plot_pa_pcs: Calculate and save figures of 'projected_area_pc' function

In lmterryn/ITSMe: Individual Tree Structural Metrics

Calculate and save figures of projected_area_pc function

Description

Calculates the projected (crown) area and saves the figures acquired when running projected_area_pc on multiple tree point clouds in a folder.

Usage

plot_pa_pcs(
  PCs_path,
  extension = ".txt",
  OUT_path = "./",
  concavity = 2,
  crown = FALSE,
  thresholdbranch = 1.5,
  minheight = 1,
  buttress = FALSE,
  thresholdR2 = 0.001,
  slice_thickness = 0.06,
  thresholdbuttress = 0.001,
  maxbuttressheight = 7,
  concavity_classify = 4,
  dtm = NA,
  r = 5,
  plotcolors = c("#000000", "#08aa7c")
)

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).
concavity	Numeric value (default=2) concavity for the computation of a concave hull based on concaveman in projected_area_pc.
crown	Logical (default=FALSE), indicates if the area is calculated based on the full point clouds (crown = FALSE) or only on the crown point clouds (crown = TRUE).
thresholdbranch	Numeric value (default=1.5) from classify_crown_pc. Only relevant when crown == TRUE.
minheight	Numeric value (default=1) from classify_crown_pc. The default value is based on non-buttressed trees. Choose a higher value (e.g. 4) for buttressed trees. Only relevant when crown == TRUE.
buttress	Logical (default=FALSE), indicates if the trees have buttresses (higher than breast height). Only relevant when crown == TRUE.
thresholdR2	Numeric value (default=0.001). Parameter of the dbh_pc function used to calculate the diameter at breast height. Only relevant when crown == TRUE and buttress == FALSE.
slice_thickness	Numeric value (default = 0.06). Parameter of the dbh_pc and dab_pc functions used to calculate the diameter at breast height and above buttresses.
thresholdbuttress	Numeric value (default=0.001). Parameter of the dab_pc function used to calculate the diameter above buttresses which is used in classify_crown_pc. Only relevant when crown == TRUE and buttress == FALSE.
maxbuttressheight	Numeric value (default=7). Parameter of the dab_pc function used to calculate the diameter above buttresses which is used in classify_crown_pc. Only relevant when crown == TRUE and buttress == FALSE.
concavity_classify	Numeric value (default=4) concavity for the computation of the functional diameter using a concave hull based on concaveman which is used in classify_crown_pc.
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 two colors for plotting. Only relevant when plot = TRUE. The stem points and the concave hull are colored by the first and second element of this list respectively.

Details

Uses read_tree_pc to read the point clouds and projected_area_pc with parameter plot = TRUE to calculate the projected area and plot the crown projection and fitting. Choose crown = TRUE, if you want to calculate and plot the projected crown area. In this case a crown classification is done using classify_crown_pc and the crown points are used as an input to projected_area_pc. For buttressed trees, first optimise the thresholdbuttress, maxbuttressheight, thresholdbranch and minheight parameter values using plot_dab_fit_pcs and plot_crown_classification_pcs and use those optimised values in this function.

Value

A list with in the first element a numeric containing the projected area values for each tree point cloud. In the second element there is the list with the plots. Figures are also saved in the output folder.

Examples

## Not run: 
# Calculate projected area with default settings and save projection figures
pas <- plot_pa_pcs(
  PCs_path = "path/to/folder/PCs/", extension = ".txt",
  OUT_path = "path/to/figure/folder/"
)
# With non-default settings and save projection figures
pas <- plot_pa_pcs(
  PCs_path = "path/to/folder/PCs/", extension = ".txt",
  OUT_path = "path/to/figure/folder/", concavity = 3
)
# Calculate projected crown area and save projection figures
pcas <- plot_pa_pcs(
  PCs_path = "path/to/folder/PCs/", extension = ".txt",
  OUT_path = "path/to/figure/folder/", concavity = 3,
  crown = TRUE, minheight = 4, buttress = TRUE
)

## End(Not run)

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