get_cum_break {LadderFuelsR}

CBH estimation using the breaking point method and the LAD percentage below and above the CBH

Description

This function calculates the canopy base height (CBH) of the vertical tree profile (VTP) using a segmented regression model fitted to the cumulative LAD values as a function of height.The function also calculates the percentage of LAD values below and above the identified CBH or breaking point.

Usage

get_cum_break(LAD_profiles, cbh_metrics, threshold=75, verbose=TRUE)

Arguments

LAD_profiles

Original tree Leaf Area Density (LAD) profile (output of [lad.profile()] function in the leafR package). An object of the class data frame.

cbh_metrics

CBH metrics based on three criteria: maximum LAD percentage, maximum distance and last distance (output of [get_cbh_metrics()] function). An object of the class data frame.

threshold

Numeric value of the LAD percentage below or above the breaking point to set the CBH (default 75).

verbose

Logical, indicating whether to display informational messages (default is TRUE).

Details

# List of tree metrics:

• treeID: tree ID with strings and numeric values

• treeID1: tree ID with only numeric values

• Hdist: Height of the distance between the ground and the CBH or breaking point (m)

• Hcbh_brpt: Height of the CBH based on the breaking point method (m)

• below_hcbhbp: Percentage of LAD values below the CBH or breaking point

• above_hcbhbp: Percentage of LAD values above the CBH or breaking point

• bp_hcbh: Height of the CBH based on the breaking point method or on the maximum LAD criterium if there is not breaking point (m)

• bp_Hdptf: Height of the canopy layer depth using the breaking point method or the maximum LAD criterium (m)

• bp_dptf: Depth of the CBH using the breaking point method or the maximum LAD criterium (m)

• bp_Hdist: Height of the distance between the CBH and the ground using the breaking point method or the maximum LAD criterium (m)

• bp_effdist: Distance between the CBH and the ground using the breaking point method or the maximum LAD criterium (m)

• bp_lad: Percentage of LAD comprised by the canopy layer

• cumlad: Cumulative LAD values at the CBH or breaking point

• max_height: Maximum height of the tree profile

Value

A data frame identifying the CBH of the vertical tree profile (VTP) based on the breaking point method and the percentage of LAD values below and above the identified CBH or breaking point.

Author(s)

Olga Viedma, Carlos Silva and JM Moreno

See Also

get_cbh_metrics

Examples

library(magrittr)
library(segmented)
library(gdata)
library(dplyr)

# LAD profiles derived from normalized ALS data after applying [lad.profile()] function
LAD_profiles <- read.table(system.file("extdata", "LAD_profiles.txt", package = "LadderFuelsR"),
header = TRUE)
LAD_profiles$treeID <- factor(LAD_profiles$treeID)

# Before running this example, make sure to run get_cbh_metrics().
if (interactive()) {
cbh_metrics <- get_cbh_dist()
LadderFuelsR::cbh_metrics$treeID <- factor(LadderFuelsR::cbh_metrics$treeID)

trees_name1 <- as.character(cbh_metrics$treeID)
trees_name2 <- factor(unique(trees_name1))

cum_LAD_metrics_list <- list()

for (i in levels(trees_name2)) {
# Filter data for each tree
tree1 <- LAD_profiles |> dplyr::filter(treeID == i)
tree2 <- cbh_metrics |> dplyr::filter(treeID == i)

# Get cumulative LAD metrics for each tree
cum_LAD_metrics <- get_cum_break(tree1, tree2, threshold=75, verbose=TRUE)
cum_LAD_metrics_list[[i]] <- cum_LAD_metrics
}

# Combine the individual data frames
cummulative_LAD <- dplyr::bind_rows(cum_LAD_metrics_list)
}