individualshrubfuel: Shrub fuel biomass

In miquelcaceres/medfuels: Fuels of Mediterranean forests and shrublands

Description

Calculates dry weight (biomass, in kg) of total or fine fuels corresponding to individual shrub data

Usage

individualshrubfuel(x, type = "total", allometric = TRUE,
  excludeSSP = TRUE, var = FALSE, agg = "none",
  customParams = NULL, outside = "warning", na.rm = TRUE)

individualshrubarea(x, excludeSSP = TRUE, var = FALSE,
  customParams = NULL, outside = "warning", na.rm = TRUE)

individualshrubvolume(x, agg = "none", na.rm = TRUE)

Arguments

x	data frame with columns 'plot', 'species', 'H' (height in cm), 'D1' and 'D2' (in cm). If 'D2' is ommitted then shrub crowns are assumed to be circular (i.e. D2 = D1). Column 'group' may be used to specify a functional group to be used when the species has not a specific allometry (see details).
type	'total' (total fuel) or 'fine' (fine fuels)
allometric	wether to use allometric equations or bulk density estimates
excludeSSP	excludes subspecies information for species matching
var	a flag to indicate that variance of estimates is desired
agg	aggregation of results. Either 'none', 'species', 'speciesplot', 'plotspecies' or 'plot'
customParams	custom allometry parameter table (for species not in default params)
outside	Treament of values outside calibration range: either 'warning' (to prompt a warning) or 'missing' (prompt a warning and return NA)
na.rm	whether to exclude missing values when aggregating biomass

Details

The function determines the allometry to be applied using the following rules, sequentially:

1. If the species name is included in the list of species with parameter values, it takes the parameters from that species.

2. If the species name is a synonym for a species included the list of species with parameter values, it takes the parameters from that species (and gives a warning).

3. If the user has specified a column 'group' and the value is included in the list of valid groups, it takes the parameters from that group.

4. If the species is listed within the checklist in 'species_groups', it takes the parameters from the group specified in that file.

5. Otherwise, it gives a warning and no allometry is applied.

Value

a vector of dry weight (biomass) in kg

Examples

plot = c(1,1,2,2,2)
species = c("Erica arborea","Genista cinerea", "Erica arborea", "Chamaerops humilis", "Genista balansae")
H = c(60,70,200,100,10)
D1 = c(60,40,100, 100,25)
D2 = D1
x = data.frame(plot, species, H, D1, D2, stringsAsFactors=FALSE)

individualshrubfuel(x)

miquelcaceres/medfuels documentation built on May 12, 2019, 6:16 p.m.