LadderFuelsR: An R Package for vertical fuel continuity analysis using Airborne Laser Scanning data
Authors: Olga Viedma, Carlos Silva, JM Moreno and A.T. Hudak
Automated tool for vertical fuel continuity analysis using Airborne Laser Scanning data that can be applied on multiple tree species and for large-scale studies.The workflow consisted of 1) calculating the Leaf Area Density (LAD) profiles of each segmented tree; 2) identifying gaps and fuel layers; 3) estimating the distance between fuel layers; and 4) retrieving the fuel layers base height (FBH) and depth. Additionally, other functions recalculate previous metrics after considering distances greater than certain threshold and calculate the CBH based on three criteria: maximum LAD, and the largest- and the last-distance. Moreover, the package calculates: i) the percentage of LAD comprised in each fuel layer and remove fuel layers below a specified threshold (default 10 % LAD) recalculating the distances among the reminder ones. On the other hand, when the LAD profiles showed only one fuel layer with CBH at the minimum base height, it identifies the CBH performing a segmented linear regression (breaking point) on the cumulative sum of LAD as a function of height. Finally, a collection of plotting functions is developed to represent all previous metrics.
#The CRAN version:
install.packages("LadderFuelsR")
# The development version:
#install.packages("remotes")
library(remotes)
install_github("https://github.com/olgaviedma/LadderFuelsR", dependencies = TRUE)
# loading LadderFuelsR package
library(LadderFuelsR)```{r pressure, echo=FALSE} if (!require(“pacman”)) install.packages(“pacman”) pacman::p_load(plyr, dplyr, tidyr, stringr, stringi, purrr, rlang, tidyverse, sf, terra, raster, data.table, rgdal, lidR, leafR, segmented, lidRplugins, ggplot2, gt, gridExtra, patchwork, SSBtools, tibble, rgl, rglwidget, LadderFuelsR, magrittr, gdata)
## 1. Computing Canopy height model (CHM) using lidR package
```{r CHM pitfree 0.5 m, echo=TRUE, message=FALSE, warning=FALSE}
LIDAR_dir <- file.path(system.file("extdata", package = "LadderFuelsR"))
lidar_file<- lidR::readLAS(file.path(LIDAR_dir, "Eglin_zone1_clipped_000000.las"), filter = "-drop_z_below 0")
chm_pitfree<- grid_canopy(lidar_file, res=0.5,pitfree( c(0,2,5,10,15,20,25,30,35,40), c(0,1.5), subcircle=0.15))
chm_pitfree[chm_pitfree > 40] <- NA
chm_pitfree[chm_pitfree < 0] <- 0
chm_pitfree1 <- projectRaster(chm_pitfree, crs=26916)
col <- height.colors(25)
plot(chm_pitfree1,col=col)
```{r Tree tops detection, echo=TRUE, message=FALSE, warning=FALSE}
# parameters ws= 2.5 hmin = 2 res=0.5 ttops_multichm = find_trees(lidar_file, multichm(res = res, dist_2d = 2,ws= ws, layer_thickness = 0.3,dist_3d = 1, hmin = hmin)) proj4string(ttops_multichm) <- CRS(‘+init=EPSG:26916’)
x<-add_treetops3d(plot(lidar_file, bg = “white”, size = 4), ttops_multichm) # Customize the plot orientation rgl.viewpoint(theta = 0, phi = 0, fov = 60, zoom = 0.75) # Convert the rgl scene to an HTML widget rglwidget(elementId = “x”, width = 800, height = 600)
## 3. Individual tree crown deliniation (Silva et al. 2016)
```{r Crowns Silva, echo=TRUE, message=FALSE, warning=FALSE}
algo_silva1 <-silva2016(chm_pitfree1, ttops_multichm, max_cr_factor = 0.6, exclusion = 0.3, ID = "treeID")
crowns_silva_las1 <-segment_trees(lidar_file, algo_silva1, attribute = "treeID", uniqueness = "incremental")
crowns_silva_las2<-filter_poi(crowns_silva_las1, !is.na(treeID))
my_palette <- colorRampPalette(col)
x1<-plot(crowns_silva_las2, color = "treeID", pal = my_palette, bg = "white")
# Customize the plot orientation
rgl.viewpoint(theta = 0, phi = 0, fov = 10, zoom = 0.75)
# Convert the rgl scene to an HTML widget
rglwidget(elementId = "x1", width = 800, height = 600)
```{r tree metrics function, echo=TRUE}
custom_crown_metrics <- function(z, i) { # user-defined function metrics <- list( dz = 1, th = 1, z_max = max(z),# max height z_min = min(z),# min height z_mean = mean(z),# mean height z_sd = sd(z), # vertical variability of points z_q1=quantile(z, probs = 0.01), z_q5=quantile(z, probs = 0.05), z_q25=quantile(z, probs = 0.25), z_q50=quantile(z, probs = 0.50), z_q75=quantile(z, probs = 0.75), z_q95=quantile(z, probs = 0.95), crr=(mean(z)-min(z))/(max(z)-min(z)) ) return(metrics) # output } ccm = ~custom_crown_metrics(z = Z, i = Intensity)
## 5.Computing crown level standard metrics within all trees detected
```{r tree and crown standard and own metrics, echo=TRUE, message=FALSE, warning=FALSE}
crowns_silva_filter<-filter_poi(crowns_silva_las2, Z >= 1)
metrics1 = crown_metrics(crowns_silva_filter,func = .stdtreemetrics, geom = "convex")
crown_diam<-data.frame(sqrt(metrics1$convhull_area/ pi) * 2)
names(crown_diam)<-"crown_diam"
metrics2 = crown_metrics(crowns_silva_filter,func = ccm, geom = "convex") #concave
metrics_all <- dplyr::bind_cols(list(metrics1,crown_diam,metrics2))
metrics_all1 <- metrics_all[,c(1:4,6,10:21)]
names(metrics_all1)<-c("treeID", "Z", "npoints", "convhull_area", "crown_diam", "z_max", "z_min", "z_mean","z_sd", "z_q1","z_q5", "z_q25","z_q50","z_q75", "z_q95", "crr", "geometry" )
tree_crowns <- st_as_sf(metrics_all1)
ttops1<-st_as_sf(ttops_multichm)
crowns1<-st_as_sf(tree_crowns)
ttops_within_crowns <- st_intersection(ttops1, crowns1)
# Set the size of the plotting device
par(mfrow = c(1, 1), mar = c(1, 1, 1, 1), pin = c(5, 4))
plot(st_geometry(crowns1), pch = 16, col = "green")
plot(ttops_within_crowns, add = TRUE, pch= 16, col = "darkblue", main = "Tree tops over the crowns")
```{r cropLAS files with no overlapping crowns, echo=TRUE, message=FALSE, warning=FALSE}
trees_ID <- tree_crowns %>% dplyr::select(treeID) n <- nrow(trees_ID)
crown_cort <- vector(“list”, length=n)
for (i in 1:n) { kk <- trees_ID[i,] crown_cort[[i]] = clip_roi(crowns_silva_las2, kk) }
my_palette <- colorRampPalette(col) x2<-plot(crown_cort[[1]], color = “Z”, pal = my_palette, bg = “black”, size = 2.5)
rgl.viewpoint(theta = 0, phi = 0, fov = 60, zoom = 0.75)
rglwidget(elementId = “x2”, width = 400, height = 600)
<p align="center">
<img src="https://github.com/olgaviedma/LadderFuelsR/blob/master/Readme/fig6.png" alt="Las file cropped by crown polygons" width="400" height="400"/>
</p>
## 7.LAI-LAD metrics by Trees
```{r LAI and LAD tree metrics, echo=TRUE, message=FALSE, warning=FALSE}
LIDAR_dir <- file.path(system.file("extdata", package = "LadderFuelsR"))
las_list1 <- list.files(LIDAR_dir, pattern = "*_CROWN.las", full.names = TRUE, ignore.case = TRUE)
# create a vector to hold the file names of .las files with more than 10 points
files_with_more_than_10_points <- c()
# loop through each file
for (file in las_list1) {
las_data <- lidR::readLAS(file)
las_data1<-filter_poi(las_data, Z >= 1)
# skip to next file if there was a problem reading
if (is.null(las_data1)) next
# check if it contains more than three points
if (las_data1@header$`Number of point records` > 10) {
files_with_more_than_10_points <- c(files_with_more_than_10_points, file)
}
}
# Creates a data frame of the 3D voxels information (xyz) with Leaf Area Density values
short_name1<-NULL
profile_list<-NULL
lidar_lai_list<-NULL
understory_lai_list<-NULL
LAHV_metric_list<-NULL
for (j in seq_along(files_with_more_than_10_points)){
short_name<-stri_sub(files_with_more_than_10_points[j], 1, -5)
short_name1<-gsub(".*/","",short_name)
normlas_file<-files_with_more_than_10_points[[j]]
VOXELS_LAD = lad.voxels(normlas_file, grain.size = 2)
lad_profile = lad.profile(VOXELS_LAD, relative = F)
lai_tot = lai(lad_profile)
understory_lai <- lai(lad_profile, min = 0.3, max = 2.5)
LAHV_metric<- LAHV(lad_profile, LAI.weighting = FALSE, height.weighting = FALSE)
lad_profile1 = data.frame(lad_profile, treeID = short_name1)
lai_tot1 = data.frame(lai_tot, treeID = short_name1)
understory_lai1 = data.frame(understory_lai, treeID = short_name1)
LAHV_metric1 = data.frame(LAHV_metric, treeID = short_name1)
profile_list<-rbind(profile_list, lad_profile1)
lidar_lai_list<-rbind(lidar_lai_list,lai_tot1)
understory_lai_list <-rbind(understory_lai_list,understory_lai1)
LAHV_metric_list<-rbind(LAHV_metric_list,LAHV_metric1)
}
head(profile_list,10)
```{r depurating LAD databases, echo=TRUE, message=FALSE, warning=FALSE}
cols <- c(‘treeID’) profile_list[cols] <- lapply(profile_list[cols], function (x) as.factor(x)) profile_list\(lad<-round(profile_list\)lad,digits = 4)
cases <- data.frame(table(profile_list\(treeID)) cases1 <-cases[cases\)Freq > 5, ] names(cases1)<-c(“treeID”, “Freq”)
profile_list1 <- profile_list[profile_list\(treeID %in% cases1\)treeID, ] profile_list2 <- data.frame(profile_list1 %>% replace(is.na(.), 0.01))
## 9.Gaps and Fuel Layers Base Height (FBH)
```{r Gaps and Fuel layers Base Height (fbh), echo=TRUE, message=FALSE, warning=FALSE}
# LAD profiles derived from normalized ALS data after applying [lad.profile()] function from leafR package
profile_list2$treeID <- factor(profile_list2$treeID)
trees_name1 <- as.character(profile_list2$treeID)
trees_name2 <- factor(unique(trees_name1))
gaps_fbhs_list<-list()
for (i in levels(trees_name2)) {
tree2 <- profile_list2 |> dplyr::filter(treeID == i)
gaps_fbhs <- get_gaps_fbhs(tree2, step=1,
min_height=1.5,
perc_gap= 25,perc_base= 25,
verbose=TRUE)
gaps_fbhs_list[[i]] <- gaps_fbhs
}
gaps_fbhs_list1 <- dplyr::bind_rows(gaps_fbhs_list)
gaps_fbhs_list1$treeID <- factor(gaps_fbhs_list1$treeID)
# Remove the row with all NA values from the original data frame
# First remove "treeID" and "treeID1" columns
gaps_fbhs_list1_no_treeID <- gaps_fbhs_list1[, -which(names(gaps_fbhs_list1) == c("treeID","treeID1"))]
# Check if any row has all NA values
rows_with_all_NA_or_zero <- apply(gaps_fbhs_list1_no_treeID, 1, function(row) all(is.na(row) | row == 0))
# Get the row index with all NA values
row_index <- which(rows_with_all_NA_or_zero)
# Remove the row with all NA values from the original data frame
if (length(row_index) > 0) {
gaps_fbhs_metrics <- gaps_fbhs_list1[-row_index, ]
} else {
gaps_fbhs_metrics <- gaps_fbhs_list1
}
rownames(gaps_fbhs_metrics) <- NULL
head(gaps_fbhs_metrics)
```{r LAD percentile of each height bin, echo=TRUE, message=FALSE, warning=FALSE}
profile_list2\(treeID <- factor(profile_list2\)treeID)
trees_name1 <- as.character(profile_list2$treeID) trees_name2 <- factor(unique(trees_name1))
gaps_perc_list <- list() # Initialize outside the loop
for (i in levels(trees_name2)) {
tree1 <- profile_list2 |> dplyr::filter(treeID == i)
percentiles <- calculate_gaps_perc(tree1, min_height=1.5)
gaps_perc_list[[i]] <- percentiles
}
gaps_perc <- dplyr::bind_rows(gaps_perc_list)head(gaps_perc)
## 11.Distance between Fuel Layers
```{r Distances (and their heights) between fuel layers, echo=TRUE, message=FALSE, warning=FALSE}
# Tree metrics derived from get_gaps_fbhs() function
numeric_vars <- setdiff(names(gaps_fbhs_metrics), c("treeID", "treeID1"))
gaps_fbhs_metrics[numeric_vars] <- lapply(gaps_fbhs_metrics[numeric_vars], function(x) as.numeric(ifelse(x == "NA", NA, x)))
gaps_fbhs_metrics$treeID <- factor(gaps_fbhs_metrics$treeID)
# Tree metrics derived from calculate_gaps_perc() function
gaps_perc$treeID <- factor(gaps_perc$treeID)
trees_name1 <- as.character(gaps_fbhs_metrics$treeID)
trees_name2 <- factor(unique(trees_name1))
metrics_distance_list <- list()
for (i in levels(trees_name2)) {
# Filter data for each tree
tree1 <- gaps_fbhs_metrics |> dplyr::filter(treeID == i)
tree2 <- gaps_perc |> dplyr::filter(treeID == i)
# Get distance metrics for each tree
metrics_distance <- get_distance(tree1,tree2,step=1, min_height=1.5)
metrics_distance_list[[i]] <- metrics_distance
}
# Combine the individual data frames
distance_metrics <- dplyr::bind_rows(metrics_distance_list)
distance_metrics <- distance_metrics[, order(names(distance_metrics))]
rownames(distance_metrics) <- NULL
head(distance_metrics)
```{r Distane between fuel layers, echo=TRUE, message=FALSE, warning=FALSE}
library(dplyr) library(magrittr)
profile_list2\(treeID <- factor(profile_list2\)treeID) # Tree metrics derived from get_distance() function distance_metrics\(treeID <- factor(distance_metrics\)treeID)
metrics_depth_list <- list()
for (i in levels(profile_list2$treeID)){
tree1 <- profile_list2 |> dplyr::filter(treeID == i) tree2 <- distance_metrics |> dplyr::filter(treeID == i)
# Get depths for each tree metrics_depth <- get_depths(tree1, tree2,step= 1,min_height= 1.5) metrics_depth_list[[i]] <- metrics_depth }
depth_metrics <- dplyr::bind_rows(metrics_depth_list)
depth_metrics <- depth_metrics[, order(names(depth_metrics))] rownames(depth_metrics) <- NULL head(depth_metrics)
## 13.Plot Gaps and Fuel Layers Base Height (FBH)
```{r Plots Gaps and Fuel layers Base Height (fbh), echo=TRUE, message=FALSE, warning=FALSE}
library(LadderFuelsR)
library(ggplot2)
library(lattice)
# LAD profiles derived from normalized ALS data after applying [lad.profile()] function
profile_list2$treeID <- factor(profile_list2$treeID)
# Tree metrics derived from get_gaps_fbhs() function
gaps_fbhs_metrics$treeID <- factor(gaps_fbhs_metrics$treeID)
# Generate plots for gaps and fbhs
plots_gaps_fbhs <- get_plots_gap_fbh(profile_list2, gaps_fbhs_metrics,min_height=1.5)
par(mfrow = c(2, 2))
# Plot in RED are the GAPS and in GREEN the FBHs
plot(plots_gaps_fbhs[[1]])
plot(plots_gaps_fbhs[[2]])
plot(plots_gaps_fbhs[[3]]) |
 |
 |
```{r Fuels base height recalculation after after considering distances greater than any number of height bin steps, echo=TRUE, message=FALSE, warning=FALSE}
library(SSBtools) library(dplyr) library(magrittr)
depth_metrics\(treeID <- factor(depth_metrics\)treeID)
trees_name1 <- as.character(depth_metrics$treeID) trees_name2 <- factor(unique(trees_name1))
fbh_corr_list <- list()
for (i in levels(trees_name2)){
# Filter data for each tree tree3 <- depth_metrics |> dplyr::filter(treeID ==i)
# Get real fbh for each tree fbh_corr <- get_real_fbh(tree3,step= 1, number_steps = 1, min_height=1.5)
# Store fbh values in a list fbh_corr_list[[i]] <- fbh_corr }
fbh_metrics_corr <- dplyr::bind_rows(fbh_corr_list) fbh_metrics_corr\(treeID <- factor(fbh_metrics_corr\)treeID)
original_column_names <- colnames(fbh_metrics_corr)
prefixes <- c(“treeID”, “Hdist”, “Hcbh”, “Hdepth”, “dist”, “depth”, “max_height”)
new_order <- c()
for (prefix in prefixes) { # Find column names matching the current prefix matching_columns <- grep(paste0(“^”, prefix), original_column_names, value = TRUE) # Append to the new order new_order <- c(new_order, matching_columns) }
fbh_metrics_corr <- fbh_metrics_corr[, new_order] rownames(fbh_metrics_corr) <- NULL head(fbh_metrics_corr)
## 15.Fuel Layers Depth after removing distances greater than the actual height bin step
```{r Fuel layers depth after considering distances greater than the actual height bin step, echo=TRUE, message=FALSE, warning=FALSE}
library(dplyr)
library(magrittr)
library(tidyr)
# Tree metrics derived from get_real_fbh() function
fbh_metrics_corr$treeID <- factor(fbh_metrics_corr$treeID)
trees_name1 <- as.character(fbh_metrics_corr$treeID)
trees_name2 <- factor(unique(trees_name1))
depth_metrics_corr_list <- lapply(levels(trees_name2), function(i) {
# Filter data for each tree
tree2 <- fbh_metrics_corr |> dplyr::filter(treeID == i)
# Get real depths for each tree
get_real_depths(tree2,step=1, min_height=1.5)
})
# Combine depth values for all trees
depth_metrics_corr <- dplyr::bind_rows(depth_metrics_corr_list)
rownames(depth_metrics_corr) <- NULL
head(depth_metrics_corr)
```{r Fuel layers distances after considering distances greater than any number of height bin steps, echo=TRUE, message=FALSE, warning=FALSE}
library(dplyr) library(magrittr) library(stringr)
depth_metrics_corr\(treeID <- factor(depth_metrics_corr\)treeID)
trees_name1 <- as.character(depth_metrics_corr$treeID) trees_name2 <- factor(unique(trees_name1))
distance_metrics_corr_list <- lapply(levels(trees_name2), function(i) { # Filter data for each tree tree2 <- depth_metrics_corr |> dplyr::filter(treeID == “1_CROWN”) # Get effective gap for each tree get_effective_gap(tree2,number_steps = 1, min_height= 1.5) })
distances_metrics_corr <- dplyr::bind_rows(distance_metrics_corr_list)
original_column_names <- colnames(distances_metrics_corr)
prefixes <- c(“treeID”, “Hcbh”, “dptf”, “Hdptf”, “effdist”, “dist”, “Hdist”, “max_Hcbh”, “max_dptf”, “max_Hdptf”, “last_Hcbh”, “last_dptf”, “last_Hdptf”, “max_height”)
new_order <- c()
for (prefix in prefixes) { # Find column names matching the current prefix matching_columns <- grep(paste0(“^”, prefix), original_column_names, value = TRUE)
# Extract numeric suffixes and order the columns based on these suffixes numeric_suffixes <- as.numeric(gsub(paste0(“^”, prefix), ““, matching_columns)) matching_columns <- matching_columns[order(numeric_suffixes)]
# Append to new order new_order <- c(new_order, matching_columns) }
distances_metrics_corr1 <- distances_metrics_corr[, new_order] # Unlist the data frame distances_metrics_corr2 <- as.data.frame(lapply(distances_metrics_corr1, function(x) unlist(x))) rownames(distances_metrics_corr2) <- NULL head(distances_metrics_corr2)
## 17.Fuels LAD percentage (greater than a threshold)
```{r Fuels LAD percentage for fuel layers with a LAD percentage above a threshold (10 %), echo=TRUE, message=FALSE, warning=FALSE}
library(dplyr)
library(magrittr)
# LAD profiles derived from normalized ALS data after applying [lad.profile()] function
profile_list2$treeID <- factor(profile_list2$treeID)
# Tree metrics derived from get_effective_gap() function
distances_metrics_corr2$treeID <- factor(distances_metrics_corr2$treeID)
trees_name1 <- as.character(distances_metrics_corr2$treeID)
trees_name2 <- factor(unique(trees_name1))
LAD_metrics1 <- list()
LAD_metrics2 <- list()
for (i in levels(trees_name2)) {
# Filter data for each tree
tree1 <- profile_list2 |> dplyr::filter(treeID == i)
tree2 <- distances_metrics_corr2 |> dplyr::filter(treeID ==i)
# Get LAD metrics for each tree
LAD_metrics <- get_layers_lad(tree1, tree2, threshold=10,
step = 1,min_height= 1.5)
LAD_metrics1[[i]] <- LAD_metrics$df1
LAD_metrics2[[i]] <- LAD_metrics$df2
}
LAD_metrics_all1 <- dplyr::bind_rows(LAD_metrics1)
LAD_metrics_all2 <- dplyr::bind_rows(LAD_metrics2)
# List of data frames
LAD_metrics_list <- list(LAD_metrics_all1, LAD_metrics_all2)
# Initialize an empty list to store reordered data frames
fuels_LAD_metrics <- list()
# Specify prefixes (adjust accordingly)
prefixes <- c("treeID", "Hdist", "Hcbh", "effdist", "dptf", "Hdptf", "max", "last", "nlayers")
# Loop over each data frame
for (i in seq_along(LAD_metrics_list)) {
LAD_metrics_all <- LAD_metrics_list[[i]]
# Get original column names
original_column_names <- colnames(LAD_metrics_all)
# Initialize vector to store new order
new_order <- c()
# Loop over prefixes
for (prefix in prefixes) {
# Find column names matching the current prefix
matching_columns <- grep(paste0("^", prefix), original_column_names, value = TRUE)
# Extract numeric suffixes and order the columns based on these suffixes
numeric_suffixes <- as.numeric(gsub(paste0("^", prefix), "", matching_columns))
# Order the columns based on numeric suffixes
matching_columns <- matching_columns[order(numeric_suffixes)]
# Append to new order
new_order <- c(new_order, matching_columns)
}
# Reorder columns
LAD_metrics_all <- LAD_metrics_all[, new_order]
# Store the reordered data frame in the list
fuels_LAD_metrics[[i]] <- LAD_metrics_all
}
rownames(fuels_LAD_metrics[[1]]) <- NULL
rownames(fuels_LAD_metrics[[2]]) <- NULL
head(fuels_LAD_metrics[[2]])
```{r Plots of fuel layers with LAD percentage greater than a threshold, echo=TRUE, message=FALSE, warning=FALSE}
library(ggplot2)
profile_list2\(treeID <- factor(profile_list2\)treeID) # Tree metrics derived from get_layers_lad() function LAD_gt10p <- fuels_LAD_metrics[[2]]
trees_name1 <- as.character(LAD_gt10p$treeID) trees_name2 <- factor(unique(trees_name1))
plots_trees_LAD <- get_plots_effective(profile_list2, LAD_gt10p, min_height=1.5)
par(mfrow = c(2, 2)) plot(plots_trees_LAD[[1]]) plot(plots_trees_LAD[[2]]) plot(plots_trees_LAD[[3]])
| | |
|----------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------|
| {alt="Plot 1"} | {alt="Plot 2"} |
| {alt="Plot 3"} | |
## 19.CBH based on different criteria: maximum LAD, maximum and last distance
```{r CBH based on different criteria: maximum LAD, maximum and last distance, echo=TRUE, message=FALSE, warning=FALSE}
library(dplyr)
library(magrittr)
# Tree metrics derived from get_layers_lad() function
LAD_gt10p <- fuels_LAD_metrics[[2]]
trees_name1 <- as.character(LAD_gt10p$treeID)
trees_name2 <- factor(unique(trees_name1))
cbh_metrics_list <- list()
for (j in levels(trees_name2)){
# Filter data for each tree
tree1 <- LAD_gt10p |> dplyr::filter(treeID == j)
cbh_metrics <- get_cbh_metrics(tree1,min_height= 1.5)
cbh_metrics_list[[j]] <- cbh_metrics
}
# Combine depth values for all trees
cbh_metrics_all <- dplyr::bind_rows(cbh_metrics_list)
# Get original column names
original_column_names <- colnames(cbh_metrics_all)
# Specify prefixes
desired_order <- c("treeID", "Hcbh", "dptf","effdist","dist", "Hdist", "Hdptf","maxlad_","max_","last_","nlayers")
# Identify unique prefixes
prefixes <- unique(sub("^([a-zA-Z]+).*", "\\1", original_column_names))
# Initialize vector to store new order
new_order <- c()
# Loop over desired order of prefixes
for (prefix in desired_order) {
# Find column names matching the current prefix
matching_columns <- grep(paste0("^", prefix), original_column_names, value = TRUE)
# Append to the new order
new_order <- c(new_order, matching_columns)
}
# Reorder columns
cbh_metrics_all <- cbh_metrics_all[, new_order]
```{r Plots of CBH based on different criteria: maximum LAD, maximum and last distance, echo=TRUE, message=FALSE, warning=FALSE} library(ggplot2)
profile_list2\(treeID <- factor(profile_list2\)treeID) # Tree metrics derived from get_cbh_metrics() function cbh_metrics_all\(treeID <- factor(cbh_metrics_all\)treeID)
trees_name1 <- as.character(cbh_metrics_all$treeID) trees_name2 <- factor(unique(trees_name1))
plots_cbh_maxlad <- get_plots_cbh_LAD(profile_list2, cbh_metrics_all,min_height=1.5) plots_cbh_maxdist <- get_plots_cbh_maxdist(profile_list2, cbh_metrics_all,min_height=1.5) plots_cbh_lastdist <- get_plots_cbh_lastdist(profile_list2, cbh_metrics_all,min_height=1.5)
par(mfrow = c(2, 2)) plot(plots_cbh_maxlad[[1]]) plot(plots_cbh_maxdist[[2]]) plot(plots_cbh_lastdist[[3]])
| | |
|----------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------|
| {alt="Plot 1"} | {alt="Plot 2"} |
| {alt="Plot 3"} | |
## 21.CBH based on the Breaking Point method and LAD percentage
```{r CBH and the LAD percentage below and above the CBH using the breaking point method, echo=TRUE, message=FALSE, warning=FALSE}
library(dplyr)
library(magrittr)
# LAD profiles derived from normalized ALS data after applying [lad.profile()] function
profile_list2$treeID <- factor(profile_list2$treeID)
# Tree metrics derived from get_cbh_metrics() function
cbh_metrics_all$treeID <- factor(cbh_metrics_all$treeID)
trees_name1 <- as.character(cbh_metrics_all$treeID)
trees_name2 <- factor(unique(trees_name1))
cum_LAD_metrics_list <- list()
for (i in levels(trees_name2)) {
# Filter data for each tree
tree1 <- profile_list2 |> dplyr::filter(treeID == i)
tree2 <- cbh_metrics_all |> dplyr::filter(treeID == "1_CROWN")
# Get cumulative LAD metrics for each tree
cum_LAD_metrics_all <- get_cum_break(tree1, tree2, threshold=75, min_height= 1.5, verbose=TRUE)
cum_LAD_metrics_list[[i]] <- cum_LAD_metrics_all
}
# Combine the individual data frames
cum_LAD_metrics <- dplyr::bind_rows(cum_LAD_metrics_list)
# =======================================================================#
# REORDER COLUMNS
# =======================================================================#
# Get original column names
original_column_names <- colnames(cum_LAD_metrics)
# Specify prefixes (adjust accordingly)
prefixes <- c("treeID", "Hcbh", "below", "above", "bp", "max", "cumlad")
# Initialize vector to store new order
new_order <- c()
# Loop over prefixes
for (prefix in prefixes) {
# Find column names matching the current prefix
matching_columns <- grep(paste0("^", prefix), original_column_names, value = TRUE)
# Extract numeric suffixes and order the columns based on these suffixes
numeric_suffixes <- as.numeric(gsub(paste0("^", prefix), "", matching_columns))
matching_columns <- matching_columns[order(numeric_suffixes)]
# Append to new order
new_order <- c(new_order, matching_columns)
}
# Reorder columns
cum_LAD_metrics <- cum_LAD_metrics[, new_order]
## when % LAD is < 75 % below or above the BP (Breaking Point), Hcbh1 is derived from CBH maximum LAD criterium
rownames(cum_LAD_metrics) <- NULL
head(cum_LAD_metrics)
```{r Plots of the CBH and the LAD percentage below and above the CBH using the breaking point method, echo=TRUE, message=FALSE, warning=FALSE}
library(ggplot2)
profile_list2\(treeID <- factor(profile_list2\)treeID)
cum_LAD_metrics\(treeID <- factor(cum_LAD_metrics\)treeID)
trees_name1 <- as.character(cum_LAD_metrics_all$treeID) trees_name2 <- factor(unique(trees_name1))
plot_list <- list()
for (j in levels(trees_name2)) {
tree1 <- profile_list2 |> dplyr::filter(treeID ==j)
tree2 <- cum_LAD_metrics |> dplyr::filter(treeID == j)
plots_cbh_bp <- get_plots_cbh_bp(tree1, tree2,min_height = 1.5)
plot_list[[j]] <- plots_cbh_bp}
par(mfrow = c(2, 2)) plot(plot_list[[1]]) plot(plot_list[[2]]) plot(plot_list[[3]])
| | |
|----------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------|
| {alt="Plot 1"} | {alt="Plot 2"} |
| {alt="Plot 3"} | |
## 23. Joinning Fuel ladder properties with Crown polygons
```{r Joining crown polygons and ladder fuels metrics, echo=TRUE, message=FALSE, warning=FALSE}
# Tree metrics derived from get_layers_lad() function
cbh_metrics_all$treeID1 <- factor(cbh_metrics_all$treeID1)
# crown polygons (output from step 4)
tree_crowns$treeID1 <- factor(tree_crowns$treeID)
crowns_properties<-merge (tree_crowns,cbh_metrics_all, by="treeID1")
crowns_properties$maxlad_Hcbh_factor <- cut(crowns_properties$maxlad_Hcbh, breaks = 5)
# Plotting with a discrete legend
palette <- colorRampPalette(c("orange", "dark green"))
ggplot() +
geom_sf(data = crowns_properties, aes(fill = maxlad_Hcbh_factor)) +
scale_fill_manual(values = palette(5)) +
theme_minimal() +
labs(title = "Tree Crowns", fill = "maxlad_Hcbh")
We gratefully acknowledge funding from project INFORICAM (PID2020-119402RB-I00), funded by the Spanish MCIN/AEI/ 10.13039/501100011033 and by the “European Union NextGenerationEU/PRTR”. Carlos Silva was supported by the NASA’s Carbon Monitoring System funding (CMS, grant 22-CMS22-0015).
Please report any issue regarding the LadderFuelsR package to Dr. Olga Viedma (olga.viedma@uclm.es)
Viedma,O.;Silva, C; Moreno, JM & Hudak, AT: LadderFuelsR: An R Package for vertical fuel continuity analysis using LiDAR data.version 0.0.1, accessed on November. 22 2023, available at: https://CRAN.R-project.org/package=LadderFuelsR
LadderFuelsR package comes with no guarantee, expressed or implied, and the authors hold no responsibility for its use or reliability of its outputs.