modelInput: Input for simulation models
In medfate: Mediterranean Forest Simulation

forest2aboveground

R Documentation

Input for simulation models

Description

Functions forest2spwbInput and forest2growthInput take an object of class forest and create input objects for simulation functions spwb (or pwb) and growth, respectively. Function forest2aboveground calculates aboveground variables such as leaf area index. Function forest2belowground calculates belowground variables such as fine root distribution.

Usage

forest2aboveground(x, SpParams, gdd = NA_real_, loading = FALSE)

forest2belowground(x, soil, SpParams)

forest2spwbInput(x, soil, SpParams, control)

forest2growthInput(x, soil, SpParams, control)

Arguments

`x`	An object of class `forest`.
`SpParams`	A data frame with species parameters (see `SpParamsDefinition` and `SpParamsMED`).
`gdd`	Growth degree days to account for leaf phenology effects (in Celsius). This should be left `NA` in most applications.
`loading`	A logical flag to indicate that fuel loading should be included (for fire hazard calculations).
`soil`	An object of class `soil`.
`control`	A list with default control parameters (see `defaultControl`).

Details

Function forest2aboveground extract height and species identity from plant cohorts of x, and calculate leaf area index and crown ratio. Functions forest2spwbInput and forest2growthInput also calculate the distribution of fine roots across soil, and finds parameter values for each plant cohort according to the parameters of its species as specified in SpParams. If control$transpirationMode = "Sperry" or control$transpirationMode = "Cochard", the forest2spwbInput and forest2growthInput also estimate the maximum conductance of rhizosphere, root xylem and stem xylem elements.

Value

Function forest2aboveground() returns a data frame with the following columns (rows are identified as specified by function plant_ID):

SP: Species identity (an integer) (first species is 0).
N: Cohort density (ind/ha) (see function plant_density).
DBH: Tree diameter at breast height (cm).
H: Plant total height (cm).
CR: Crown ratio (crown length to total height) (between 0 and 1).
LAI_live: Live leaf area index (m2/m2) (one-side leaf area relative to plot area), includes leaves in winter dormant buds.
LAI_expanded: Leaf area index of expanded leaves (m2/m2) (one-side leaf area relative to plot area).
LAI_dead: Dead leaf area index (m2/m2) (one-side leaf area relative to plot area).
Loading: Fine fuel loading (kg/m2), only if loading = TRUE.

Function forest2spwbInput() 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).
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 = "Cochard" 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 = "Cochard" 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$transpirationMode = "Granier", columns are:
- Gswmin: Minimum stomatal conductance to water vapor (in mol H2O·m-2·s-1).
- Tmax_LAI: Coefficient relating LAI with the ratio of maximum transpiration over potential evapotranspiration.
- Tmax_LAIsq: Coefficient relating squared LAI with the ratio of maximum transpiration over potential evapotranspiration.
- Psi_Extract: Water potential corresponding to 50% relative transpiration (in MPa).
- Exp_Extract: Parameter of the Weibull function regulating transpiration reduction.
- VCstem_c, VCstem_d: Parameters of the stem xylem vulnerability curve.
- WUE: Daily water use efficiency (gross photosynthesis over transpiration) under no light, water or CO2 limitations and VPD = 1kPa (g C/mm water).
- WUE_par: Coefficient regulating the influence of % PAR on gross photosynthesis.
- WUE_par: Coefficient regulating the influence of atmospheric CO2 concentration on gross photosynthesis.
- WUE_par: Coefficient regulating the influence of vapor pressure deficit (VPD) on gross photosynthesis.
If control$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-2).
- Kmax_rootxylem: Sapwood-specific hydraulic conductivity of root xylem (in kg H2O·s-1·m-2).
- VCleaf_kmax: Maximum leaf hydraulic conductance.
- VCleaf_c, VCleaf_d: Parameters of the leaf vulnerability curve.
- VCstem_kmax: Maximum stem xylem conductance.
- VCstem_c, VCstem_d: Parameters of the stem xylem vulnerability curve.
- VCroot_c, VCroot_d: Parameters of the root xylem vulnerability curve.
- Plant_kmax: Maximum whole-plant conductance.
If control$transpirationMode = "Cochard" 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-2).
- Kmax_rootxylem: Sapwood-specific hydraulic conductivity of root xylem (in kg H2O·s-1·m-2).
- VCleaf_kmax: Maximum leaf hydraulic conductance.
- VCleaf_c, VCleaf_d: Parameters of the leaf vulnerability curve.
- VCstem_kmax: Maximum stem xylem conductance.
- VCstem_c, VCstem_d: Parameters of the stem xylem vulnerability curve.
- VCroot_c, VCroot_d: Parameters of the root xylem vulnerability curve.
- Plant_kmax: Maximum whole-plant conductance.
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 forest2growthInput 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

Examples

#Load example plot plant data
data(exampleforestMED)

#Default species parameterization
data(SpParamsMED)

# Aboveground parameters
forest2aboveground(exampleforestMED, SpParamsMED)

# Example of aboveground parameters taken from a forest
# described using LAI and crown ratio
data(exampleforestMED2)
forest2aboveground(exampleforestMED2, SpParamsMED)

# Initialize soil with default soil params
examplesoil <- soil(defaultSoilParams())

# Bewowground parameters (distribution of fine roots)
forest2belowground(exampleforestMED, examplesoil, SpParamsMED)

# Initialize control parameters using 'Granier' transpiration mode
control <- defaultControl("Granier")

# Prepare spwb input
forest2spwbInput(exampleforestMED, examplesoil, SpParamsMED, control)
                
# Prepare input for 'Sperry' transpiration mode
control <- defaultControl("Sperry")
forest2spwbInput(exampleforestMED,examplesoil,SpParamsMED, control)

# Prepare input for 'Cochard' transpiration mode
control <- defaultControl("Cochard")
forest2spwbInput(exampleforestMED,examplesoil,SpParamsMED, control)

# Example of initialization from a forest 
# described using LAI and crown ratio
control <- defaultControl("Granier")
forest2spwbInput(exampleforestMED2, examplesoil, SpParamsMED, control)

medfate documentation built on Aug. 29, 2023, 5:07 p.m.