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

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_)

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

plant_equilibriumLeafLitter(x, SpParams, AET = 800)

  smallBranchDecompositionRate = 0.81

plant_phytovolume(x, SpParams)

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

plant_characterParameter(x, SpParams, parName)

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



An object of class forest.


A data frame with species parameters (see SpParamsMED).

treeOffset, shrubOffset

Integers to offset cohort IDs.


Proportion of the target cohort included in the assessment


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


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


Actual annual evapotranspiration (in mm).


Decomposition rate of small branches.


A boolean flag to indicate that extreme values should be prevented (maximum tree LAI = 7 and maximum shrub LAI = 3)


A string with a parameter name.


A boolean flag to try imputation on missing values.


A boolean flag to try imputation of missing values using genus values.


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).


Miquel De Cáceres Ainsa, CREAF


#Default species parameterization

#Load example plot

#A plant-level way to obtain stand basal area
sum(plant_basalArea(exampleforest, SpParamsMED), na.rm=TRUE)
#> [1] 25.0333

#The analogous plant-level function for LAI
sum(plant_LAI(exampleforest, SpParamsMED))
#> [1] 1.584948
#The analogous plant-level function for fuel loading
sum(plant_fuelLoading(exampleforest, SpParamsMED))
#> [1] 0.5395798
#Summary function for 'forest' objects can be also used
summary(exampleforest, SpParamsMED)
#> Tree BA (m2/ha): 25.0333016  adult trees: 25.0333016  saplings: 0 
#> Density (ind/ha) adult trees: 552  saplings: 0  shrubs (estimated): 749.4923076 
#> Cover (%) adult trees: 100  saplings: 0  shrubs: 3.75  herbs: 10 
#> LAI (m2/m2) total: 1.7585845  adult trees: 1.5543216  saplings: 0  shrubs: 0.030626  herbs: 0.1736369 
#> Fuel loading (kg/m2) total: 0.5588728  adult trees: 0.5255004  saplings: 0  shrubs: 0.0140795  herbs: 0.019293 
#> PAR ground (%): NA  SWR ground (%): NA 

#Cohort IDs in the models
plant_ID(exampleforest, SpParamsMED)
#> [1] "T1_148" "T2_168" "S1_165"