treestats

1.71.12

Phylogenetic Tree Statistics

1packages depend

7.2Kdownloads / year

95.2%test coverage

13/13checks pass

Overview

About

Maintained by Thijs JanzenFirst published 2024-01-128 releasesCRAN page ↗GitHub ↗

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.

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.

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).

Health

CRAN checks

13OK

Slowest check: 8.0 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.94

95.2%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-19
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
WARNING2026-06-17
12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-30
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
WARNING2026-04-23
11 OK · 2 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 1,395 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 97%
References docs: 65%

Downloads

7.2K

CRAN downloads in the past year

Rank #3,518 · ~20/day · ~600/mo

Releases R versions

Daily download trend is not available in this view yet.

59530 days

3.2K90 days

7.2K1 year

Compare downloads with other packages →

Also on474 r2u31 autocran

Repository

GitHub ↗ thijsjanzen/treestats

21Stars

2Forks

0Open issues

0Open PRs

4Releases

823Commits

2Contributors

823 commits · Last activity 2026-07-04 · 0% stars, 30d

Stars over time

2025-06-19 · 182026-07-07 · 21

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/thijsjanzen/treestats on 2026-07-19.

Continuous integration (1)

GitHub Actions

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

29 external dependencies (excludes base and recommended)

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

secsse

Code & Tests

Code Composition

R 8,056 (60%)C++ 2,420 (18%)Rd 2,373 (18%)Vignettes 511 (4%)

Code characteristics

Cyclomatic complexity: 1.0 median / 16 max
Test cases: 171 / 0.94 per code line
System requirements: 1 external

Test coverage

Line coverage

95%

Expression

95.1%

Tests / Examples

95.2% / 23% ex

Functions

381 79 exported

Complexity

2.7 avg / 16 max

Call network

381 nodes / 388 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

381 functions

Function	Cyclo	Coverage
minmax_adj exp	7	76%
diameter exp	5	76%
beta_statistic exp	3	77%
minmax_laplace exp	8	79%
slow_calc	3	83%
check_tree	16	88%

People & History

People (1)

Maintainer (1)

Thijs Janzen

Maintainer, Author

Authors (1)

Thijs Janzen

Maintainer, Author

Package Timeline

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

1.71.12Latest
2026-06-16 · current release · diff ↗
1.70.11
2026-05-20 · diff ↗
R
R 4.6.0 released · 2026-04-24
1.70.8
2025-11-12 · diff ↗
1.70.7
2025-09-11 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.70.5
2024-08-26 · diff ↗
1.70.4
2024-07-17 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.0.5
2024-01-30 · diff ↗
1.0.3
2024-01-12
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2024-01-12
Total releases: 8 / 2 yrs
License: GPL-3 OSI
Download size: 2.1 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Phylogenetics

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