R Observatory: Metrics for rTwig version 1.4.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

rTwig

1.4.0Package record

Realistic Quantitative Structure Models

0packages depend

2.9Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Aidan MoralesCRAN page ↗GitHub ↗Website ↗Issues ↗

Real Twig is a method to correct branch overestimation in quantitative structure models. Overestimated cylinders are correctly tapered using measured twig diameters of corresponding tree species. Supported quantitative structure modeling software includes 'TreeQSM', 'SimpleForest', 'Treegraph', and 'aRchi'. Also included is a novel database of twig diameters and tools for fractal analysis of point clouds.

Changes in 1.4.0

New Features

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.
New database called 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():
Leaf meshes from 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.
Now accepts random color palettes for cylinders, points, or triangulation meshes by setting the *_palette = "random". Additionally, the user can set a random color for each cylinder by setting both color and palette to "random".
Transparency options added for point clouds and main stem triangulation mesh with pt_alpha and tri_alpha.
Point clouds can now be colored by any variable or palette using 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.
Any 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.

Show all changes in 1.4.0Hide the rest of the changes in 1.4.0

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.

Improvements

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().

Breaking Changes

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.

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)

install.packages("rTwig", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("aidanmorales/rTwig")

Development version from aidanmorales/rTwig. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-rtwig

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-rTwig

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 9.0 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-08
ERROR12 OK, 1 ERROR2026-06-07
OK12 OK2026-04-25

Show 5 earlier changesHide 5 earlier changes

NOTE12 OK, 2 NOTE2026-04-22
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-18
NOTE12 OK, 2 NOTE2026-04-10
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-09
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.4.0

READMEYes · 809 wordsVignettesYes · 6 · dynamicNEWSYes · 100% structured · mentions 1.4.0Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 21 (1 internal)includes a package overview page
Examples that run: 88%14 run in a plain check · 2 never run
Exported functions with examples: 89%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 33% with a bibliography file

Vignettes (6)

How these are measured

Downloads

2.9K

CRAN downloads in the past year

Rank #10,237 · ~8/day · ~243/mo

Releases R versions

Daily download trend is not available in this view yet.

39330 days

99690 days

2.9K1 year

Compare downloads with other packages →

Also on338 r2u

How downloads are counted

Repository

aidanmorales/rtwig ↗Account: aidanmorales

22Stars

0Forks

1Open issues

0Open PRs

6Releases

293Commits

1Commit identities

forestrylidarqsmrrcpprpackagemodelingr-package

293 commits · Last activity 2026-10-16 · 0% stars, 30d · Default branch at 1.4.0.9000, ahead of CRAN 1.4.0 (checked 2026-10-18)

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 3
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2025-10-22 · 122026-09-07 · 22

How these are measured

PracticesBeta

9 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/aidanmorales/rtwig on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-10-16 · The repository has a site deploy workflow

pkgdown site last built 2026-10-16

CRAN release process (2)

cran-comments.mdrevdep/

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

23 external dependencies (excludes base and recommended)

Installing rTwig adds 61 packages (33 with compiled code, 62 MB of source tarballs). Heaviest: BH 14 MB, data.table 5.7 MB, bslib 5.6 MB.

Depends (1)

R >= 3.5.0

Imports (12)

R.matlab rmatio tidytable cobs igraph rgl colourvalues Rdpack rlang Rcpp RcppSimdJson geometry

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (9)

knitr rmarkdown ggplot2 ggpmisc ggpubr gt yardstick dplyr tidyr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (2)

Aidan Morales

David W. MacFarlane

Author, Copyright holder

Releases (5)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.4.0Latest
record
2025-03-03 · current release · diff ↗ ·
added 5 exports
import_leaves, import_treeqsm, standardise_qsm, summarise_qsm, summarize_qsm
1.3.0
record
2024-11-21 · diff ↗
1.2.0
record
2024-11-08 · diff ↗ ·
added 2 exports
cluster_cloud, prune_qsm
1.1.0
record
2024-08-21 · diff ↗ ·
removed 1 export
plot_stand

added 4 exports
import_treegraph, run_rtwig, standardize_qsm, tree_metrics
R
R 4.4.0 released · 2024-04-24
1.0.2
record
2024-04-08
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2024-04-08
Total releases: 5 / 2 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.5.0
Bundled data: 2.4 KB / 2 files
Download size: 899 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("rTwig")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for rTwig version 1.4.0 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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