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)

plant_equilibriumSmallBranchLitter(
  x,
  SpParams,
  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)

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).

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

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)
#> [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"