R Observatory: Metrics for phylosignalDB version 0.4.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

phylosignalDB

0.4.2Package record

Explore Phylogenetic Signals Using Distance-Based Methods

0packages depend

2.2Kdownloads / year

71.8%test coverage

13/13flavors OK

Overview

About

Maintained by Liang YaoCRAN page ↗GitHub ↗Issues ↗

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.

Changes in 0.4.2

This release removes the restriction to ultrametric trees and adds a CITATION file specifying the reference users should cite.

From NEWS.md in the release

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. 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-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). 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: 1.3 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.4.2

READMEYes · 407 wordsVignettesNoNEWSYes · 100% structured · mentions 0.4.2Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 6 (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: 100%
Help pages citing references: 83%

How these are measured

Downloads

2.2K

CRAN downloads in the past year

Rank #22,588 · ~6/day · ~187/mo

Releases R versions

Daily download trend is not available in this view yet.

22630 days

58990 days

2.2K1 year

Compare downloads with other packages →

Also on79 r2u3 autocran

How downloads are counted

Repository

anonymous-eco/phylosignaldb ↗Account: anonymous-eco

1Stars

0Forks

1Open issues

0Open PRs

1Releases

14Commits

1Commit identities

License file reads as GPL-3.0 · 14 commits · Last activity 2025-01-16 · 0% stars, 30d · The default branch showed an older version (0.2.2) than CRAN on 2026-10-21

Responsiveness

not measured

Stars over time

2026-07-07 · 02026-07-16 · 1

How these are measured

PracticesBeta

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

Checks run against github.com/anonymous-eco/phylosignaldb on 2026-10-21.

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Installing phylosignalDB adds 11 packages (7 with compiled code, 7.7 MB of source tarballs). Heaviest: Rcpp 1.8 MB, RcppEigen 1.7 MB, ape 1.4 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (2)

Liang Yao

Author, Maintainer since 0.2.2 (2025)

Ye Yuan

Author

Releases (2)

Pick two releases to compare their code metrics.

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

Cite

Cite this package

Run in R for the authors' entry:

citation("phylosignalDB")

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

It points to 10.1002/ece3.71106.

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 v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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