R Observatory: Metrics for phylosignalDB version 0.4.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

phylosignalDB

0.4.2

Explore Phylogenetic Signals Using Distance-Based Methods

0packages depend

2.1Kdownloads / year

71.8%test coverage

13/13checks pass

Overview

About

Maintained by Liang YaoFirst published 2025-01-162 releasesCRAN page ↗GitHub ↗

A unified method, called M statistic, is provided for detecting phylogenetic signals in continuous traits, discrete traits, and multi-trait combinations. Blomberg and Garland (2002) doi:10.1046/j.1420-9101.2002.00472.x provided a widely accepted statistical definition of the phylogenetic signal, which is the "tendency for related species to resemble each other more than they resemble species drawn at random from the tree". The M statistic strictly adheres to the definition of phylogenetic signal, formulating an index and developing a method of testing in strict accordance with the definition, instead of relying on correlation analysis or evolutionary models. The novel method equivalently expressed the textual definition of the phylogenetic signal as an inequality equation of the phylogenetic and trait distances and constructed the M statistic. The M statistic implemented in this package is based on the methodology described in Yao and Yuan (2025) doi:10.1002/ece3.71106. If you use this method in your research, please cite the paper.

Install

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

install.packages("phylosignalDB", 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("anonymous-eco/phylosignalDB")

Development version from anonymous-eco/phylosignalDB. 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-phylosignaldb

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-phylosignalDB

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-phylosignalDB

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

Health

CRAN checks

13OK

Slowest check: 1.3 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.10

71.8%

Coverage · measured lines

100%

Documentation · exports

5

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 407 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 83%

Downloads

2.1K

CRAN downloads in the past year

Rank #22,187 · ~6/day · ~173/mo

Releases R versions

Daily download trend is not available in this view yet.

12430 days

47990 days

2.1K1 year

Compare downloads with other packages →

Also on109 r2u9 autocran

Repository

GitHub ↗ anonymous-eco/phylosignaldb

1Stars

0Forks

1Open issues

0Open PRs

1Releases

14Commits

1Contributors

License GPL-3.0 · 14 commits · Last activity 2025-01-18

Stars over time

2026-07-07 · 02026-07-16 · 1

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/anonymous-eco/phylosignaldb on 2026-08-03.

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0

Imports (5)

ape castorclusterdoParallel foreach

LinkingTo (0)

none

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (2)

Maintainer (1)

Liang Yao

Author, Maintainer

Authors (2)

Liang Yao

Author, Maintainer

Ye Yuan

Author

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
0.4.2Latest
2026-01-29 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
0.2.2
2025-01-16
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2025-01-16
Total releases: 2 / 1 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.0
Bundled data: 16 KB / 1 file
Download size: 28 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("phylosignalDB")

Format

Yao, L., & Yuan, Y. (2026). phylosignalDB: Explore Phylogenetic Signals Using Distance-Based Methods (Version 0.4.2) [Computer software]. https://doi.org/10.32614/CRAN.package.phylosignalDB

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 phylosignalDB version 0.4.2 [Data set]. HJJB, LLC. Data release v2026-08-09. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-09, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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