R Observatory: Metrics for treestats version 1.71.13

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

treestats

1.71.13Package record

Phylogenetic Tree Statistics

1packages depend

9.1Kdownloads / year

95.4%test coverage

13/13flavors OK

Overview

About

Maintained by Thijs JanzenCRAN page ↗GitHub ↗Website ↗Issues ↗

Collection of phylogenetic tree statistics, collected throughout the literature. All functions have been written to maximize computation speed. The package includes umbrella functions to calculate all statistics, all balance associated statistics, or all branching time related statistics. Furthermore, the 'treestats' package supports summary statistic calculations on Ltables, provides speed-improved coding of branching times, Ltable conversion and includes algorithms to create intermediately balanced trees. Full description can be found in Janzen (2024) doi:10.1016/j.ympev.2024.108168.

Changes in 1.71.13

Polytomies were not handled correctly, and code for the following statistics

was adjusted accordingly: ILnumber, entropy_j, tot_internal_path, tot_path,

max_width, max_del_width, max_depth, mw_over_md, phylogenetic_diversity,

var_pair_dist and var_leaf_depth.

Furthermore, several statistics previously not available for non-binary trees

Several statistics previously not available for non-binary trees

were expanded to be applicable to non-binary trees as well (use at your own

discretion, as normalization constants might not be applicable): b1, b2,

cherries, pitchforks, double_cherries, sackin index, total cophenetic index,

area_per_pair and average_leaf_depth.

max_closeness, area_per_pair and average_leaf_depth.

For an overview of which statistics can be used with non-binary trees, please

Show all changes in 1.71.13Hide the rest of the changes in 1.71.13

consult the table in the README file, which has been updated accordingly.

From NEWS.md in the release

Install

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

install.packages("treestats", 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("thijsjanzen/treestats")

Development version from thijsjanzen/treestats. 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-treestats

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-treestats

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-treestats

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: 9.1 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-10-17
WARNING12 OK, 1 WARNING2026-10-01
OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-19

Show 6 earlier changesHide 6 earlier changes

WARNING12 OK, 1 WARNING2026-06-17
OK13 OK2026-04-30
WARNING11 OK, 2 NOTE, 1 WARNING2026-04-23
NOTE12 OK, 2 NOTE2026-04-22
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-18
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.71.13

READMEYes · 1,309 wordsVignettesYes · 4 · dynamicNEWSYes · 100% structured · mentions 1.71.13Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 81includes a package overview page
Examples that run: 100%18 run in a plain check
Exported functions with examples: 23%
Documented parameters: 100%
Return-value docs: 96%
Help pages citing references: 64%

Vignettes (4)

How these are measured

Downloads

9.1K

CRAN downloads in the past year

Rank #3,249 · ~25/day · ~757/mo

Releases R versions

Daily download trend is not available in this view yet.

49330 days

3.6K90 days

9.1K1 year

Compare downloads with other packages →

Also on459 r2u4 autocran

How downloads are counted

Repository

thijsjanzen/treestats ↗Account: thijsjanzen

21Stars

2Forks

1Open issues

0Open PRs

5Releases

831Commits

2Commit identities

831 commits · Last activity 2026-08-24 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 80%
Median days to close, 50 most recently updated closed issues: 14
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-06-19 · 182026-07-07 · 21

How these are measured

PracticesBeta

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

Checks run against github.com/thijsjanzen/treestats on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-08-24 · The repository has a site deploy workflow

pkgdown site last built 2026-08-24

Coverage (1)

Coverage reporting

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

29 external dependencies (excludes base and recommended)

Installing treestats adds 45 packages (27 with compiled code, 40 MB of source tarballs). Heaviest: BH 14 MB, igraph 4.8 MB, maps 2.2 MB.

Depends (1)

Rcpp

Imports (5)

ape nloptr treebalance DDD RSpectra

LinkingTo (3)

Rcpp RcppArmadillo nloptr

Suggests (23)

phytools phyloTop testthat geiger nLTT castor adephylo ggplot2 tibble dplyr tidyr picante lintr rmarkdown knitr igraphMatrixpheatmap ggdendro dendextendMatrixTreeSimnlme

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

secsse

How these are counted

Code & Tests

People & History

People (1)

Thijs Janzen

Maintainer since 1.0.3 (2024), Author

Releases (9)

Pick two releases to compare their code metrics.

1.71.13Latest
record
2026-08-24 · current release · diff ↗ ·
added 1 export
check_binary
1.71.12
record
2026-06-16 · diff ↗ ·
added 1 export
inv_branch_dist
1.70.11
record
2026-05-20 · diff ↗
R
R 4.6.0 released · 2026-04-24
1.70.8
record
2025-11-12 · diff ↗
1.70.7
record
2025-09-11 · diff ↗ ·
added 2 exports
i_stat, sshape
R
R 4.5.0 released · 2025-04-11
1.70.5
record
2024-08-26 · diff ↗
1.70.4
record
2024-07-17 · diff ↗ ·
removed 3 exports
calc_balance_stats, eigen_vector, prep_lapl_spec

added 16 exports
avg_vert_depth, calc_topology_stats, colless_corr, colless_quad, create_fully_balanced_tree, create_fully_unbalanced_tree, double_cherries, eigen_centrality, four_prong, minmax_adj, minmax_laplace, mw_over_md, root_imbalance, tot_internal_path, tot_path_length, treeness
R
R 4.4.0 released · 2024-04-24
1.0.5
record
2024-01-30 · diff ↗
1.0.3
record
2024-01-12
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2024-01-12
Total releases: 9 / 2 yrs
License: GPL-3 OSI
Download size: 5.2 MB

Appears in task views

Phylogenetics

Cite

Cite this package

Run in R for the authors' entry:

citation("treestats")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1016/j.ympev.2024.108168.

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 treestats version 1.71.13 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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