R Observatory: Metrics for GUniFrac version 1.9

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

GUniFrac

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

4packages dependsuggested by 1

25.9Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Jun ChenCRAN 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. 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-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). 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: 4.6 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-04-22
ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.9

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 19
Examples that run: 74%14 run in a plain check · 5 never run
Exported functions with examples: 100%
Documented parameters: 93%
Return-value docs: 100%
Help pages citing references: 74%

Vignettes (1)

Performing differential abundance analysis using ZicoSeq HTML

How these are measured

Downloads

25.9K

CRAN downloads in the past year

Rank #2,957 · ~71/day · ~2.2K/mo

Releases R versions

Daily download trend is not available in this view yet.

1.5K30 days

4.7K90 days

25.9K1 year

Compare downloads with other packages →

Also on675 r2u4 autocran4.4K conda_forge179 c2d4u

How downloads are counted

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Installing GUniFrac adds 39 packages (20 with compiled code, 24 MB of source tarballs). Heaviest: ggplot2 6.0 MB, Rcpp 1.8 MB, isoband 1.5 MB.

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

4direct

1indirect

Imports 4

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

MiRKAT LDM chemodiv mecoturn

Suggests, most downloaded first

microeco

How these are counted

Code & Tests

Datasets

People & History

People (4)

Jun Chen

Author, Maintainer since 1.0 (2012)

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

Releases (10)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.9Latest
record
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
record
2023-09-14 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.7
record
2022-10-23 · diff ↗ ·
added 1 export
SimulateMSeqC
1.6
record
2022-05-17 · diff ↗ ·
added 3 exports
dICC, dICC.SE.asympt, dICC.SE.bt
R
R 4.2.0 released · 2022-04-22
1.5
record
2022-04-06 · diff ↗ ·
removed 2 exports
linda, linda.plot

added 1 export
ZicoSeq.plot
1.4
record
2021-11-10 · diff ↗ ·
added 2 exports
linda, linda.plot
1.3
record
2021-08-18 · diff ↗ ·
added 3 exports
SimulateMSeq, ZicoSeq, GMPR
R
R 4.1.0 released · 2021-05-18
1.2
record
2021-05-03 · diff ↗ ·
removed 1 export
pattern:^[[:alpha:]]+

added 6 exports
GUniFrac, Rarefy, PermanovaG, PermanovaG2, dmanova, adonis3
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26

Show 11 earlier eventsHide 11 earlier events

R
R 3.5.0 released · 2018-04-23
1.1
record
2018-02-13 · diff ↗ ·
removed 1 export
pattern:.

added 1 export
pattern:^[[:alpha:]]+
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
record
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

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 package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →