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.
import_qsm()