medfate (version 2.9.3)

plant_values: Plant description functions

Description

Functions to calculate attributes of 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, mode = "MED")
plant_species(x, SpParams)
plant_speciesName(x, SpParams)
plant_density(x, SpParams, mode = "MED")
plant_height(x, SpParams)
plant_individualArea(x, SpParams, mode = "MED")
plant_crownRatio(x, SpParams, mode = "MED")
plant_crownBaseHeight(x, SpParams, mode = "MED")
plant_crownLength(x, SpParams, mode = "MED")
plant_foliarBiomass(x, SpParams, gdd = NA_real_, mode = "MED")
plant_fuel(x, SpParams, gdd = NA_real_, includeDead = TRUE, mode = "MED")
plant_equilibriumLeafLitter(x, SpParams, AET = 800, mode = "MED")
plant_equilibriumSmallBranchLitter(
  x,
  SpParams,
  smallBranchDecompositionRate = 0.81,
  mode = "MED"
)
plant_phytovolume(x, SpParams)
plant_LAI(x, SpParams, gdd = NA_real_, mode = "MED", bounded = TRUE)
plant_characterParameter(x, SpParams, parName)
plant_parameter(x, SpParams, parName, fillMissing = TRUE)

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).

treeOffset, shrubOffset

Integers to offset cohort IDs.

self_proportion

Proportion of the target cohort included in the assessment

mode

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

gdd

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

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.

Author

Miquel De Cáceres Ainsa, CREAF

See Also

spwb, forest, summary.forest

Examples

#Default species parameterization
data(SpParamsMED)

#Load example plot
data(exampleforestMED)

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

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

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