R Observatory: Metrics for permubiome version 1.3.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

permubiome

1.3.2Package record

A Permutation Based Test for Biomarker Discovery in Microbiome Data

0packages depend

2.6Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Alfonso Benitez-PaezCRAN page ↗

The permubiome R package was created to perform a permutation-based non-parametric analysis on microbiome data for biomarker discovery aims. This test executes thousands of comparisons in a pairwise manner, after a random shuffling of data into the different groups of study with a prior selection of the microbiome features with the largest variation among groups. Previous to the permutation test itself, data can be normalized according to different methods proposed to handle microbiome data ('proportions' or 'Anders'). The median-based differences between groups resulting from the multiple simulations are fitted to a normal distribution with the aim to calculate their significance. A multiple testing correction based on Benjamini-Hochberg method (fdr) is finally applied to extract the differentially presented features between groups of your dataset. LATEST UPDATES: v1.1 and olders incorporates function to parse COLUMN format; v1.2 and olders incorporates -optimize- function to maximize evaluation of features with largest inter-class variation; v1.3 and olders includes the -size.effect- function to perform estimation statistics using the bootstrap-coupled approach implemented in the 'dabestr' (>=0.3.0) R package. Current v1.3.2 fixed bug with "Class" recognition and updated 'dabestr' functions.

Install

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

install.packages("permubiome", 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-permubiome

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-permubiome

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-permubiome

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

2NOTE11OK

Check messages

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

Maintainer: ‘Alfonso Benitez-Paez <alfbenpa@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Alfonso",
                    family = "Benitez-Paez",
                    role = c("aut", "cre"),
                    email = "alfbenpa@gmail.com")
as necessary.

CRAN check page ↗

Slowest check: 2.1 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.3.2

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 6
Examples that run: 100%6 run in a plain check
Exported functions with examples: 100%
Documented parameters: not tracked
Return-value docs: not tracked
Help pages citing references: 100%

How these are measured

Downloads

2.6K

CRAN downloads in the past year

Rank #17,761 · ~7/day · ~216/mo

Releases R versions

Daily download trend is not available in this view yet.

29830 days

72990 days

2.6K1 year

Compare downloads with other packages →

Also on69 r2u1 autocran

How downloads are counted

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Installing permubiome adds 38 packages (17 with compiled code, 41 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, vipor 4.5 MB.

Depends (0)

none

Imports (6)

ggplot2 rlang dabestr gridExtraMatrixdplyr

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

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

Alfonso Benitez-Paez

Maintainer since 1.0 (2016)

Releases (6)

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
1.3.2Latest
record
2023-10-16 · 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
1.3.1
record
2020-07-31 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.3
record
2019-12-10 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.2
record
2018-08-18 · diff ↗
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
1.1
record
2016-03-23 · diff ↗

Show 2 earlier eventsHide 2 earlier events

1.0
record
2016-02-08
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2016-02-08
Total releases: 6 / 10 yrs
License: GPL-3 OSI
Download size: 12 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("permubiome")

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 permubiome version 1.3.2 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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