Functions forest2spwbInput and forest2growthInput take an object of class forest and calculate input data for functions spwb, pwb and growth, respectively. Functions spwbInput and growthInput do the same but starting from different input data. Function forest2aboveground calculates aboveground variables that may be used in spwbInput and growthInput functions. Function forest2belowground calculates belowground fine root distribution.
forest2aboveground(x, SpParams, gdd = NA, mode = "MED")
forest2belowground(x, soil)
forest2growthInput(x, soil, SpParams, control)
forest2spwbInput(x, soil, SpParams, control, mode = "MED")
growthInput(above, Z50, Z95, soil, SpParams, control)
spwbInput(above, Z50, Z95, soil, SpParams, control)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).
Functions forest2spwbInput() and spwbInput() return 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).
control$transpirationMode = "Sperry" there are the following additional elements:
VGrhizo_kmax: A matrix with maximum rhizosphere conductance values of each cohort (in rows) in each soil layer (in columns).
VGroot_kmax: A matrix with maximum root xylem conductance values of each cohort (in rows) in each soil layer (in columns).
RhizoPsi: A matrix with the water potential around the rhizosphere of each cohort (in rows) in each soil layer (in columns).
paramsPhenology: A data frame with leaf phenology parameters:
PhenologyType: Leaf phenology type.
LeafDuration: Leaf duration (in years).
Sgdd: Degree days needed for leaf budburst (for winter decideous species).
Tbgdd: Base temperature for the calculation of degree days to leaf budburst.
Ssen: Degree days corresponding to leaf senescence.
Phsen: Photoperiod corresponding to start counting senescence degree-days.
Tbsen: Base temperature for the calculation of degree days to leaf senescence.
paramsAnatomy: A data frame with plant anatomy parameters for each cohort:
Hmax: Maximum plant height (cm).
Hmed: Median plant height (cm).
Al2As: Leaf area to sapwood area ratio (in m2·m-2).
Ar2Al: Fine root area to leaf area ratio (in m2·m-2).
SLA: Specific leaf area (mm2/mg = m2/kg).
LeafWidth: Leaf width (in cm).
LeafDensity: Density of leaf tissue (dry weight over volume).
WoodDensity: Density of wood tissue (dry weight over volume).
FineRootDensity: Density of fine root tissue (dry weight over volume).
SRL: Specific Root length (cm·g-1).
RLD: Root length density (cm·cm-3).
r635: Ratio between the weight of leaves plus branches and the weight of leaves alone for branches of 6.35 mm.
paramsInterception: A data frame with rain interception and light extinction parameters for each cohort:
kPAR: PAR extinction coefficient.
g: Canopy water retention capacity per LAI unit (mm/LAI).
control$transpirationMode = "Sperry" 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$transpirationMode = "Granier", columns are:
Gswmin: Minimum stomatal conductance to water vapor (in mol H2O·m-2·s-1).
Tmax_LAI: Coefficient relating LAI with the ratio of maximum transpiration over potential evapotranspiration.
Tmax_LAIsq: Coefficient relating squared LAI with the ratio of maximum transpiration over potential evapotranspiration.
Psi_Extract: Water potential corresponding to 50% relative conductance (in MPa).
Psi_Critic: Water potential corresponding to 50% of stem cavitation (in MPa).
WUE: Daily water use efficiency (gross photosynthesis over transpiration) under no light, water or CO2 limitations and VPD = 1kPa (g C/mm water).
WUE_par: Coefficient regulating the influence of % PAR on gross photosynthesis.
WUE_par: Coefficient regulating the influence of atmospheric CO2 concentration on gross photosynthesis.
WUE_par: Coefficient regulating the influence of vapor pressure deficit (VPD) on gross photosynthesis.
control$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.
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.
Functions forest2growthInput and growthInput return 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).
MortalityBaselineRate: Deterministic proportion or probability specifying the baseline reduction of cohort's density occurring in a year.
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.
fineRootBiomassTarget: Target fine root biomass (g dry) per individual (only if transpirationMode = "Sperry").
internalCarbon and internalRings: data structures to store other internal state variables.
An object of class forest.
A data frame with species parameters (see SpParamsDefinition and SpParamsMED).
Growth degree days to account for leaf phenology effects (in Celsius). This should be left NA in most applications.
Calculation mode, either "MED" or "US".
An object of class soil.
A list with default control parameters (see defaultControl).
A data frame with aboveground plant information (see the return value of forest2aboveground below). In the case of spwbInput the variables should include SP, N, LAI_live, LAI_dead, H and CR. In the case of growthInput variables should include DBH and Cover.
Numeric vectors with cohort depths (in mm) corresponding to 50% and 95% of fine roots.
Miquel De Cáceres Ainsa, CREAF
Functions forest2spwbInput and forest2abovegroundInput extracts height and species identity from plant cohorts of x, and calculate leaf area index and crown ratio.forest2spwbInput also calculates the distribution of fine roots across soil. Both forest2spwbInput and spwbInput find parameter values for each plant cohort according to the parameters of its species as specified in SpParams. If control$transpirationMode = "Sperry" the functions also estimate the maximum conductance of rhizosphere, root xylem and stem xylem elements.
resetInputs, spwb, soil, forest, SpParamsMED, defaultSoilParams, plant_ID
#Load example plot plant data
data(exampleforestMED)
#Default species parameterization
data(SpParamsMED)
# Aboveground parameters
above = forest2aboveground(exampleforestMED, SpParamsMED)
above
# Initialize soil with default soil params
examplesoil = soil(defaultSoilParams())
# Rooting depths
Z50 = c(exampleforestMED$treeData$Z50, exampleforestMED$shrubData$Z50)
Z95 = c(exampleforestMED$treeData$Z95, exampleforestMED$shrubData$Z95)
# Initialize control parameters
control = defaultControl("Granier")
# Prepare spwb input
spwbInput(above, Z50, Z95, examplesoil,SpParamsMED, control)
# When starting from an object of class 'forest' the whole process
# can be simplified:
forest2spwbInput(exampleforestMED, examplesoil, SpParamsMED, control)
# Prepare input for Sperry transpiration mode
control = defaultControl("Sperry")
forest2spwbInput(exampleforestMED,examplesoil,SpParamsMED, control)
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