R Observatory: Metrics for treestructure version 1.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

treestructure

1.0.1

Detect Population Structure Within Phylogenetic Trees

0packages depend

2.8Kdownloads / year

57.7%test coverage

13/13checks pass

Overview

About

Maintained by Erik VolzFirst published 2020-02-173 releasesCRAN page ↗GitHub ↗

Algorithms for detecting population structure from the history of coalescent events recorded in phylogenetic trees. This method classifies each tip and internal node of a tree into disjoint sets characterized by similar coalescent patterns.

Install

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

install.packages("treestructure", 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("emvolz-phylodynamics/treestructure")

Development version from emvolz-phylodynamics/treestructure. 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-treestructure

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

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-treestructure

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

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

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-treestructure

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 3.5 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.09

57.7%

Coverage · measured lines

100%

Documentation · exports

2

Dependencies · direct

Check history

OK2026-08-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-27
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-21
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 8 earlier snapshots

ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-10
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-03
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-16
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 67%
References docs: 20%

Downloads

2.8K

CRAN downloads in the past year

Rank #11,295 · ~8/day · ~234/mo

Releases R versions

Daily download trend is not available in this view yet.

25430 days

87990 days

2.8K1 year

Compare downloads with other packages →

Also on409 r2u24 autocran

Repository

GitHub ↗ emvolz-phylodynamics/treestructure

23Stars

3Forks

5Open issues

0Open PRs

1Releases

117Commits

6Contributors

117 commits · Last activity 2026-07-05 · 0% stars, 30d

Stars over time

2025-07-15 · 172026-07-07 · 23

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/emvolz-phylodynamics/treestructure on 2026-08-23.

Continuous integration (1)

GitHub Actions

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (2)

ape rlang

LinkingTo (1)

Rcpp

Suggests (8)

ggtree ggplot2 knitr rmarkdown getopt phangorn treeio testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (3)

Maintainer (1)

Erik Volz

Author, Maintainer

Authors (1)

Erik Volz

Author, Maintainer

Contributors (2)

Vinicius B. Franceschi

Contributor · added in 0.7.0

Fabricia F. Nascimento

Contributor · added in 0.7.0

Package Timeline

3 releases. Pick two to compare their code metrics. R releases are shown for context.

1.0.1Latest
2026-07-05 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
0.7.0
2025-09-27 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
0.1.0
2020-02-17
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2020-02-17
Total releases: 3 / 6 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.1.0
Download size: 1.7 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("treestructure")

Format

Volz, E., B. Franceschi, V., & F. Nascimento, F. (2026). treestructure: Detect Population Structure Within Phylogenetic Trees (Version 1.0.1) [Computer software]. https://doi.org/10.32614/CRAN.package.treestructure

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 treestructure version 1.0.1 [Data set]. HJJB, LLC. Data release v2026-08-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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