R Observatory: Metrics for phyloseqGraphTest version 0.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

phyloseqGraphTest

0.1.1

Graph-Based Permutation Tests for Microbiome Data

2packages depend

6.4Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Julia FukuyamaFirst published 2018-03-154 releasesCRAN page ↗GitHub ↗

Provides functions for graph-based multiple-sample testing and visualization of microbiome data, in particular data stored in 'phyloseq' objects. The tests are based on those described in Friedman and Rafsky (1979) http://www.jstor.org/stable/2958919, and the tests are described in more detail in Callahan et al. (2016) doi:10.12688/f1000research.8986.1.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("phyloseqGraphTest", 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("jfukuyama/phyloseqGraphTest")

Development version from jfukuyama/phyloseqGraphTest. 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-phyloseqgraphtest

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

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 5.6 min · r-devel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

4

Dependencies · direct

Check history

NOTE2026-06-09
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
11 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-16
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-13
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-12
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 1 earlier snapshots

ERROR2026-03-10
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

6.4K

CRAN downloads in the past year

Rank #5,156 · ~18/day · ~534/mo

Releases R versions

Daily download trend is not available in this view yet.

34630 days

1.5K90 days

6.4K1 year

Compare downloads with other packages →

Also on104 r2u

Repository

GitHub ↗ jfukuyama/phyloseqgraphtest

4Stars

4Forks

3Open issues

1Open PRs

0Releases

45Commits

2Contributors

45 commits · Last activity 2024-02-05

Stars over time

2022-08-18 · 42026-07-07 · 4

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/jfukuyama/phyloseqgraphtest on 2026-08-16.

Continuous integration (1)

Travis CI

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

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (3)

R >= 3.5.0ggplot2 phyloseq

Imports (2)

ggnetwork igraph

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

MiscMetabar pctax

Code & Tests

People & History

People (0)

Author records are not tracked yet for this package.

Listed in earlier versions (1)

Julia Fukuyama

no longer listed · 0.0.1 to 0.1.1

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.1.1Latest
2024-02-05 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
0.1.0
2020-02-07 · diff ↗
R
R 3.6.0 released · 2019-04-26
0.0.2
2018-06-27 · diff ↗
R
R 3.5.0 released · 2018-04-23
0.0.1
2018-03-15
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2018-03-15
Total releases: 4 / 8 yrs
License: CC0
Minimum R: ≥ 3.5.0
Download size: 466 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("phyloseqGraphTest")

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 phyloseqGraphTest version 0.1.1 [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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