Skip to contents

Summary basic structural metrics tree point cloud for one tree.

Source: R/summary_metrics.R
summary_basic_pointcloud_metrics_pertree.Rd

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 of one tree.

Usage

summary_basic_pointcloud_metrics_pertree(
  PC_path,
  metrics = c("tree position", "stem diameter", "tree height", "projected area",
    "alpha volume"),
  dtm = NA,
  r = 5,
  crown = FALSE,
  thresholdbranch = 1.5,
  minheight = 1,
  concavity = 2,
  alpha = 1,
  buttress = FALSE,
  h_cutoff = 20,
  thresholdR2 = 0.001,
  slice_thickness = 0.06,
  thresholdbuttress = 0.001,
  maxbuttressheight = 7,
  functional = TRUE,
  concavity_fdiameter = 4,
  how = "median",
  arc_min_length_cm = NULL,
  arc_min_angle = 18,
  arc_tolerance = 0.05,
  min_inner_buffer = 0.06,
  inner_buffer_fraction = 0.5,
  OUT_path = FALSE,
  overwrite = FALSE,
  plot = FALSE,
  plotcolors = c("#000000", "#808080", "#1c027a", "#08aa7c", "#fac87f")
)

Arguments

PC_path

A character with the path to the tree point cloud.

metrics

A list of strings referring to the metrics you want to calculate. The possibilities are "tree position", "stem diameter", "tree height", "projected area", and "alpha volume".

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).

h_cutoff

Numeric value (default=15), height threshold where dab is measured when buttress == TRUE.

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.

how

Method used to summarise point-to-centre radii when estimating DBH with dbh_pc. Use "mean" for the original ITSMe behaviour, "median" for the median radius, or a numeric value such as 10 to trim 5 percent of radii on each side before taking the mean. Only relevant when buttress == FALSE.

arc_min_length_cm

Optional numeric. Minimum arc length, in centimetres, represented by one angular sector when calculating arc coverage with dbh_pc. If supplied, this is converted to degrees based on the fitted radius. Only relevant when buttress == FALSE.

arc_min_angle

Numeric. Minimum angular sector width in degrees used to calculate arc coverage with dbh_pc. Default is 18, corresponding to 20 sectors. Only relevant when buttress == FALSE.

arc_tolerance

Numeric. Radial tolerance, in metres, around the fitted DBH circle. Points within radius +/- arc_tolerance are counted as supporting the fitted circle when calculating arc coverage with dbh_pc. Only relevant when buttress == FALSE.

min_inner_buffer

Numeric. Minimum buffer distance, in metres, excluded from the fitted DBH radius before checking whether the inner circle is empty with dbh_pc. Only relevant when buttress == FALSE.

inner_buffer_fraction

Numeric. Fraction of the fitted DBH radius used as buffer before checking whether the inner circle is empty with dbh_pc. The effective buffer is max(min_inner_buffer, inner_buffer_fraction * radius). Only relevant when buttress == FALSE.

OUT_path

A character with name of the output folder where the summary figures should be saved or logical (default=FALSE) in this case no figures are saved.

overwrite

Logical (default=FALSE), indicates if the output file can be overwritten.

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.

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.

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.

Examples

if (FALSE) { # \dontrun{
# Calculate the summary with default parameters and export summary figure
summary <- summary_basic_pointcloud_metrics(
  PC_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(
  PC_path = "path/to/folder/PCs/",
  metrics = c("tree position", "stem diameter"),
  crown = TRUE, minheight = 4, buttress = TRUE
)
} # }