Changelog • rTwig

rTwig (development version)

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()
- Complete refactor with Rcpp and tidyeval for massive performance improvements
- New QSM skeleton plotting option
- Supports plotting multiple QSMs in the same plot
- Cylinder and cloud colors can now be set to random
- bg_color can change the background color of the plot
export_mesh()
- Complete refactor with Rcpp and tidyeval for massive performance improvements
- Cylinder color parameter can now be set to random, or FALSE to disable exporting colors
- Note: color exporting will be fixed in a future rgl package update

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.

CRAN release: 2024-04-08

Changes for CRAN re-submission
- Reduced package size
- Allow user to run all examples
- Small text formatting changes
Vignette and webpage typo fixes
Improved treedata import in import_qsm()