plantAreaDensity: Plant Area Density (PAD)

Description

Computes Plant Area Density either from transmittance or attenuation coefficient estimates. Details of calculation and underlying assumptions can be found online at tools:::Rd_expr_doi("10.23708/1AJNMP"). PAD is defind as the plant area per unit volume ( PAD plant area / voxel volume = m^2 / m^3).

Usage

plantAreaDensity(
  vxsp,
  vx,
  lad = "spherical",
  angle.name = "angleMean",
  variable.name = c("transmittance", "attenuation_FPL_unbiasedMLE",
    "attenuation_PPL_MLE"),
  pad.max = 5,
  pulse.min = 5,
  ...
)

Value

A voxel space object with the requested PAD variables.

Arguments

vxsp: a VoxelSpace object.
vx: a subset of voxel index. A data.table with i, j, k columns. Missing parameter means whole voxel space.
lad: the name of the probability density function of the leaf angle distribution. One of AMAPVox:::leafAngleDistribution.
angle.name: the name of the mean angle variable in the VoxelSpace object.
variable.name: the name of the transmittance/attenuation variables in the VoxelSpace object. Transmittance variables are expected to start with "tra" and attenuation variables with "att".
pad.max: a float, the maximal PAD value
pulse.min: an integer, the minimal number of pulses in a voxel for computing the PAD. PAD set to NA otherwise.
...: additional parameters which will be passed to the leaf angle distribution functions. Details in computeG().

References

VINCENT, Gregoire; PIMONT, François; VERLEY, Philippe, 2021, "A note on PAD/LAD estimators implemented in AMAPVox 1.7", tools:::Rd_expr_doi("10.23708/1AJNMP"), DataSuds, V1

Examples

Run this code

# load a voxel file
vxsp <- readVoxelSpace(system.file("extdata", "tls_sample.vox", package = "AMAPVox"))
# compute PAD
pad <- plantAreaDensity(vxsp, variable.name = "attenuation_PPL_MLE")
# merge pad variables into voxel space
vxsp@data <- merge(vxsp@data, pad, by = c("i", "j", "k"))
grep("^pad", names(vxsp), value = TRUE) # print PAD variables in vxsp
# PAD on a subset
pad.i2j3 <- plantAreaDensity(vxsp, vxsp@data[i ==2 & j==3, .(i, j, k)])
pad.i2j3[["ground_distance"]] <- vxsp@data[i ==2 & j==3]$ground_distance
if (FALSE) {
# plot vertical profile
library(ggplot2)
# meld data.table (wide-to-long reshaping)
pad <- data.table::melt(pad.i2j3,
  id.vars = "ground_distance",
  measure.vars = c("pad_transmittance", "pad_attenuation_FPL_unbiasedMLE",
    "pad_attenuation_PPL_MLE"))
ggplot(data = pad, aes(x=value, y=ground_distance, color=variable)) +
  geom_path() + geom_point()
}