modelInput {medfate}

Input for simulation models

Description

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).

Details

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

IMPORTANT NOTE: Older function names forest2spwbInput and forest2growthInput are now deprecated, but they can still be used for back-compatibility.

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 H, CR and LAI (see function forest2aboveground).

• below: A data frame with columns Z50, Z95. If control$transpirationMode = "Sperry" additional columns are fineRootBiomass and coarseRootSoilVolume.

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

  • Gs_P50, Gs_slope: Parameters of the curve describing the decrease in stomatal conductance as a function of leaf water potential (sigmoid).

  • Vmax298: Maximum Rubisco carboxylation rate at 25ºC (in micromol CO2·s-1·m-2).

  • Jmax298: Maximum rate of electron transport at 25ºC (in micromol photons·s-1·m-2).

  • Kmax_stemxylem: Sapwood-specific hydraulic conductivity of stem xylem (in kg H2O·s-1·m-1·MPa-1).

  • Kmax_rootxylem: Sapwood-specific hydraulic conductivity of root xylem (in kg H2O·s-1·m-1·MPa-1).

  • VCleaf_kmax: Maximum leaf hydraulic conductance (in mmol H2O·s-1·m-2·MPa-1).

  • VCleaf_c, VCleaf_d: Parameters of the leaf vulnerability curve (Weibull).

  • VCleaf_P50, VCleaf_slope: Parameters of the leaf vulnerability curve (sigmoid).

  • VCstem_kmax: Maximum stem xylem conductance (in mmol H2O·s-1·m-2·MPa-1).

  • VCstem_c, VCstem_d: Parameters of the stem xylem vulnerability curve (Weibull).

  • VCstem_P50, VCstem_slope: Parameters of the stem xylem vulnerability curve (sigmoid).

  • VCroot_c, VCroot_d: Parameters of the root xylem vulnerability curve (Weibull).

  • VCroot_P50, VCroot_slope: Parameters of the root xylem vulnerability curve (sigmoid).

  • Plant_kmax: Maximum whole-plant conductance (in mmol H2O·s-1·m-2·MPa-1).

  • FR_leaf, FR_stem, FR_root: Fraction of whole-plant resistance corresponding to each segment.

• paramsWaterStorage: A data frame with plant water storage parameters for each cohort:

  • LeafPI0: Osmotic potential at full turgor of leaves (MPa).

  • LeafEPS: Modulus of elasticity (capacity of the cell wall to resist changes in volume in response to changes in turgor) of leaves (MPa).

  • LeafAF: Apoplastic fraction (proportion of water outside the living cells) in leaves.

  • Vleaf: Storage water capacity in leaves, per leaf area (L/m2).

  • StemPI0: Osmotic potential at full turgor of symplastic xylem tissue (MPa).

  • StemEPS: Modulus of elasticity (capacity of the cell wall to resist changes in volume in response to changes in turgor) of symplastic xylem tissue (Mpa).

  • StemAF: Apoplastic fraction (proportion of water outside the living cells) in stem xylem.

  • Vstem: Storage water capacity in sapwood, per leaf area (L/m2).

• 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).

• paramsAllometry: A data frame with allometric parameters for each cohort:

  • Aash: Regression coefficient relating the square of shrub height with shrub area.

  • Absh, Bbsh: Allometric coefficients relating phytovolume with dry weight of shrub individuals.

  • Acr, B1cr, B2cr, B3cr, C1cr, C2cr: Regression coefficients used to calculate crown ratio of trees.

  • Acw, Bcw: Regression coefficients used to calculated crown width of trees.

• internalAllocation: A data frame with internal allocation variables for each cohort:

  • allocationTarget: Value of the allocation target variable.

  • leafAreaTarget: Target leaf area (m2) per individual.

  • sapwoodAreaTarget: Target sapwood area (cm2) per individual.

  • fineRootBiomassTarget: Target fine root biomass (g dry) per individual.

  • crownBudPercent: Percentage of the crown with buds.

• internalCarbon: A data frame with the concentration (mol·gluc·l-1) of metabolic and storage carbon compartments for leaves and sapwood.

• internalMortality: A data frame to store the cumulative mortality (density for trees and cover for shrubs) predicted during the simulation, also distinguishing mortality due to starvation or dessication.

Author(s)

Miquel De Cáceres Ainsa, CREAF

See Also

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

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)
                
# Prepare input for 'Sperry' transpiration mode
control <- defaultControl("Sperry")
spwbInput(exampleforest,examplesoil,SpParamsMED, control)

# Prepare input for 'Sureau' transpiration mode
control <- defaultControl("Sureau")
spwbInput(exampleforest,examplesoil,SpParamsMED, control)

# Example of initialization from a forest 
# described using LAI and crown ratio
control <- defaultControl("Granier")
spwbInput(exampleforest2, examplesoil, SpParamsMED, control)