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Calculate and save figures of alpha_volume_pc function

Source: R/plotting_metrics_pc.R
plot_av_pcs.Rd

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

Usage

plot_av_pcs(
  PCs_path,
  extension = ".txt",
  OUT_path = "./",
  alpha = 1,
  crown = FALSE,
  thresholdbranch = 1.5,
  minheight = 1,
  buttress = FALSE,
  thresholdR2 = 0.001,
  slice_thickness = 0.06,
  thresholdbuttress = 0.001,
  maxbuttressheight = 7,
  concavity = 4,
  dtm = NA,
  r = 5,
  plotcolor = "#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).

alpha

Numeric value (default=1) alpha for the computation of the 3D alpha-shape of the tree crown based on ashape3d in alpha_volume_pc.

crown

Logical (default=FALSE), indicates if the volume 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.

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

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.

plotcolor

color for plotting 3D shape. Only relevant when plot = TRUE.

Value

a numeric containing the volume values for each tree point cloud. Figures are saved in the output folder.

Details

Uses read_tree_pc to read the point clouds and alpha_volume_pc with parameter plot = TRUE to calculate the volume and plot the 3D the alpha-shape fitting. Choose crown = TRUE, if you want to calculate and plot the crown volume. In this case a crown classification is done using classify_crown_pc and the crown points are used as an input to alpha_volume_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 the volume with default settings and save alpha shape figures
vs <- plot_av_pcs(
  PCs_path = "path/to/folder/PCs/", extension = ".txt",
  OUT_path = "path/to/figure/folder/"
)
# Calculate the volume with non-default settings and save alpha shape figures
vs <- plot_av_pcs(
  PCs_path = "path/to/folder/PCs/", extension = ".txt",
  OUT_path = "path/to/figure/folder/", alpha = 2
)
# Calculate crown volume and save alpha shape figures
cvs <- plot_av_pcs(
  PCs_path = "path/to/folder/PCs/", extension = ".txt",
  OUT_path = "path/to/figure/folder/", alpha = 2,
  crown = TRUE, minheight = 4, buttress = TRUE
)
}