rTwig 1.3.0

New Features

• 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.

Improvements

• 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.

rTwig 1.2.0

New Features

• 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.

  • triangulation: The user can now plot TreeQSM triangulation meshes by passing in the triangulation list from import_qsm(). The user can also control the color and palette with tri_color and tri_palette.
  • pan: The right mouse button now pans the plot instead of zooming by default. The functionality mimics pan3d() from RGL, but rewritten with Rcpp for better responsiveness.
  • lit: Enable or disable plot lighting
  • alpha: Set cylinder transparency. Note: can degrade performance with large numbers of cylinders or facets.
  • axes_color: The axes color can now be set by the user.
  • skeleton_lwd: Set the line width of the skeleton plots.
  • normalize: Center the cylinders around 0,0,0. Defaults to FALSE.

• 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

Improvements

• correct_radii(): Complete refactor with Rcpp and tidyeval for better maintainability.
  • ~ 2 - 3x performance improvement!
  • The outlier and broken branch filters are rewritten in Rcpp, for massive performance gains.
  • Parallel processing has been removed, eliminating overhead and excessive memory usage.
• update_cylinders(): Fix a bug in path metrics for SimpleForest QSMs (issue #4).
• qsm_summary():
  • Refactored with tidyeval.
  • Fix bug where triangulation was not using the correct ending cylinder.
• box_dimension(): The 3D plot now pans on right mouse button.
• run_rtwig(): Fix missing Treegraph parameter (issue #5).
• tree_metrics():
  • Fix a bug where the start x,y,z values were incorrect.
  • Fix a bug where NA cylinder orientation values would cause the calculations to fail.
  • NA values are removed and the user sees a warning promoting them to check the QSM.
• The QSM network is now cached in the temp folder to avoid repeat calculations.
• Data checking and helpful error messages are now included for every function.
• Add the Real Twig Method paper citation in the package and readme.
• New website look.
• Update vignettes.
• Update twig data base.
• Reduced package dependencies.

Breaking Changes

• 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.
• file has been changed to filename in run_rtwig(), import_qsm(), and import_treegraph() to be consistent with other functions.

rTwig 1.1.0

New Features

• 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

Improvements

• 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

Breaking Changes

• 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.

rTwig 1.0.2

• 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()

v1.0.0

Initial public release of rTwig.