plot_av_pcs: Calculate and save figures of 'alpha_volume_pc' function

In lmterryn/ITSMe: Individual Tree Structural Metrics

Calculate and save figures of alpha_volume_pc function

Description

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.

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.

Value

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

Examples

## Not run: 
# 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
)

## End(Not run)

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