R Observatory: Metrics for GUniFrac version 1.9

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

GUniFrac

1.9

Generalized UniFrac Distances, Distance-Based Multivariate Methods and Feature-Based Univariate Methods for Microbiome Data Analysis

5packages depend

36Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Jun ChenFirst published 2012-04-2810 releasesCRAN page ↗

A suite of methods for powerful and robust microbiome data analysis including data normalization, data simulation, community-level association testing and differential abundance analysis. It implements generalized UniFrac distances, Geometric Mean of Pairwise Ratios (GMPR) normalization, semiparametric data simulator, distance-based statistical methods, and feature-based statistical methods. The distance-based statistical methods include three extensions of PERMANOVA: (1) PERMANOVA using the Freedman-Lane permutation scheme, (2) PERMANOVA omnibus test using multiple matrices, and (3) analytical approach to approximating PERMANOVA p-value. Feature-based statistical methods include linear model-based methods for differential abundance analysis of zero-inflated high-dimensional compositional data.

Install

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

install.packages("GUniFrac", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-gunifrac

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-GUniFrac

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-GUniFrac

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

Health

CRAN checks

13OK

Slowest check: 5.0 min · r-devel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

18

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
OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 74%
Documented parameters: 93%
Return-value docs: 100%
References docs: 74%

Downloads

36K

CRAN downloads in the past year

Rank #2,895 · ~99/day · ~3K/mo

Releases R versions

Daily download trend is not available in this view yet.

1.4K30 days

4.9K90 days

36K1 year

Compare downloads with other packages →

Also on537 r2u24 autocran4.6K conda_forge61 c2d4u

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (18)

Rcpp vegan ggplot2 matrixStatsMatrixapeparallelstatsutilsstatmod rmutil dirmultMASSggrepel foreach modeest inlinemethods

LinkingTo (1)

Rcpp

Suggests (4)

ade4 knitr markdown ggpubr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

5direct

1indirect

LDM MiRKAT chemodiv mecoturn microeco

Code & Tests

Datasets

People & History

People (4)

Maintainer (1)

Jun Chen

Author, Maintainer

Authors (4)

Jun Chen

Author, Maintainer

Lu Yang

Author · added in 1.5

Lujun Zhang

Author · added in 1.8

Xianyang Zhang

Author · added in 1.4

Listed in earlier versions (1)

Huijuan Zhou

no longer listed · 1.4

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.9Latest
2025-08-25 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.8
2023-09-14 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.7
2022-10-23 · diff ↗
1.6
2022-05-17 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.5
2022-04-06 · diff ↗
1.4
2021-11-10 · diff ↗
1.3
2021-08-18 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.2
2021-05-03 · diff ↗
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26

Show 11 earlier events

R
R 3.5.0 released · 2018-04-23
1.1
2018-02-13 · diff ↗
unarchivedReturned to CRAN
2018-02-12
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16
orphanedOrphaned by its maintainer
2014-12-07
maintainer address <chenjun@mail.med.upenn.edu> bounced
R
R 3.1.0 released · 2014-04-10
R
R 3.0.0 released · 2013-04-03
1.0
2012-04-28
R
R 2.15.0 released · 2012-03-30

Package metadata

First published: 2012-04-28
Total releases: 10 / 14 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 263 KB / 5 files
Download size: 823 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Phylogenetics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("GUniFrac")

Format

Chen, J., Yang, L., Zhang, L., & Zhang, X. (2025). GUniFrac: Generalized UniFrac Distances, Distance-Based Multivariate Methods and Feature-Based Univariate Methods for Microbiome Data Analysis (Version 1.9) [Computer software]. https://doi.org/10.32614/CRAN.package.GUniFrac

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 GUniFrac version 1.9 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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