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Calculate and save figures of projected_area_pc function

Source: R/plotting_metrics_pc.R
plot_pa_pcs.Rd

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.

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.

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.

Examples

if (FALSE) {
# 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
)
}