get_gaps_fbhs {LadderFuelsR}R Documentation

Gaps and Fuel layers Base Height (FBH)

Description

This function calculates gaps and fuel layers base height (FBH) as the difference in percentiles between consecutive LAD values along the vertical tree profile (VTP). Negative differences are linked to gaps and positive differences to fuel base height.

Usage

get_gaps_fbhs (LAD_profiles, 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 text.

verbose

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

Details

# List of tree metrics:

Value

A data frame giving the height of gaps and fuel layers bases in meters.

Author(s)

Olga Viedma, Carlos Silva and JM Moreno

Examples

library(magrittr)
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)

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

metrics_precentile_list1<-list()

for (i in levels(trees_name2)) {
tree1 <- LAD_profiles |> dplyr::filter(treeID == i)
metrics_precentil <- get_gaps_fbhs(tree1, verbose=TRUE)
metrics_precentile_list1[[i]] <- metrics_precentil
}

metrics_all_percentil <- dplyr::bind_rows(metrics_precentile_list1)
metrics_all_percentil$treeID <- factor(metrics_all_percentil$treeID)

# Remove the row with all NA values from the original data frame
# First remove "treeID" and "treeID1" columns
no_treeID <- metrics_all_percentil[, -which(names(metrics_all_percentil) == c("treeID","treeID1"))]

# Check if any row has all NA values
NA_or_zero <- apply(no_treeID, 1, function(row) all(is.na(row) | row == 0))

# Get the row index with all NA values
row_index <- which(NA_or_zero)

# Remove the row with all NA values from the original data frame
if (length(row_index) > 0) {
gap_cbh_metrics <- metrics_all_percentil[-row_index, ]
} else {
gap_cbh_metrics <- metrics_all_percentil
}

[Package LadderFuelsR version 0.0.4 Index]