medfate (version 2.8.0)

Plant values: Plant description functions

Description

Functions to calculate attributes of plants in a forest object.

Usage

plant_basalArea(x)
plant_largerTreeBasalArea(x)
plant_characterParameter(x, SpParams, parName)
plant_cover(x, SpParams, mode = "MED")
plant_crownBaseHeight(x, SpParams, mode = "MED")
plant_crownLength(x, SpParams, mode = "MED")
plant_crownRatio(x, SpParams, mode = "MED")
plant_density(x, SpParams, mode = "MED")
plant_equilibriumLeafLitter(x, SpParams, AET = 800, mode = "MED")
plant_equilibriumSmallBranchLitter(x, SpParams, 
                                   smallBranchDecompositionRate = 0.81, mode = "MED")
plant_foliarBiomass(x, SpParams, gdd = NA, mode = "MED")
plant_fuel(x, SpParams, gdd = NA, includeDead = TRUE, mode = "MED")
plant_height(x)
plant_ID(x, treeOffset = 0, shrubOffset = 0)
plant_LAI(x, SpParams, gdd = NA, mode = "MED")
plant_individualArea(x, SpParams, mode = "MED")
plant_parameter(x, SpParams, parName, fillMissing = TRUE)
plant_phytovolume(x, SpParams)
plant_species(x)
plant_speciesName(x, SpParams)

Value

A vector with values for each plant of the input forest object:

• plant_basalArea: Tree basal area (m2/ha).

• plant_largerTreeBasalArea: Basal area (m2/ha) of trees larger (in diameter) than the tree. Half of the trees of the same record are included.

• plant_characterParameter: The parameter values of each plant, as strings.

• plant_cover: Shrub cover (in percent).

• plant_crownBaseHeight: The height corresponding to the start of the crown (in cm).

• plant_crownLength: The difference between crown base height and total height (in cm).

• plant_crownRatio: The ratio between crown length and total height (between 0 and 1).

• plant_density: Plant density (ind/ha). Tree density is directly taken from the forest object, while the shrub density is estimated from cover and height by calculating the area of a single individual.

• plant_equilibriumLeafLitter: Litter biomass of leaves at equilibrium (in kg/m2).

• plant_equilibriumSmallBranchLitter: Litter biomass of small branches (< 6.35 mm diameter) at equilibrium (in kg/m2).

• plant_foliarBiomass: Standing biomass of leaves (in kg/m2).

• plant_fuel: Fine fuel load (in kg/m2).

• plant_height: Total height (in cm).

• plant_ID: Cohort coding for simulation functions (concatenation of 'T' (Trees) or 'S' (Shrub), cohort index and species index).

• plant_LAI: Leaf area index (m2/m2).

• plant_individualArea: Area (m2) occupied by a shrub individual.

• plant_parameter: The parameter values of each plant, as numeric.

• plant_phytovolume: Shrub phytovolume (m3/m2).

• plant_species: Species identity integer (indices start with 0).

• plant_speciesName: String with species taxonomic name (or a functional group).

Arguments

x

An object of class forest.

SpParams

A data frame with species parameters (see SpParamsMED).

parName

A string with a parameter name.

mode

Calculation mode, either "MED" or "US".

gdd

Growth degree days (to account for leaf phenology effects).

AET

Actual annual evapotranspiration (in mm).

smallBranchDecompositionRate

Decomposition rate of small branches.

includeDead

A flag to indicate that standing dead fuels (dead branches) are included.

treeOffset, shrubOffset

Integers to offset cohort IDs.

fillMissing

A boolean flag to try imputation on missing values.

Author

Miquel De Cáceres Ainsa, CREAF

See Also

spwb, forest, summary.forest

Examples

#Default species parameterization
data(SpParamsMED)

#Load example plot
data(exampleforestMED)

#A short way to obtain total basal area
sum(plant_basalArea(exampleforestMED), na.rm=TRUE)

#The same forest level function for LAI
sum(plant_LAI(exampleforestMED, SpParamsMED))

#The same forest level function for fuel loading
sum(plant_fuel(exampleforestMED, SpParamsMED))

#Summary function for 'forest' objects can be also used
summary(exampleforestMED, SpParamsMED)

plant_speciesName(exampleforestMED, SpParamsMED)

plant_ID(exampleforestMED)