> S1_165       0.26    3.497202     9.773996  -7.000000  2.132799 -8.312465
#>        VGrhizo_kmax Plant_kmax   FR_leaf   FR_stem   FR_root
#> T1_148     36831905  0.7598454 0.1899614 0.5672339 0.2428047
#> T2_168     48037860  1.3675461 0.3418865 0.2739468 0.3841667
#> S1_165    202246943  1.8603342 0.2191231 0.2489276 0.5319493
#> 
#> $paramsWaterStorage
#>           maxFMC maxMCleaf maxMCstem   LeafPI0  LeafEPS    LeafAF     Vleaf
#> T1_148 122.16441  142.2755 101.30719 -1.236151 10.52923 0.3447917 0.5488595
#> T2_168 109.23042  159.3801  47.00007 -2.070000 18.27000 0.4580000 0.1347648
#> S1_165  98.39177  132.9039  71.62682 -2.370000 17.23000 0.2400000 0.2902653
#>        StemPI0  StemEPS    StemAF Vsapwood
#> T1_148 -1.9760 12.82234 0.9258273 6.306451
#> T2_168 -3.1824 44.33022 0.6263370 1.318710
#> S1_165 -2.5168 22.41056 0.6263370 1.384287
#> 
#> $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 Emist Elim Emin_L Emin_S RootCrownPsi LeafPsi StemPsi LeafSympPsi
#> T1_148     0     0    0      0      0       -0.033  -0.033  -0.033      -0.033
#> T2_168     0     0    0      0      0       -0.033  -0.033  -0.033      -0.033
#> S1_165     0     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] NA NA NA
#> 
#> $internalLAIDistribution$PrevLAIdead
#> [1] NA NA NA
#> 
#> $internalLAIDistribution$PrevLAImistletoe
#> [1] NA NA NA
#> 
#> $internalLAIDistribution$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
#> 
#> $internalLAIDistribution$mistletoe
#>    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
#> 
#> $version
#> [1] "5.1.0"
#> 
#> 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
#> 
#> $control$soilPoolResults
#> [1] FALSE
#> 
#> $control$snowResults
#> [1] TRUE
#> 
#> $control$plantResults
#> [1] TRUE
#> 
#> $control$labileCarbonBalanceResults
#> [1] TRUE
#> 
#> $control$plantStructureResults
#> [1] TRUE
#> 
#> $control$growthMortalityResults
#> [1] TRUE
#> 
#> $control$decompositionPoolResults
#> [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"
#> 
#> $control$soilDomains
#> [1] "buckets"
#> 
#> $control$rhizosphereOverlap
#> [1] "partial"
#> 
#> $control$truncateRootDistribution
#> [1] FALSE
#> 
#> $control$fullRhizosphereOverlapConductivity
#> [1] 0.01
#> 
#> $control$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
#> 
#> $control$unfoldingDD
#> [1] 300
#> 
#> $control$verticalLayerSize
#> [1] 100
#> 
#> $control$windMeasurementHeight
#> [1] 200
#> 
#> $control$segmentedXylemVulnerability
#> [1] TRUE
#> 
#> $control$stemCavitationRecovery
#> [1] "rate"
#> 
#> $control$leafCavitationRecovery
#> [1] "rate"
#> 
#> $control$lfmcComponent
#> [1] "fine"
#> 
#> $control$mistletoeParams
#> $control$mistletoeParams$kPAR
#> [1] 0.5
#> 
#> $control$mistletoeParams$g
#> [1] 0.8
#> 
#> $control$mistletoeParams$LeafWidth
#> [1] 1
#> 
#> $control$mistletoeParams$Tmax_LAI
#> [1] 0.134
#> 
#> $control$mistletoeParams$Tmax_LAIsq
#> [1] -0.006
#> 
#> $control$mistletoeParams$Gsw_P50_Baldocchi
#> [1] -2.5
#> 
#> $control$mistletoeParams$Gsw_slope_Baldocchi
#> [1] 30
#> 
#> $control$mistletoeParams$Gsw_AC_slope_Baldocchi
#> [1] 8
#> 
#> $control$mistletoeParams$Vmax298
#> [1] 80
#> 
#> $control$mistletoeParams$Jmax298
#> [1] 120
#> 
#> 
#> $control$defoliationParams
#> $control$defoliationParams$cavitationInducedDefoliation
#> [1] TRUE
#> 
#> $control$defoliationParams$criticalLeafPLC
#> [1] 0.88
#> 
#> $control$defoliationParams$cvLeafP50
#> [1] 10
#> 
#> 
#> $control$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
#> 
#> $control$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
#> 
#> $control$decompositionAnnualBaseRates
#>     SurfaceMetabolic BelowgroundMetabolic               Leaves 
#>               8.0000              18.5000               2.0000 
#>            FineRoots                Twigs        SmallBranches 
#>               4.9000               1.8000               1.5000 
#>            LargeWood          CoarseRoots        SurfaceActive 
#>               0.0200               0.1000               6.0000 
#>    BelowgroundActive          SurfaceSlow      BelowgroundSlow 
#>              11.0000               0.0800               0.4000 
#>   BelowgroundPassive 
#>               0.0033 
#> 
#> $control$decompositionAnnualTurnoverRate
#> [1] 0.1
#> 
#> $control$allowSeedBankDynamics
#> [1] TRUE
#> 
#> $control$allowRecruitment
#> [1] TRUE
#> 
#> $control$allowResprouting
#> [1] TRUE
#> 
#> $control$recruitmentMode
#> [1] "annual/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
#> 
#> $control$recrAge
#> [1] 5
#> 
#> $control$recrTreeHeight
#> [1] 620
#> 
#> $control$recrShrubCover
#> [1] 1
#> 
#> $control$recrShrubHeight
#> [1] 25
#> 
#> 
#> $soil
#>   widths sand clay      usda om nitrogen ph  bd rfc  macro     Ksat VG_alpha
#> 1    300   25   25 Silt loam NA       NA NA 1.5  25 0.0485 5401.471 89.16112
#> 2    700   25   25 Silt loam NA       NA NA 1.5  45 0.0485 5401.471 89.16112
#> 3   1000   25   25 Silt loam NA       NA NA 1.5  75 0.0485 5401.471 89.16112
#> 4   2000   25   25 Silt loam NA       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 LAImistletoe Tair Cair VPair
#> 1     0   50  100      NA          NA      NA           NA   NA   NA    NA
#> 2   100  150  200      NA          NA      NA           NA   NA   NA    NA
#> 3   200  250  300      NA          NA      NA           NA   NA   NA    NA
#> 4   300  350  400      NA          NA      NA           NA   NA   NA    NA
#> 5   400  450  500      NA          NA      NA           NA   NA   NA    NA
#> 6   500  550  600      NA          NA      NA           NA   NA   NA    NA
#> 7   600  650  700      NA          NA      NA           NA   NA   NA    NA
#> 8   700  750  800      NA          NA      NA           NA   NA   NA    NA
#> 9   800  850  900      NA          NA      NA           NA   NA   NA    NA
#> 10  900  950 1000      NA          NA      NA           NA   NA   NA    NA
#> 11 1000 1050 1100      NA          NA      NA           NA   NA   NA    NA
#> 12 1100 1150 1200      NA          NA      NA           NA   NA   NA    NA
#> 13 1200 1250 1300      NA          NA      NA           NA   NA   NA    NA
#> 14 1300 1350 1400      NA          NA      NA           NA   NA   NA    NA
#> 15 1400 1450 1500      NA          NA      NA           NA   NA   NA    NA
#> 16 1500 1550 1600      NA          NA      NA           NA   NA   NA    NA
#> 17 1600 1650 1700      NA          NA      NA           NA   NA   NA    NA
#> 18 1700 1750 1800      NA          NA      NA           NA   NA   NA    NA
#> 19 1800 1850 1900      NA          NA      NA           NA   NA   NA    NA
#> 20 1900 1950 2000      NA          NA      NA           NA   NA   NA    NA
#> 21 2000 2050 2100      NA          NA      NA           NA   NA   NA    NA
#> 22 2100 2150 2200      NA          NA      NA           NA   NA   NA    NA
#> 23 2200 2250 2300      NA          NA      NA           NA   NA   NA    NA
#> 24 2300 2350 2400      NA          NA      NA           NA   NA   NA    NA
#> 25 2400 2450 2500      NA          NA      NA           NA   NA   NA    NA
#> 26 2500 2550 2600      NA          NA      NA           NA   NA   NA    NA
#> 27 2600 2650 2700      NA          NA      NA           NA   NA   NA    NA
#> 28 2700 2750 2800      NA          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 LAI_mistletoe Age ObsID
#> T1_148 800 0.66     0.80         0.80        0             0  NA  <NA>
#> T2_168 660 0.60     0.50         0.50        0             0  NA  <NA>
#> S1_165  80 0.80     0.03         0.03        0             0  NA  <NA>
#> 
#> $below
#>        Z50  Z95 Z100 poolProportions
#> T1_148 100  300   NA      0.60150376
#> T2_168 300 1000   NA      0.37593985
#> S1_165 200 1000   NA      0.02255639
#> 
#> $belowLayers
#> $belowLayers$V
#>                1          2           3            4
#> T1_148 0.9498377 0.04811006 0.001774047 0.0002781442
#> T2_168 0.5008953 0.45059411 0.040648313 0.0078622840
#> S1_165 0.6799879 0.27379114 0.035676316 0.0105446776
#> 
#> $belowLayers$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
#> 
#> $belowLayers$RHOP
#> $belowLayers$RHOP$T1_148
#>                 1          2          3          4
#> T1_148 0.60150376 0.60150376 0.60150376 0.60150376
#> T2_168 0.37593985 0.37593985 0.37593985 0.37593985
#> S1_165 0.02255639 0.02255639 0.02255639 0.02255639
#> 
#> $belowLayers$RHOP$T2_168
#>                 1          2          3          4
#> T1_148 0.60150376 0.60150376 0.60150376 0.60150376
#> T2_168 0.37593985 0.37593985 0.37593985 0.37593985
#> S1_165 0.02255639 0.02255639 0.02255639 0.02255639
#> 
#> $belowLayers$RHOP$S1_165
#>                 1          2          3          4
#> T1_148 0.60150376 0.60150376 0.60150376 0.60150376
#> T2_168 0.37593985 0.37593985 0.37593985 0.37593985
#> S1_165 0.02255639 0.02255639 0.02255639 0.02255639
#> 
#> 
#> 
#> $paramsPhenology
#>             PhenologyType LeafDuration t0gdd Sgdd Tbgdd Ssen Phsen Tbsen xsen
#> T1_148 oneflush-evergreen     2.083333    50  200     0 8268  12.5  28.5    2
#> T2_168 oneflush-evergreen     2.000000    50  200     0 8268  12.5  28.5    2
#> S1_165 oneflush-evergreen     1.341667    50  200     0 8268  12.5  28.5    2
#>        ysen
#> T1_148    2
#> T2_168    2
#> S1_165    2
#> 
#> $paramsAnatomy
#>           Al2As Ar2Al      SLA LeafDensity WoodDensity FineRootDensity
#> T1_148 1317.523     1 5.140523   0.2881200        0.60       0.2881200
#> T2_168 3908.823     1 6.340000   0.6650000        0.89       0.6650000
#> S1_165 2436.475     1 7.152702   0.3669009        0.73       0.3669009
#>              SRL RLD     r635
#> T1_148 2115.0874  10 1.964226
#> T2_168  735.7025  10 1.805872
#> S1_165  996.2760  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  -1.0913031    1.300000  4.412593
#>         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 -3.284789  2.132799 -8.312465 7.900000 0.3643000 0.002757000 -0.4636000
#> 
#> $paramsWaterStorage
#>           maxFMC maxMCleaf maxMCstem   LeafPI0  LeafEPS    LeafAF     Vleaf
#> T1_148 122.16441  142.2755 101.30719 -1.236151 10.52923 0.3447917 0.5488595
#> T2_168 109.23042  159.3801  47.00007 -2.070000 18.27000 0.4580000 0.1347648
#> S1_165  98.39177  132.9039  71.62682 -2.370000 17.23000 0.2400000 0.2902653
#>        StemPI0  StemEPS    StemAF  Vsapwood
#> T1_148 -1.9760 12.82234 0.9258273 4.1672242
#> T2_168 -3.1824 44.33022 0.6263370 0.8201071
#> S1_165 -2.5168 22.41056 0.6263370 0.3874813
#> 
#> $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] NA NA NA
#> 
#> $internalLAIDistribution$PrevLAIdead
#> [1] NA NA NA
#> 
#> $internalLAIDistribution$PrevLAImistletoe
#> [1] NA NA NA
#> 
#> $internalLAIDistribution$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
#> 
#> $internalLAIDistribution$mistletoe
#>    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
#> 
#> $version
#> [1] "5.1.0"
#> 
#> attr(,"class")
#> [1] "spwbInput" "list"