Returns the diameter at breast height (DBH) and functional diameter at breast height (fDBH) of a tree measured from a tree point cloud. There should be only one stem at breast height.
Usage
dbh_pc(
pc,
thresholdR2 = 0.001,
slice_thickness = 0.06,
functional = TRUE,
concavity = 4,
dtm = NA,
r = 5,
plot = FALSE,
plotcolors = c("#000000", "#1c027a", "#08aa7c", "#fac87f")
)Arguments
- pc
The tree point cloud as a data.frame with columns X,Y,Z. Output of
read_tree_pc.- thresholdR2
Numeric value (default=0.001) that is multiplied with the radius to determine if at breast height (1.3 m above the lowest point of the point cloud) the circle fit is influenced by branches. If the resulting value is exceeded, the lower trunk without branches is extracted using
extract_lower_trunk_pc. Increase the thresholdR2 if your point cloud quality is low (for example, errors in co-registration of point clouds in multi-scan due to wind-effect).- slice_thickness
Numeric value (default = 0.06) that determines the thickness of the slice which is used to measure the diameter.
- functional
Logical (default=FALSE), indicates if the functional diameter should be calculated.
- concavity
Numeric value (default=4) concavity for the computation of the functional diameter using a concave hull based on
concaveman.- dtm
The digital terrain model as a data.frame with columns X,Y,Z (default = NA). If the digital terrain model is in the same format as a point cloud it can also be read with
read_tree_pc.- r
Numeric value (default=5) r which determines the range taken for the dtm. Should be at least the resolution of the dtm. Only relevant when a dtm is provided.
- plot
Logical (default=FALSE), indicates if the optimised circle fitting is plotted.
- plotcolors
list of four colors for plotting. Only relevant when plot = TRUE. The stem points, fitted circle, the concave hull and the estimated center are colored by the first, second and third and fourth element of this list respectively.
Value
List with the diameter of the stem at breast height, the residuals on the fitting, and the functional diameter at breast height. Also optionally (plot=TRUE) plots the circle fitting on the horizontal slice which is then included in the list output.
Details
The DBH is measured as the diameter of the optimal circle fitted through a
6mm thick horizontal slice (from 1.27 m to 1.33 m above the lowest tree
point) using diameter_slice_pc. A least squares circle fitting
algorithm is applied to find the optimal fit. Also the functional diameter at
breast height (fDBH) is determined using diameter_slice_pc. For
this the area of the concave hull with (concavity 4) is determined on the
slice. From this area the diameter is determined as the diameter of a circle
with this area. In case there are branches or foliage at this height, the
lower trunk is extracted using extract_lower_trunk_pc. Wether
this is the case is determined using the thresholdR2 parameter. When the
bottom of the point cloud is incomplete or obstructed you can choose to add a
digital terrain model as an input which is used to estimate lowest point of
the point cloud in order to obtain slices at the correct height of the tree.
Examples
if (FALSE) {
# Read tree point cloud and calculate the DBH
pc_tree <- read_tree_pc(PC_path = "path/to/point_cloud.txt")
dbh <- dbh_pc(pc = pc_tree)
# and plot the circle fitting
output <- dbh_pc(pc = pc_tree, plot = TRUE)
dbh <- output$dbh
}