summary_basic_pointcloud_metrics: Summary basic structural metrics tree point cloud

In lmterryn/ITSMe: Individual Tree Structural Metrics

Summary basic structural metrics tree point cloud

Description

Returns a summary data.frame containing the tree position (X,Y-coordinates), tree height, diameter at breast height, functional diameter at breast height, diameter above buttresses, functional diameter above buttresses, projected (crown) area and (crown) volume.

Usage

summary_basic_pointcloud_metrics(
  PCs_path,
  extension = ".txt",
  dtm = NA,
  r = 5,
  crown = FALSE,
  thresholdbranch = 1.5,
  minheight = 1,
  concavity = 2,
  alpha = 1,
  buttress = FALSE,
  thresholdR2 = 0.001,
  slice_thickness = 0.06,
  thresholdbuttress = 0.001,
  maxbuttressheight = 7,
  functional = TRUE,
  concavity_fdiameter = 4,
  OUT_path = FALSE,
  plot = FALSE,
  plotcolors = c("#000000", "#808080", "#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". Only relevant if the tree point clouds are available.
dtm	The digital terrain model from tree_height_pc.
r	Numeric value (default=5) r which determines the range taken for the dtm from tree_height_pc. Only relevant if a dtm is provided.
crown	Logical (default=FALSE), indicates if the area and 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. Only relevant when crown == TRUE.
concavity	Numeric value (default=2). Parameter of the projected_area_pc function used to calculate the projected crown area.
alpha	Numeric value (default=1). Parameter of the alpha_volume_pc function used to calculate the crown volume.
buttress	Logical (default=FALSE), indicates if the trees have buttresses (higher than breast height).
thresholdR2	Numeric value (default=0.001). Parameter of the dbh_pc function used to calculate the diameter at breast height. Only relevant if 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. Only relevant when buttress == TRUE.
maxbuttressheight	Numeric value (default=7). Parameter of the dab_pc function used to calculate the diameter above buttresses. Only relevant when buttress == TRUE.
functional	Logical (default=FALSE), indicates if the functional diameter should be calculated.
concavity_fdiameter	Numeric value (default=4) concavity for the computation of the functional diameter using a concave hull based on concaveman. This concavity value is used in the functions diameter_slice_pc, dbh_pc, dab_pc, and classify_crown_pc.
OUT_path	A character with name of the output file (including the path to the folder), where the summary csv file should be saved or logical (default=FALSE) in this case no csv file is produced.
plot	Logical (default=FALSE), indicates if summary figure for each tree point cloud is plotted. If an OUT_path is provided, the figures are saved in the OUT_path.
plotcolors	list of five colors for plotting. Only relevant when plot = TRUE. The stem points above buttresses, stem points at breast height, fitted circle, the concave hull and the estimated center are colored by the first, second, third, fourth and fifth element of this list respectively.

Details

The tree position, tree height, diameter at breast height, functional diameter at breast height, diameter above buttresses, functional diameter above buttresses, projected (crown) area and (crown) volume are otained with tree_position_pc, tree_height_pc, dbh_pc, dab_pc, projected_area_pc and alpha_volume_pc respectively.

Value

The summary of the basic structural metrics for multiple tree point clouds as a data.frame. Includes the tree height, diameter at breast height, diameter above buttresses, projected (crown) area and (crown) volume. The summary is saved in a csv file if an output folder is provided.

Examples

## Not run: 
# Calculate the summary with default parameters and export to csv
summary <- summary_basic_pointcloud_metrics(
  PCs_path = "path/to/folder/PCs/",
  OUT_path = "path/to/out/folder/"
)
# Calculate the summary with non-default parameter values
# recommended for buttressed trees
summary <- summary_basic_pointcloud_metrics(
  PCs_path = "path/to/folder/PCs/",
  extension = ".ply", crown = TRUE,
  minheight = 4, buttress = TRUE
)

## End(Not run)

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