process_pcl: Process single PCL transects.
In forestr: Ecosystem and Canopy Structural Complexity Metrics from LiDAR

Description Usage Arguments Details Value See Also Examples

process_pcl imports and processes a single PCL transect.

process_pcl(
  f,
  user_height,
  marker.spacing,
  max.vai,
  pavd = FALSE,
  hist = FALSE,
  save_output = TRUE
)

`f`	the name of the filename to input <character> or a data frame <data frame>.
`user_height`	the height of the laser off the ground as mounted on the user in meters. default is 1 m
`marker.spacing`	distance between markers, defaults is 10 m
`max.vai`	the maximum value of column VAI. The default is 8. Should be a max value, not a mean.
`pavd`	logical input to include Plant Area Volume Density Plot from plot_pavd, if TRUE it is included, if FALSE, it is not.
`hist`	logical input to include histogram of VAI with PAVD plot, if TRUE it is included, if FALSE, it is not.
`save_output`	the name of the output folder where to write all the output fiels.

This function imports raw pcl data or existing data frames of pcl data and writes all data and analysis to a series of .csv files in an output directory (output) keeping nothing in the workspace.

process_pcl uses a workflow that cuts the data into 1 meter segments with z and x positions in coordinate space where x referes to distance along the ground and z refers to distance above the ground. Data are normalized based on light extinction assumptions from the Beer-Lambert Law to account for light saturation. Data are then summarized and metrics of canopy structure complexity are calculated.

process_pcl will write multiple output files to disk in an output directory that process_pcl creates within the work directing. These files include:

1. an output variables file that contains a list of CSC variables and is written by the subfunction write_pcl_to_csv 2. a summary matrix, that includes detailed information on each vertical column of LiDAR data written by the subfunction write_summary_matrix_to_csv 3. a hit matrix, which is a matrix of VAI at each x and z position, written by the subfunction write_hit_matrix_to_pcl 4. a hit grid, which is a graphical representation of VAI along the x and z coordinate space. 5. optionally, plant area/volume density profiles can be created by including pavd = TRUE that include an additional histogram with the optional hist = TRUE in the process_pcl call.

writes the hit matrix, summary matrix, and output variables to csv in an output folder, along with hit grid plot

process_multi_pcl

# Run process complete PCL transect without storing to disk
uva.pcl <- system.file("extdata", "UVAX_A4_01W.csv", package = "forestr")

process_pcl(uva.pcl, marker.spacing = 10, user_height = 1.05,
max.vai = 8, pavd = FALSE, hist = FALSE, save_output = FALSE)

# with data frame
process_pcl(osbs, marker.spacing = 10, user_height = 1.05,
max.vai = 8, pavd = FALSE, hist = FALSE, save_output = FALSE)