import_leaves(): a new function to import leaves from QSM-FaNNI. The leaves are stored as an rgl::mesh3d() object.export_mesh(): The function now supports multiple 3d mesh formats including, .ply, .obj and .stl. It also supports exporting a QSM to Blender using the QSM Blender Addons format .txt.twigs_index. This is based on qualitative size classes supported by the literature, making it easier to select a twig radius for tree species without twig measurements. More info can be found in the Twigs vignette.plot_qsm():
import_leaves() or aRchi::add_leaves() can now be plotted with the leaves parameter. Leaf color and transparency can be controlled with lf_color and lf_alpha respectively.*_palette = "random". Additionally, the user can set a random color for each cylinder by setting both color and palette to "random".pt_alpha and tri_alpha.pt_color and pt_palette. The user can set a random color for each point by setting both pt_color and pt_palette to random.rgl::mesh3d() objects can now be passed to plot_qsm() with the mesh parameter.tree_metrics():
modified is a standard output in the tree data frame. This is an average of the binary index of the cylinders modified by Real Twig. The rTwig version and run date are now also saved as version and run_date.
volume_change_pct and area_change_pct are standard outputs of the tree data frame. These represent the percent change in total tree volume and surface area using radius and raw_radius.
vessel_volume, pipe_area, pipe_radius, and twig_distance_m are standard outputs taken from the base of the QSM.
Added first order branches to the branch distribution metrics to better match the output of TreeQSM. These columns include _1 in their column names.
path_fraction is now a standard output.
export_mesh(): The function was entirely reworked using Rcpp for fast and efficient mesh export. All functionality that was dependent on rgl has been implemented in custom C++ functions.
Function names now use British English to be consistent with R standards. American spelling will still work interchangeably (e.g. standardize_qsm() vs standardise_qsm().
Some functions have been renamed to follow tidy guidelines and have consistency within rTwig and other R packages (e.g. qsm_summary() -> summarise_qsm()).
Fixed a bug in plot_qsm(), where certain variable names conflicted with internal functions, resulting in an error (issue #12).
Fixed multiple bugs in tree_metrics():
Empty azimuth and zenith factors are now filled with 0, instead of being missing.
Issue #15 occurred because the cylinder verification was at too high a level and could not properly create the cylinder network when an error condition was met.
Fixed an issue when only a single branch or segment was provided as filtered data, causing the calculations to fail. The user is now show a warning when these edge cases occur.
Fixed an issue where crown base height calculations would fail if there was only one first order branch present.
Fixed an issue where disconnected data using verify = FALSE would fail crown base calculations due to missing branches (issue #18).
run_rtwig(): The user can now use standardize and standardise interchangeably.
Updated Twigs vignette with new info and plots.
Updated Dictionary vignette describing all standard outputs from tree_metrics().
import_qsm() is deprecated and has been replaced with import_treeqsm(). The functionality is unchanged, but the name changed to be explicit about its use. import_qsm() still functions, but will be removed in a future rTwig release.
qsm_summary() is deprecated and has been replaced with summarise_qsm(). The functionality is unchanged, but the name changed to be consistent with tidy guidelines. qsm_summary() still functions, but will be removed in a future rTwig release.
tree_metrics() now outputs the base diameters as a standard output in the tree data frame. The new variables are d_base_qsm_cm and d_base_raw_cm, which are the modified and unmodified diameter of the base of the tree or branch.tree_metrics() is now dynamic and can accept filtered data. The QSM must be a connected structure (e.g. a whole tree or single branch). If the main stem is shorter than DBH (1.37 m), DBH will be NA, and the user will be notified. If DBH is NA, the base diameter will be used in calculations instead. If a branch is provided, the lowest order will be considered as the main stem, and the standard summary will be calculated. Previously, trying to summarize any filtered data would throw an error (issue #8).
qsm_summary() is now dynamic and can accept filtered data. If the filtered QSM data is a connected structure (e.g. a branch), the lowest order will be considered as the main stem, and the standard summary will be calculated. If the QSM data is disconnected (e.g. several pruned branches), only total volume and surface area will be calculated, and the user will be notified. Additionally, DBH calculations are also dynamic. If the main stem of a tree or branch is shorter than DBH (1.37 m), DBH will be NA, and the user will be notified. Previously, trying to summarize any filtered data would throw an error (issue #7).
Fixed a bug in plot_qsm() where color vectors or a vector element would throw an unintended error (issue #9).
Fixed a bug in update_cylinders() where distanceFromBase was being joined with the wrong index values (issue #10).
Fix an issue for CRAN, where Fedora with the clang compiler threw an error.
Random colors are now consistently brighter.
Update Validation vignette with more data.
Add start-up message on package load.
Polish up documentation.
cluster_cloud(): A new function to transfer QSM variables to the input point cloud or simulate a point cloud from the QSM. Efficient nearest neighbor searching is done with the C++ nanoflann library: https://github.com/jlblancoc/nanoflann
prune_qsm(): A new function to efficiently and easily prune QSMs using multiple pruning criteria and return options.
aRchi QSMs are now supported in the package.
Users can now pass radius or color column variables either unquoted or quoted to user facing functions like plot_qsm(), qsm_summary(), or export_mesh(). Piping the QSM cylinders into these functions allows the user to easily select unquoted columns.
update_cylinders(): Three new allometric scaling variables as standard outputs - vessel_volume, pipe_area, pipe_radius.
plot_qsm(): Point clouds and stem triangulation meshes can now be plotted independently of a QSM.
import_qsm(). The user can also control the color and palette with tri_color and tri_palette.pan3d() from RGL, but rewritten with Rcpp for better responsiveness.correct_radii():
The broken branch filter can now be disabled, with broken_branch = FALSE
Now returns modified, an index of what cylinders were modified by Real Twig.
run_rtwig(): The broken branch filter can now be disabled, with broken_branch = FALSE
correct_radii(): Complete refactor with Rcpp and tidyeval for better maintainability.
update_cylinders(): Fix a bug in path metrics for SimpleForest QSMs (issue #4).qsm_summary():
box_dimension(): The 3D plot now pans on right mouse button.run_rtwig(): Fix missing Treegraph parameter (issue #5).tree_metrics():
qsm_summary(): User can pass radius as either a quoted or unquoted column name, so there is no longer any default value. Failing to provide a radius will throw an error prompting the user for a radius column name.correct_radii(): parallel processing has been removed, so backend is no longer a parameter.run_rtwig():parallel processing has been removed, so backend is no longer a parameter.run_rtwig(), import_qsm(), and import_treegraph() to be consistent with other functions.run_rtwig(): New function to run the Real Twig method and calculate tree metrics in one simple function.
standardize_qsm(): New function to standardize variable names across all supported QSM software. See the dictionary vignette for more details on the variable names.
tree_metrics(): New function to calculate all the standard outputs of TreeQSM, plus new variables, metrics, and simulated point clouds reconstructed entirely from the QSM. Computationally expensive tasks are implemented with Rcpp for maximum performance.
import_treegraph(): New function to import Treegraph QSM. Treegraph support is implemented throughout the package!
update_cylinders(): New variables: distanceFromBase, distanceToTwig, branch_alt. QSM topology is now verified and corrected if there are any topological errors.
plot_qsm()
export_mesh()
Implement Rcpp across package
plot_qsm() > 10x performance improvement!
smooth_qsm() > 10x performance improvement!
export_mesh() > 10x performance improvement!
box_dimension() ~ 3x performance improvement
update_cylinder()
~2x performance improvement with better vectorization
Cleaned variable names and removed repeat calculations
Verify and correct QSM topology
Reduced package dependencies
Cleanup function imports
Update twig data base
Update vignettes
Update citations
All parent child cylinder IDs, nodes, and branches begin numbering at 1 to ensure compatibility with R indexing and igraph. This affects SimpleForest and Treegraph.
Redefined SimpleForest branch structure to begin at a new branch order and end in a twig. This ensures consistency in the code and calculations between TreeQSM, Treegraph, and SimpleForest. The old branch definition is saved as a new variable called branch_alt, and is changed to begin at zero to be consistent with the new branch_alt variable from Real Twig.
Renamed twigRad function parameter to twig_radius to be consistent with tidy style guidelines
Renamed GrowthLength to growthLength to be consistent with SimpleForest
Variable names in qsm_summary() updated to be explicit and consistent with the outputs of tree_metrics()
plot_qsm() now takes input column parameters as quoted variables. cyl_color and cyl_palette have been changed to color and palette respectively. cyl_sides has been renamed to facets.
export_mesh() now takes input column parameters as quoted variables. cyl_color and cyl_palette have been changed to color and palette respectively. cyl_sides has been renamed to facets.
plot_stand() has been deprecated as all of its functionality is now incorporated into plot_qsm()
twigs: renamed scientific.name to scientific_name and radius.mm to radius_mm for consistent naming conventions across the package.
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