plot_dab_fit_pcs: Calculate and save figures of 'dab_pc' function

In lmterryn/ITSMe: Individual Tree Structural Metrics

Calculate and save figures of dab_pc function

Description

Calculates the dab and saves the figures acquired when running dab_pc on multiple tree point clouds in a folder. Use different values for the thresholdbuttress and maxbuttressheight parameter to optimise dab calculation for your tree point clouds.

Usage

plot_dab_fit_pcs(
  PCs_path,
  extension = ".txt",
  OUT_path = "./",
  thresholdbuttress = 0.001,
  maxbuttressheight = 7,
  slice_thickness = 0.06,
  functional = TRUE,
  concavity = 4,
  dtm = NA,
  r = 5,
  plotcolors = c("#000000", "#808080", "#1c027a", "#08aa7c", "#fac87f")
)

Arguments

PCs_path	A character with the path to the folder that contains the tree point clouds.
extension	A character refering to the file extension of the point cloud files (default=".txt"). Can be ".txt", ".ply" or ".las".
OUT_path	A character with the path to the folder where the figures should be saved (default = current folder).
thresholdbuttress	Numeric value (default=0.001). Parameter of the dab_pc function used to calculate the diameter above buttresses.
maxbuttressheight	Numeric value (default=7). Parameter of the dab_pc function used to calculate the diameter above buttresses.
slice_thickness	Numeric value (default = 0.06) that determines the thickness of the slice which is used to measure the diameter.
functional	Logical (default=FALSE), indicates if the functional diameter should be calculated.
concavity	Numeric value (default=4) concavity for the computation of the functional diameter using a concave hull based on concaveman.
dtm	The digital terrain model (default = NA), parameter of tree_height_pc.
r	Numeric value (default=5) r, parameter of tree_height_pc. Only relevant if a dtm is provided.
plotcolors	list of three colors for plotting. Only relevant when plot = TRUE. The stem points above buttresses, stem points at breast height, fitted circle, the concave hull and the estimated center are colored by the first, second, third, fourth and fifth element of this list respectively.

Details

Uses read_tree_pc to read the point clouds and dab_pc with parameter plot = TRUE to calculate the dab and plot the circle fitting.

Value

A list with in the first element a numeric containing the dab values for each tree point cloud, the second element the residuals on the circle fittings, the third element the functional diameters. In the fourth element there is the list with the plots. Figures are also saved in the output folder.

Examples

## Not run: 
# Calculate DABs with default settings and save circle fitting figures
dab_values <- plot_dab_fit_pcs(
  PCs_path = "path/to/folder/PCs/",
  extension = ".txt",
  OUT_path = "path/to/figure/folder/"
)
# Calculate DABs with non-default settings and save circle fitting figures
dab_values <- plot_dab_fit_pcs(
  PCs_path = "path/to/folder/PCs/",
  extension = ".txt",
  OUT_path = "path/to/figure/folder/",
  thresholdbuttress = 0.002,
  maxbuttressheight = 5
)

## End(Not run)

lmterryn/ITSMe documentation built on Feb. 4, 2025, 2:21 a.m.