plot_dbh_fit_pcs: Calculate and save figures of 'dbh_pc' function

In lmterryn/ITSMe: Individual Tree Structural Metrics

Calculate and save figures of dbh_pc function

Description

Calculates the dbh and saves the figures acquired when running dbh_pc on multiple tree point clouds in a folder.

Usage

plot_dbh_fit_pcs(
  PCs_path,
  extension = ".txt",
  thresholdR2 = 0.001,
  slice_thickness = 0.06,
  functional = TRUE,
  concavity = 4,
  dtm = NA,
  r = 5,
  OUT_path = "./",
  plotcolors = c("#000000", "#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".
thresholdR2	Numeric value (default=0.001). Parameter of the dbh_pc function used to calculate the diameter at breast height.
slice_thickness	Numeric value (default = 0.06). Parameter of the dbh_pc function used to calculate the diameter at breast height.
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.
OUT_path	A character with the path to the folder where the figures should be saved (default = current folder).
plotcolors	list of three colors for plotting. Only relevant when plot = TRUE. The stem points, fitted circle, the concave hull and the estimated center are colored by the first, second and third and fourth element of this list respectively.

Details

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

Value

A list with in the first element a numeric containing the dbh 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 DBHs and save circle fitting figures
dbh_values <- plot_dbh_fit_pcs(
  PCs_path = "path/to/folder/PCs/",
  extension = ".txt",
  OUT_path = "path/to/figure/folder/"
)

## End(Not run)

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