High-Performance Open-Source Archive
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.
import_qsm()
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