plant_values: Woody plant cohort description functions
In medfate: Mediterranean Forest Simulation

plant_values

R Documentation

Woody plant cohort description functions

Description

Functions to calculate attributes of woody plants in a forest object.

Usage

plant_ID(x, SpParams, treeOffset = 0L, shrubOffset = 0L)

plant_basalArea(x, SpParams)

plant_largerTreeBasalArea(x, SpParams, self_proportion = 0.5)

plant_cover(x, SpParams)

plant_species(x, SpParams)

plant_speciesName(x, SpParams)

plant_density(x, SpParams)

plant_height(x, SpParams)

plant_individualArea(x, SpParams)

plant_crownRatio(x, SpParams)

plant_crownBaseHeight(x, SpParams)

plant_crownLength(x, SpParams)

plant_foliarBiomass(x, SpParams, gdd = NA_real_, competitionEffect = TRUE)

plant_fuelLoading(x, SpParams, gdd = NA_real_, includeDead = TRUE)

plant_equilibriumLeafLitter(x, SpParams, AET = 800)

plant_equilibriumSmallBranchLitter(
  x,
  SpParams,
  smallBranchDecompositionRate = 0.81
)

plant_phytovolume(x, SpParams)

plant_LAI(
  x,
  SpParams,
  gdd = NA_real_,
  bounded = TRUE,
  competitionEffect = TRUE
)

plant_characterParameter(x, SpParams, parName)

plant_parameter(x, SpParams, parName, fillMissing = TRUE, fillWithGenus = TRUE)

Arguments

`x`	An object of class `forest`.
`SpParams`	A data frame with species parameters (see `SpParamsMED`).
`treeOffset`, `shrubOffset`	Integers to offset cohort IDs.
`self_proportion`	Proportion of the target cohort included in the assessment
`gdd`	Growth degree days (to account for leaf phenology effects).
`competitionEffect`	Logical flag to indicate the inclusion of competition effect on LAI estimates.
`includeDead`	A flag to indicate that standing dead fuels (dead branches) are included.
`AET`	Actual annual evapotranspiration (in mm).
`smallBranchDecompositionRate`	Decomposition rate of small branches.
`bounded`	A boolean flag to indicate that extreme values should be prevented (maximum tree LAI = 7 and maximum shrub LAI = 3)
`parName`	A string with a parameter name.
`fillMissing`	A boolean flag to try imputation on missing values.
`fillWithGenus`	A boolean flag to try imputation of missing values using genus values.

Value

A vector with values for each woody plant cohort 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_fuelLoading: 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).

Author(s)

Miquel De Cáceres Ainsa, CREAF

Examples

#Default species parameterization
data(SpParamsMED)

#Load example plot
data(exampleforest)

#A plant-level way to obtain stand basal area
sum(plant_basalArea(exampleforest, SpParamsMED), na.rm=TRUE)

#The analogous plant-level function for LAI
sum(plant_LAI(exampleforest, SpParamsMED))
  
#The analogous plant-level function for fuel loading
sum(plant_fuelLoading(exampleforest, SpParamsMED))
      
#Summary function for 'forest' objects can be also used
summary(exampleforest, SpParamsMED)

#Cohort IDs in the models
plant_ID(exampleforest, SpParamsMED)

medfate documentation built on April 4, 2025, 2:01 a.m.