R Observatory: Metrics for phyloseqGraphTest version 0.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

phyloseqGraphTest

0.1.1Package record

Graph-Based Permutation Tests for Microbiome Data

0packages dependsuggested by 2

6.2Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Julia FukuyamaCRAN 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. 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

Health

CRAN checks

2NOTE11OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Julia Fukuyama <julia.fukuyama@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Julia",
                    family = "Fukuyama",
                    role = c("aut", "cre"),
                    email = "julia.fukuyama@gmail.com")
as necessary.

CRAN check page ↗

Slowest check: 5.7 min · r-devel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTE2026-06-09
ERROR11 OK, 1 NOTE, 1 ERROR2026-06-08
NOTE12 OK, 2 NOTE2026-03-16
ERROR11 OK, 2 NOTE, 1 ERROR2026-03-13
NOTE12 OK, 2 NOTE2026-03-12

Show 1 earlier changeHide 1 earlier change

ERROR11 OK, 2 NOTE, 1 ERROR2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.1

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 10 (3 internal)includes a package overview page
Examples that run: 100%3 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

Graph Testing Vignette

How these are measured

Downloads

6.2K

CRAN downloads in the past year

Rank #6,329 · ~17/day · ~513/mo

Releases R versions

Daily download trend is not available in this view yet.

49930 days

1.3K90 days

6.2K1 year

Compare downloads with other packages →

Also on114 r2u

How downloads are counted

Repository

jfukuyama/phyloseqgraphtest ↗Account: jfukuyama

4Stars

4Forks

3Open issues

1Open PRs

0Releases

45Commits

2Commit identities

45 commits · Last activity 2024-02-05

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 30
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2022-08-18 · 42026-07-07 · 4

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/jfukuyama/phyloseqgraphtest on 2026-10-11.

Continuous integration (1)

Travis CI (config file)

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing phyloseqGraphTest adds 30 packages (16 with compiled code, 25 MB of source tarballs). Heaviest: ggplot2 6.0 MB, igraph 4.8 MB, Rcpp 1.8 MB. 1 more not on CRAN is not measured.

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

0direct

0indirect

Suggested by 2

Suggests, most downloaded first

MiscMetabar pctax

How these are counted

Code & Tests

People & History

People (from the free-text Author field) (1)

Julia Fukuyama

Author, Maintainer since 0.0.1 (2018)

Releases (4)

Pick two releases to compare their code metrics.

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
record
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
record
2020-02-07 · diff ↗
R
R 3.6.0 released · 2019-04-26
0.0.2
record
2018-06-27 · diff ↗
R
R 3.5.0 released · 2018-04-23
0.0.1
record
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

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 v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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