Title: | Realistic Quantitative Structure Models |
---|---|
Description: | Real Twig is a method to correct branch overestimation in quantitative structure models. Overestimated cylinders are correctly tapered using measured twig diameters of corresponding tree species. Supported quantitative structure modeling software includes 'TreeQSM', 'SimpleForest', 'Treegraph', and 'aRchi'. Also included is a novel database of twig diameters and tools for fractal analysis of point clouds. |
Authors: | Aidan Morales [aut, cre, cph] |
Maintainer: | Aidan Morales <[email protected]> |
License: | GPL (>= 3) |
Version: | 1.4.0.9000 |
Built: | 2025-03-03 17:22:43 UTC |
Source: | https://github.com/aidanmorales/rtwig |
R port of Dominik Seidel's fractal analysis "box-dimension" metric.
box_dimension(cloud, lowercutoff = 0.01, rm_int_box = FALSE, plot = FALSE)
box_dimension(cloud, lowercutoff = 0.01, rm_int_box = FALSE, plot = FALSE)
cloud |
A point cloud matrix size n x 3. Non-matrices are automatically converted to a matrix. |
lowercutoff |
The smallest box size determined by the point spacing of the cloud in meters. Defaults to 1 cm. |
rm_int_box |
Remove the initial box as TRUE or FALSE. Defaults to FALSE. |
plot |
Plot the results. The user can specify "2D", "3D", or "ALL" plots. FALSE disables plotting. Defaults to FALSE. |
Returns a list
Arseniou G, MacFarlane DW, Seidel D (2021). “Measuring the Contribution of Leaves to the Structural Complexity of Urban Tree Crowns with Terrestrial Laser Scanning.” Remote Sensing, 13(14). doi:10.3390/rs13142773.
Mandelbrot BB (1983). The fractal geometry of nature. Freeman.
Saarinen N, Calders K, Kankare V, Yrttimaa T, Junttila S, Luoma V, Huuskonen S, Hynynen J, Verbeeck H (2021). “Understanding 3D structural complexity of individual Scots pine trees with different management history.” Ecology and Evolution, 11(6), 2561-2572. doi:10.1002/ece3.7216.
Seidel D (2018). “A holistic approach to determine tree structural complexity based on laser scanning data and fractal analysis.” Ecology and Evolution, 8(1), 128-134. doi:10.1002/ece3.3661.
Seidel D, Annighöfer P, Stiers M, Zemp CD, Burkardt K, Ehbrecht M, Willim K, Kreft H, Hölscher D, Ammer C (2019). “How a measure of tree structural complexity relates to architectural benefit-to-cost ratio, light availability, and growth of trees.” Ecology and Evolution, 9(12), 7134-7142. doi:10.1002/ece3.5281.
## Calculate Box Dimension file <- system.file("extdata/cloud.txt", package = "rTwig") cloud <- read.table(file, header = FALSE) output <- box_dimension(cloud, plot = "ALL") output
## Calculate Box Dimension file <- system.file("extdata/cloud.txt", package = "rTwig") cloud <- read.table(file, header = FALSE) output <- box_dimension(cloud, plot = "ALL") output
Cluster a point cloud or simulate a point cloud based on its QSM. If using the input point cloud, the cylinder ids are transferred to the cloud using the nearest neighbors. If simulating a cloud, the points are built directly from the cylinders with user controlled spacing. The cylinder id can be used to easily join the desired variables from the QSM to the cloud. The nearest neighbor search uses the C++ nanoflann library.
cluster_cloud(cylinder, cloud = NULL, spacing = NULL)
cluster_cloud(cylinder, cloud = NULL, spacing = NULL)
cylinder |
A QSM cylinder data frame. |
cloud |
The input point cloud for the QSM to cluster. If NULL (default), the simulated cloud is returned. |
spacing |
The point spacing in meters for the simulated cloud. Defaults to 0.02 meters. |
A point cloud data frame
Blanco JL, Rai PK (2014). “nanoflann: a C++ header-only fork of FLANN, a library for Nearest Neighbor (NN) with KD-trees.” https://github.com/jlblancoc/nanoflann.
## Load Data file <- system.file("extdata/QSM.mat", package = "rTwig") file2 <- system.file("extdata/cloud.txt", package = "rTwig") qsm <- run_rtwig(file, twig_radius = 4.23, metrics = FALSE) cloud <- read.table(file2) ## Clustered Cloud clustered_cloud <- cluster_cloud(cylinder = qsm, cloud = cloud) # # Join QSM variables and export # filename <- tempfile(pattern = "clustered_cloud", fileext = ".txt") # clustered_cloud %>% # left_join(qsm) %>% # fwrite(file = filename) ## Simulated Cloud simulated_cloud <- cluster_cloud(cylinder = qsm, spacing = 0.01) # Plot Simulated Cloud plot_qsm(cloud = simulated_cloud) # # Join QSM variables and export # filename2 <- tempfile(pattern = "simulated_cloud", fileext = ".txt") # simulated_cloud %>% # left_join(qsm) %>% # fwrite(file = filename2)
## Load Data file <- system.file("extdata/QSM.mat", package = "rTwig") file2 <- system.file("extdata/cloud.txt", package = "rTwig") qsm <- run_rtwig(file, twig_radius = 4.23, metrics = FALSE) cloud <- read.table(file2) ## Clustered Cloud clustered_cloud <- cluster_cloud(cylinder = qsm, cloud = cloud) # # Join QSM variables and export # filename <- tempfile(pattern = "clustered_cloud", fileext = ".txt") # clustered_cloud %>% # left_join(qsm) %>% # fwrite(file = filename) ## Simulated Cloud simulated_cloud <- cluster_cloud(cylinder = qsm, spacing = 0.01) # Plot Simulated Cloud plot_qsm(cloud = simulated_cloud) # # Join QSM variables and export # filename2 <- tempfile(pattern = "simulated_cloud", fileext = ".txt") # simulated_cloud %>% # left_join(qsm) %>% # fwrite(file = filename2)
Corrects cylinder radii
correct_radii(cylinder, twig_radius, broken_branch = TRUE)
correct_radii(cylinder, twig_radius, broken_branch = TRUE)
cylinder |
QSM cylinder data frame |
twig_radius |
Twig radius in millimeters |
broken_branch |
Enable or disable the broken branch filter. Defaults to enabled (TRUE). |
Returns a data frame
## TreeQSM Processing Chain file <- system.file("extdata/QSM.mat", package = "rTwig") qsm <- import_treeqsm(file) cylinder <- qsm$cylinder cylinder <- update_cylinders(cylinder) cylinder <- correct_radii(cylinder, twig_radius = 4.23) str(cylinder)
## TreeQSM Processing Chain file <- system.file("extdata/QSM.mat", package = "rTwig") qsm <- import_treeqsm(file) cylinder <- qsm$cylinder cylinder <- update_cylinders(cylinder) cylinder <- correct_radii(cylinder, twig_radius = 4.23) str(cylinder)
Exports the cylinder data to the format used by TreeQSM
export_mat(cylinder, filename)
export_mat(cylinder, filename)
cylinder |
QSM cylinder data frame |
filename |
Desired name of file |
Returns a .mat file
## TreeQSM Processing Chain file <- system.file("extdata/QSM.mat", package = "rTwig") qsm <- import_treeqsm(file) cylinder <- qsm$cylinder cylinder <- update_cylinders(cylinder) filename <- tempfile(pattern = "TreeQSM_QSM", fileext = ".mat") export_mat(cylinder, filename) ## SimpleForest Processing Chain file <- system.file("extdata/QSM.csv", package = "rTwig") cylinder <- read.csv(file) cylinder <- update_cylinders(cylinder) filename <- tempfile(pattern = "SimpleForest_QSM", fileext = ".mat") export_mat(cylinder, filename)
## TreeQSM Processing Chain file <- system.file("extdata/QSM.mat", package = "rTwig") qsm <- import_treeqsm(file) cylinder <- qsm$cylinder cylinder <- update_cylinders(cylinder) filename <- tempfile(pattern = "TreeQSM_QSM", fileext = ".mat") export_mat(cylinder, filename) ## SimpleForest Processing Chain file <- system.file("extdata/QSM.csv", package = "rTwig") cylinder <- read.csv(file) cylinder <- update_cylinders(cylinder) filename <- tempfile(pattern = "SimpleForest_QSM", fileext = ".mat") export_mat(cylinder, filename)
Exports a QSM cylinder mesh in various formats
export_mesh( cylinder, filename, format = "ply", radius = NULL, color = NULL, palette = NULL, facets = 6, normals = FALSE, alpha = 1 )
export_mesh( cylinder, filename, format = "ply", radius = NULL, color = NULL, palette = NULL, facets = 6, normals = FALSE, alpha = 1 )
cylinder |
QSM cylinder data frame. |
filename |
File name and path for exporting. The file extension is automatically added if not present. |
format |
Mesh file format. Defaults to |
radius |
Radius column name either quoted or unquoted. Defaults to the modified radii. |
color |
Optional cylinder color parameter.
|
palette |
Optional cylinder color palette for numerical data.
Palettes include |
facets |
The number of facets in the polygon cross section. Defaults to 6. A higher number of facets improves visual smoothness at the cost of plotting speed, performance and memory. |
normals |
Export surface normals per vertex. Defaults to FALSE. |
alpha |
Set the transparency of the cylinders used in the "ply" format. Defaults to 1. 1 is opaque and 0 is fully transparent. |
A mesh file
## Load QSM file <- system.file("extdata/QSM.mat", package = "rTwig") qsm <- import_treeqsm(file) cylinder <- qsm$cylinder cylinder <- update_cylinders(cylinder) # PLY filename <- tempfile(pattern = "QSM_ply") export_mesh( cylinder = cylinder, filename = filename, format = "ply", color = "distanceToTwig", palette = "viridis", normals = TRUE ) # OBJ filename <- tempfile(pattern = "QSM_obj") export_mesh( cylinder = cylinder, filename = filename, format = "obj", normals = TRUE ) # STL filename <- tempfile(pattern = "QSM_stl") export_mesh( cylinder = cylinder, filename = filename, format = "stl", normals = TRUE ) # QSM Blender Addons filename <- tempfile(pattern = "QSM_blender") export_mesh( cylinder = cylinder, filename = filename, format = "blender", normals = TRUE )
## Load QSM file <- system.file("extdata/QSM.mat", package = "rTwig") qsm <- import_treeqsm(file) cylinder <- qsm$cylinder cylinder <- update_cylinders(cylinder) # PLY filename <- tempfile(pattern = "QSM_ply") export_mesh( cylinder = cylinder, filename = filename, format = "ply", color = "distanceToTwig", palette = "viridis", normals = TRUE ) # OBJ filename <- tempfile(pattern = "QSM_obj") export_mesh( cylinder = cylinder, filename = filename, format = "obj", normals = TRUE ) # STL filename <- tempfile(pattern = "QSM_stl") export_mesh( cylinder = cylinder, filename = filename, format = "stl", normals = TRUE ) # QSM Blender Addons filename <- tempfile(pattern = "QSM_blender") export_mesh( cylinder = cylinder, filename = filename, format = "blender", normals = TRUE )
Imports leaves created by the QSM foliage and needles naive insertion (QSM-FaNNI) algorithm. The leaves are stored as a triangular mesh, compatible with both rTwig and RGL functions.
import_leaves(filename, format = "obj", simplify = FALSE)
import_leaves(filename, format = "obj", simplify = FALSE)
filename |
a QSM-FaNNI .obj file |
format |
.obj file format. Valid formats include |
simplify |
simplify the mesh by removing duplicate vertices. This can reduce memory usage at the cost of import speed. Defaults to FALSE. |
rgl::mesh3d object
Åkerblom M, Raumonen P, Casella E, Disney MI, Danson FM, Gaulton R, Schofield LA, Kaasalainen M (2018). “An algorithm to insert leaves into quantitative structure models of trees.” Interface Focus, 8(2), 20170045. ISSN 2042-8898, doi:10.1098/rsfs.2017.0045, 20180216.
## Not run: ## Import FaNNI leaves from the standard obj format file <- "path_to_leaves.obj" qsm <- import_leaves(file, format = "obj") ## Import FaNNI leaves from the extended obj format file <- "path_to_leaves_extended.obj" qsm <- import_leaves(file, format = "obj_ext") ## End(Not run)
## Not run: ## Import FaNNI leaves from the standard obj format file <- "path_to_leaves.obj" qsm <- import_leaves(file, format = "obj") ## Import FaNNI leaves from the extended obj format file <- "path_to_leaves_extended.obj" qsm <- import_leaves(file, format = "obj_ext") ## End(Not run)
import_qsm()
is deprecated and will be removed in a future version. Use import_treeqsm()
instead.
import_qsm(...)
import_qsm(...)
... |
function inputs |
Returns a list
Imports a QSM created by treegraph
import_treegraph(filename)
import_treegraph(filename)
filename |
a treegraph .json file |
Returns a list
Yang W, Wilkes P, Vicari MB, Hand K, Calders K, Disney M (2024). “Treegraph: tree architecture from terrestrial laser scanning point clouds.” Remote Sensing in Ecology and Conservation. ISSN 2056-3485, doi:10.1002/rse2.399.
Wilkes P, Shenkin A, Disney M, Malhi Y, Bentley LP, Vicari MB (2021). “Terrestrial laser scanning to reconstruct branch architecture from harvested branches.” Methods in Ecology and Evolution, 12, 2487-2500. doi:10.1111/2041-210X.13709.
## Not run: # Import a treegraph QSM qsm <- import_treegraph("path/to/json/file") ## End(Not run)
## Not run: # Import a treegraph QSM qsm <- import_treegraph("path/to/json/file") ## End(Not run)
Imports a QSM created by TreeQSM
import_treeqsm(filename, version = "2.x.x")
import_treeqsm(filename, version = "2.x.x")
filename |
a TreeQSM .mat MATLAB file |
version |
TreeQSM version. Valid versions include |
Returns a list
Raumonen P, Kaasalainen M, Åkerblom M, Kaasalainen S, Kaartinen H, Vastaranta M, Holopainen M, Disney M, Lewis P (2013). “Fast Automatic Precision Tree Models from Terrestrial Laser Scanner Data.” Remote Sensing, 5(2), 491–520. doi:10.3390/rs5020491.
## Read a TreeQSM MATLAB file in the 2.3.x - 2.4.x format file <- system.file("extdata/QSM.mat", package = "rTwig") qsm <- import_treeqsm(file, version = "2.x.x") summary(qsm) ## Read a TreeQSM MATLAB file in the 2.0 format file <- system.file("extdata/QSM_2.mat", package = "rTwig") qsm <- import_treeqsm(file, version = "2.0") names(qsm)
## Read a TreeQSM MATLAB file in the 2.3.x - 2.4.x format file <- system.file("extdata/QSM.mat", package = "rTwig") qsm <- import_treeqsm(file, version = "2.x.x") summary(qsm) ## Read a TreeQSM MATLAB file in the 2.0 format file <- system.file("extdata/QSM_2.mat", package = "rTwig") qsm <- import_treeqsm(file, version = "2.0") names(qsm)
Efficiently plot QSMs, point clouds, leaves, and stem triangulation meshes. Plots can be combined and extensively customized.
plot_qsm( cylinder = NULL, radius = NULL, color = NULL, palette = NULL, alpha = 1, facets = 6, skeleton = FALSE, skeleton_lwd = 1, cloud = NULL, pt_color = "#000000", pt_palette = NULL, pt_size = NULL, pt_alpha = 1, triangulation = NULL, tri_color = NULL, tri_palette = NULL, tri_alpha = 1, leaves = NULL, lf_color = "#5BA803", lf_alpha = 1, axes = TRUE, axes_color = "#000000", grid = FALSE, grid_color = "#D3D3D3", hover = FALSE, bg_color = "#FFFFFF", lit = FALSE, pan = TRUE, normalize = FALSE, mesh = NULL )
plot_qsm( cylinder = NULL, radius = NULL, color = NULL, palette = NULL, alpha = 1, facets = 6, skeleton = FALSE, skeleton_lwd = 1, cloud = NULL, pt_color = "#000000", pt_palette = NULL, pt_size = NULL, pt_alpha = 1, triangulation = NULL, tri_color = NULL, tri_palette = NULL, tri_alpha = 1, leaves = NULL, lf_color = "#5BA803", lf_alpha = 1, axes = TRUE, axes_color = "#000000", grid = FALSE, grid_color = "#D3D3D3", hover = FALSE, bg_color = "#FFFFFF", lit = FALSE, pan = TRUE, normalize = FALSE, mesh = NULL )
cylinder |
QSM cylinder data frame. |
radius |
Radius column name either quoted or unquoted. Defaults to the modified radii. |
color |
Optional cylinder color parameter.
|
palette |
Optional cylinder color palette for numerical data.
Palettes include |
alpha |
Set the transparency of the cylinders. Defaults to 1. 1 is opaque and 0 is fully transparent. |
facets |
The number of facets in the polygon cross section. Defaults to 6. A higher number of facets improves visual smoothness at the cost of plotting speed, performance and memory. |
skeleton |
Plot the QSM skeleton instead of cylinders. Defaults to FALSE. |
skeleton_lwd |
Skeleton line width. Defaults to 1. |
cloud |
Point cloud data frame or matrix where the first three columns are the x, y, and z coordinates. |
pt_color |
Optional point cloud color parameter.
|
pt_palette |
Optional point cloud color palette for numerical data.
|
pt_size |
Size of the points. Defaults to 0.1. |
pt_alpha |
Set the transparency of the point cloud. Defaults to 1. 1 is opaque and 0 is fully transparent. |
triangulation |
Stem triangulation mesh from TreeQSM. Defaults to NULL. |
tri_color |
Color of the triangulation mesh.
Accepts hex colors, |
tri_palette |
Optional triangulation color palette for z values. Supports the same inputs as palette. |
tri_alpha |
Set the transparency of the triangulation mesh. Defaults to 1. 1 is opaque and 0 is fully transparent. |
leaves |
Leaf mesh in the |
lf_color |
Color of the leaves. Defaults to leaf green.
Accepts hex colors, |
lf_alpha |
Set the transparency of the leaves. Defaults to 1. 1 is opaque and 0 is fully transparent. |
axes |
Show plot axes. Defaults to TRUE. |
axes_color |
Set the axes color. Defaults to black. |
grid |
Show plot grid lines. Defaults to FALSE. |
grid_color |
Set grid lines color. Defaults to grey. |
hover |
Show cylinder and branch id on mouse hover. Defaults to FALSE. |
bg_color |
Set the background color of the plot.
Accepts hex colors or |
lit |
Enable light source in plot. Defaults to FALSE. |
pan |
Use right mouse button to pan the plot. Defaults to TRUE.
Panning is disabled when |
normalize |
Normalize the cylinders to 0,0,0. Defaults to FALSE. |
mesh |
Plot any |
An rgl::open3d()
plot
## TreeQSM file <- system.file("extdata/QSM.mat", package = "rTwig") qsm <- import_treeqsm(file) cylinder <- qsm$cylinder cylinder <- update_cylinders(cylinder) plot_qsm(cylinder) triangulation <- qsm$triangulation plot_qsm(triangulation = triangulation)
## TreeQSM file <- system.file("extdata/QSM.mat", package = "rTwig") qsm <- import_treeqsm(file) cylinder <- qsm$cylinder cylinder <- update_cylinders(cylinder) plot_qsm(cylinder) triangulation <- qsm$triangulation plot_qsm(triangulation = triangulation)
Efficiently prune a QSM. The user can prune by cylinder, branch, and segment ids, or by height or diameter classes, individually, or all at the same time, and return either the pruned data, the remaining data, or a binary index of which cylinders are pruned.
prune_qsm( cylinder, cylinder_ids = NULL, branch_ids = NULL, segment_ids = NULL, height_m = NULL, diameter_cm = NULL, invert = FALSE, index = FALSE )
prune_qsm( cylinder, cylinder_ids = NULL, branch_ids = NULL, segment_ids = NULL, height_m = NULL, diameter_cm = NULL, invert = FALSE, index = FALSE )
cylinder |
QSM cylinder data frame |
cylinder_ids |
A single or vector of cylinder ids. Everything connected above the cylinder is pruned. |
branch_ids |
A single or vector of branch ids. Everything connected to the branch is pruned. |
segment_ids |
A single or vector of segment ids. Everything connected above the segment is pruned. |
height_m |
Height class in meters below which all cylinders are pruned. Valid inputs are numeric to one decimal. |
diameter_cm |
Branch diameter class in centimeters below which all cylinders are pruned. Valid inputs are numeric to one decimal. |
invert |
Return the remaining or pruned data. Defaults to TRUE (the remaining data), but can be set to FALSE. |
index |
Returns a column index called |
a data frame
## Load QSM file <- system.file("extdata/QSM.mat", package = "rTwig") qsm <- import_treeqsm(file) cylinder <- qsm$cylinder cylinder <- update_cylinders(cylinder) ## Pruning Index prune1 <- prune_qsm(cylinder, height_m = 2, index = TRUE) plot_qsm(prune1, color = pruning, palette = "blue2red") ## Remaining prune2 <- prune_qsm(cylinder, height_m = 2, invert = FALSE) plot_qsm(prune2) ## Pruned prune3 <- prune_qsm(cylinder, height_m = 2, invert = TRUE) plot_qsm(prune3)
## Load QSM file <- system.file("extdata/QSM.mat", package = "rTwig") qsm <- import_treeqsm(file) cylinder <- qsm$cylinder cylinder <- update_cylinders(cylinder) ## Pruning Index prune1 <- prune_qsm(cylinder, height_m = 2, index = TRUE) plot_qsm(prune1, color = pruning, palette = "blue2red") ## Remaining prune2 <- prune_qsm(cylinder, height_m = 2, invert = FALSE) plot_qsm(prune2) ## Pruned prune3 <- prune_qsm(cylinder, height_m = 2, invert = TRUE) plot_qsm(prune3)
qsm_summary
is deprecated and will be removed in a future version. Use summarise_qsm()
instead.
qsm_summary(...)
qsm_summary(...)
... |
function inputs |
Returns a list
Run the Real Twig correction and calculate tree metrics for supported QSM formats.
run_rtwig( filename, twig_radius, metrics = TRUE, version = NULL, smooth = TRUE, standardise = FALSE, broken_branch = TRUE, ... )
run_rtwig( filename, twig_radius, metrics = TRUE, version = NULL, smooth = TRUE, standardise = FALSE, broken_branch = TRUE, ... )
filename |
file path to QSM (.mat, .csv, .json) |
twig_radius |
Twig radius in millimeters |
metrics |
Calculate tree metrics. Defaults to TRUE. |
version |
If using a specific version of TreeQSM, the user can specify the version (e.g. 2.4.1, 2.0, etc.). |
smooth |
Defaults to TRUE if using TreeQSM. Can be set to FALSE. |
standardise |
Standardise QSM cylinder data. Defaults to FALSE, but can be set to TRUE. |
broken_branch |
Enable or disable the broken branch filter. Defaults to TRUE. |
... |
Additional arguments allowing standardise and standardize to be used as synonyms. |
Returns cylinder data frame or list if metrics is true.
## TreeQSM file <- system.file("extdata/QSM.mat", package = "rTwig") qsm <- run_rtwig(file, twig_radius = 4.23) str(qsm$cylinder)
## TreeQSM file <- system.file("extdata/QSM.mat", package = "rTwig") qsm <- run_rtwig(file, twig_radius = 4.23) str(qsm$cylinder)
Visually smooth a QSM by ensuring the midpoints of all cylinders are connected. Only TreeQSM is supported.
smooth_qsm(cylinder)
smooth_qsm(cylinder)
cylinder |
QSM cylinder data frame |
Returns a data frame
file <- system.file("extdata/QSM.mat", package = "rTwig") qsm <- import_treeqsm(file) cylinder <- qsm$cylinder cylinder <- update_cylinders(cylinder) ## Before Smoothing plot_qsm(cylinder) ## After Smoothing cylinder <- smooth_qsm(cylinder) plot_qsm(cylinder)
file <- system.file("extdata/QSM.mat", package = "rTwig") qsm <- import_treeqsm(file) cylinder <- qsm$cylinder cylinder <- update_cylinders(cylinder) ## Before Smoothing plot_qsm(cylinder) ## After Smoothing cylinder <- smooth_qsm(cylinder) plot_qsm(cylinder)
All QSM variables are renamed and reordered a standardised format across the supported QSM software for a consistent experience. All internal rTwig functions use these standardised names for consistency.
standardise_qsm(cylinder) standardize_qsm(cylinder)
standardise_qsm(cylinder) standardize_qsm(cylinder)
cylinder |
QSM cylinder data frame |
Renames supported QSM software output columns to be consistent.
All names are lower case and underscore delimited. See the dictionary
vignette for a detailed description of column names. A consistent QSM format
ensures maximum compatibility when analyzing QSMs made with different
software. This function can be run either before or after
update_cylinders()
has been run, or at any stage.
standardise_qsm()
and standardise_qsm()
are synonyms.
Returns a data frame
## TreeQSM Processing Chain file <- system.file("extdata/QSM.mat", package = "rTwig") qsm <- import_treeqsm(file) cylinder <- qsm$cylinder cylinder <- standardise_qsm(cylinder) str(cylinder) ## SimpleForest Processing Chain file <- system.file("extdata/QSM.csv", package = "rTwig") cylinder <- read.csv(file) cylinder <- standardise_qsm(cylinder) str(cylinder) ## aRchi Processing Chain file <- system.file("extdata/QSM2.csv", package = "rTwig") cylinder <- read.csv(file) cylinder <- standardise_qsm(cylinder) str(cylinder)
## TreeQSM Processing Chain file <- system.file("extdata/QSM.mat", package = "rTwig") qsm <- import_treeqsm(file) cylinder <- qsm$cylinder cylinder <- standardise_qsm(cylinder) str(cylinder) ## SimpleForest Processing Chain file <- system.file("extdata/QSM.csv", package = "rTwig") cylinder <- read.csv(file) cylinder <- standardise_qsm(cylinder) str(cylinder) ## aRchi Processing Chain file <- system.file("extdata/QSM2.csv", package = "rTwig") cylinder <- read.csv(file) cylinder <- standardise_qsm(cylinder) str(cylinder)
Generates a simple QSM summary. The summary includes basic tree metrics, such as DBH, total height, and also volume and surface area arranged by totals and branching order.
summarise_qsm(cylinder, radius, triangulation = NULL) summarize_qsm(cylinder, radius, triangulation = NULL)
summarise_qsm(cylinder, radius, triangulation = NULL) summarize_qsm(cylinder, radius, triangulation = NULL)
cylinder |
QSM cylinder data frame |
radius |
Radius column name either quoted or unquoted. |
triangulation |
Optional QSM triangulation list. Only supports TreeQSM. |
summarise_qsm()
and summarize_qsm()
are synonyms.
Returns a list
## SimpleForest Processing Chain file <- system.file("extdata/QSM.csv", package = "rTwig") cylinder <- read.csv(file) cylinder <- update_cylinders(cylinder) summarise_qsm(cylinder, radius) # TreeQSM Triangulation file <- system.file("extdata/QSM.mat", package = "rTwig") qsm <- import_treeqsm(file) cylinder <- qsm$cylinder cylinder <- update_cylinders(cylinder) summarise_qsm(cylinder, radius, triangulation = qsm$triangulation)
## SimpleForest Processing Chain file <- system.file("extdata/QSM.csv", package = "rTwig") cylinder <- read.csv(file) cylinder <- update_cylinders(cylinder) summarise_qsm(cylinder, radius) # TreeQSM Triangulation file <- system.file("extdata/QSM.mat", package = "rTwig") qsm <- import_treeqsm(file) cylinder <- qsm$cylinder cylinder <- update_cylinders(cylinder) summarise_qsm(cylinder, radius, triangulation = qsm$triangulation)
Calculates tree metrics from a QSM
tree_metrics(cylinder, verify = TRUE)
tree_metrics(cylinder, verify = TRUE)
cylinder |
QSM cylinder data frame |
verify |
Verify QSM topology. Defaults to TRUE. If |
Calculates detailed tree, branch, and segment metrics from a QSM. Valid inputs require a connected QSM, which can be a whole tree or an individual branch. The outputs include all of the standard outputs from TreeQSM, and also additional variables, including, but not limited to, growth length, reverse branch order, branch segment or node relationships, and distances from twigs and the base of the tree, across various distribution metrics. Also included is a simulated point cloud of the tree, based on the QSM cylinder radii. When corrected with Real Twig, this allows for the testing and validation of point cloud diameter overestimation throughout the tree.
Returns a list of tree metric data frames and a synthetic point cloud
Raumonen P, Kaasalainen M, Åkerblom M, Kaasalainen S, Kaartinen H, Vastaranta M, Holopainen M, Disney M, Lewis P (2013). “Fast Automatic Precision Tree Models from Terrestrial Laser Scanner Data.” Remote Sensing, 5(2), 491–520. doi:10.3390/rs5020491.
Hackenberg J, Spiecker H, Calders K, Disney M, Raumonen P (2015). “SimpleTree —An Efficient Open Source Tool to Build Tree Models from TLS Clouds.” Forests, 6(11), 4245–4294. doi:10.3390/f6114245.
Hackenberg J, Bontemps J (2023). “Improving quantitative structure models with filters based on allometric scaling theory.” Applied Geomatics, 15. doi:10.1007/s12518-023-00537-4.
Yang W, Wilkes P, Vicari MB, Hand K, Calders K, Disney M (2024). “Treegraph: tree architecture from terrestrial laser scanning point clouds.” Remote Sensing in Ecology and Conservation. ISSN 2056-3485, doi:10.1002/rse2.399.
Smith D, Sperry J, Enquist B, Savage V, McCulloh K, Bentley L (2013). “Deviation from symmetrically self-similar branching in trees predicts altered hydraulics, mechanics, light interception and metabolic scaling.” The New phytologist, 201. doi:10.1111/nph.12487.
## TreeQSM Processing Chain file <- system.file("extdata/QSM.mat", package = "rTwig") cylinder <- import_treeqsm(file)$cylinder cylinder <- update_cylinders(cylinder) metrics <- tree_metrics(cylinder) names(metrics) ## SimpleForest Processing Chain file <- system.file("extdata/QSM.csv", package = "rTwig") cylinder <- read.csv(file) cylinder <- update_cylinders(cylinder) metrics <- tree_metrics(cylinder) names(metrics)
## TreeQSM Processing Chain file <- system.file("extdata/QSM.mat", package = "rTwig") cylinder <- import_treeqsm(file)$cylinder cylinder <- update_cylinders(cylinder) metrics <- tree_metrics(cylinder) names(metrics) ## SimpleForest Processing Chain file <- system.file("extdata/QSM.csv", package = "rTwig") cylinder <- read.csv(file) cylinder <- update_cylinders(cylinder) metrics <- tree_metrics(cylinder) names(metrics)
Database of twig radii by tree species
twigs
twigs
twigs
A data frame containing twig radii measurements
The tree's genus and species
The average twig radius in millimeters
The twig measurement sample size
The minimum twig radii from the samples
The maximum twig radii from the samples
The standard deviation of twig radii
The coefficient of variation of twig radii
Database of twig radii by size index
twigs_index
twigs_index
twigs_index
A data frame containing twig radii measurements
The twig size index
The average twig radius in millimeters
The twig measurement sample size
The minimum twig radii from the samples
The maximum twig radii from the samples
The standard deviation of twig radii
The coefficient of variation of twig radii
Updates the QSM cylinder data in preparation for radii correction
update_cylinders(cylinder)
update_cylinders(cylinder)
cylinder |
QSM cylinder data frame |
Updates and verifies parent-child cylinder relationships and
calculates new variables and metrics found throughout the supported QSM
software. update_cylinders()
is required to run all rTwig functions, and
is run automatically if rTwig detects a new QSM.
Returns a data frame
Hackenberg J, Spiecker H, Calders K, Disney M, Raumonen P (2015). “SimpleTree —An Efficient Open Source Tool to Build Tree Models from TLS Clouds.” Forests, 6(11), 4245–4294. doi:10.3390/f6114245.
Hackenberg J, Bontemps J (2023). “Improving quantitative structure models with filters based on allometric scaling theory.” Applied Geomatics, 15. doi:10.1007/s12518-023-00537-4.
## TreeQSM Processing Chain file <- system.file("extdata/QSM.mat", package = "rTwig") qsm <- import_treeqsm(file) cylinder <- qsm$cylinder cylinder <- update_cylinders(cylinder) str(cylinder) ## SimpleForest Processing Chain file <- system.file("extdata/QSM.csv", package = "rTwig") cylinder <- read.csv(file) cylinder <- update_cylinders(cylinder) str(cylinder) ## aRchi Processing Chain file <- system.file("extdata/QSM2.csv", package = "rTwig") cylinder <- read.csv(file) cylinder <- update_cylinders(cylinder) str(cylinder)
## TreeQSM Processing Chain file <- system.file("extdata/QSM.mat", package = "rTwig") qsm <- import_treeqsm(file) cylinder <- qsm$cylinder cylinder <- update_cylinders(cylinder) str(cylinder) ## SimpleForest Processing Chain file <- system.file("extdata/QSM.csv", package = "rTwig") cylinder <- read.csv(file) cylinder <- update_cylinders(cylinder) str(cylinder) ## aRchi Processing Chain file <- system.file("extdata/QSM2.csv", package = "rTwig") cylinder <- read.csv(file) cylinder <- update_cylinders(cylinder) str(cylinder)