R Observatory: Metrics for treestructure version 1.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

treestructure

1.0.1Package record

Detect Population Structure Within Phylogenetic Trees

0packages depend

2.8Kdownloads / year

57.7%test coverage

13/13flavors OK

Overview

About

Maintained by Erik VolzCRAN page ↗GitHub ↗Website ↗Issues ↗

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.

Changes in 1.0.1

The default target false discovery rate is now fdr = 0.2 (was 0.1). The stricter 0.1 default was conservative on real trees and interacted awkwardly with minCladeSize; at 0.2 the number of designated clusters decreases monotonically as minCladeSize grows, and more genuine structure is recovered while the whole-tree error rate remains controlled.
The node-support vignette was revised to the new default (fdr = 0.2).

From NEWS.md in the release

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. 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-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). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 3.8 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-27
ERROR12 OK, 1 ERROR2026-06-21
OK13 OK2026-06-09

Show 8 earlier changesHide 8 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-10
ERROR12 OK, 1 ERROR2026-05-03
OK14 OK2026-04-22
ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-04-16
ERROR13 OK, 1 ERROR2026-04-09
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.1

README· In the repository, left out of the releaseVignettesYes · 4 · dynamicNEWSYes · 100% structured · mentions 1.0.1Citation fileNoWebsiteYes · pkgdown

Help pages: 5 (1 internal)includes a package overview page
Examples that run: 100%4 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 67%
Help pages citing references: 20%

Vignettes (4)

How these are measured

Downloads

2.8K

CRAN downloads in the past year

Rank #11,524 · ~8/day · ~236/mo

Releases R versions

Daily download trend is not available in this view yet.

34730 days

94790 days

2.8K1 year

Compare downloads with other packages →

Also on377 r2u

How downloads are counted

Repository

emvolz-phylodynamics/treestructure ↗Organization: emvolz-phylodynamics

23Stars

3Forks

5Open issues

1Open PRs

1Releases

117Commits

6Commit identities

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

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 4
Median days to close, 50 most recently updated closed PRs: 2

Stars over time

2025-07-15 · 172026-09-19 · 23

How these are measured

PracticesBeta

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

Checks run against github.com/emvolz-phylodynamics/treestructure on 2026-10-25.

Continuous integration (1)

GitHub Actions

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-07-05 · The repository has a site deploy workflow

pkgdown site last built 2026-07-05

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

How this is detected·Detection ruleset v4 (2026-10-20)

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen on or before 2026-07-02
Commits: at least 3 crediting it in the message

Models named in its commits

Claude Opus 4.83 commits · Jul 2026

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Installing treestructure adds 4 packages (4 with compiled code, 4.2 MB of source tarballs). Heaviest: Rcpp 1.8 MB, ape 1.4 MB, rlang 766 KB.

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.

How these are counted

Code & Tests

People & History

People (3)

Erik Volz

Author, Maintainer since 0.1.0 (2020)

Vinicius B. Franceschi

Contributor · added in 0.7.0

Fabricia F. Nascimento

Contributor · added in 0.7.0

Releases (3)

Pick two releases to compare their code metrics.

1.0.1Latest
record
2026-07-05 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
0.7.0
record
2025-09-27 · diff ↗ ·
added 2 exports
addtips, treestructure.test
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
record
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

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 package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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