rbiom

3.1.0

Integrated Analysis and Visualization of Microbiome Data

1packages depend

101.7Kdownloads / year

91.9%test coverage

13/13checks pass

Overview

About

Maintained by Daniel P. SmithFirst published 2020-05-2611 releasesCRAN page ↗GitHub ↗

A toolkit for working with Biological Observation Matrix ('BIOM') files. Read/write all 'BIOM' formats. Compute rarefaction, alpha diversity, and beta diversity (including 'UniFrac'). Summarize counts by taxonomic level. Subset based on metadata. Generate visualizations and statistical analyses.

Install

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

install.packages("rbiom", 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("cmmr/rbiom")

Development version from cmmr/rbiom. 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-rbiom

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-rbiom

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-rbiom

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

Health

CRAN checks

13OK

Slowest check: 8.4 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.08

91.9%

Coverage · measured lines

25%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-07
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-28
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-27
11 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-11
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

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

Documentation

READMEYes · 179 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 98%
Documented parameters: not tracked
Return-value docs: 0%
References docs: 0%

Downloads

101.7K

CRAN downloads in the past year

Rank #2,593 · ~279/day · ~8.5K/mo

Releases R versions

Daily download trend is not available in this view yet.

2.3K30 days

8.3K90 days

101.7K1 year

Compare downloads with other packages →

Also on745 r2u30 autocran20.5K conda_forge

Repository

GitHub ↗ cmmr/rbiom

19Stars

1Forks

3Open issues

0Open PRs

6Releases

421Commits

2Contributors

421 commits · Last activity 2026-05-07 · 0% stars, 30d

Stars over time

2025-07-07 · 182026-07-07 · 19

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/cmmr/rbiom on 2026-07-19.

Continuous integration (1)

GitHub Actions

Docs source (1)

README.Rmd

Lint, format, editor (1)

lintr

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

Dependencies

Declared dependencies

36 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.3.0

Imports (22)

methodsmgcvstatsutilsape dplyr ecodive emmeans fillpattern ggbeeswarm ggnewscale ggplot2 ggrepel ggtext jsonlite magrittr patchwork pillar plyr readr readxl vegan

LinkingTo (0)

none

Suggests (19)

cli crayon ggdensity glue h5lite labeling lifecycleMatrixopenxlsx optparse pkgconfig prettycode R6 rlang scales testthat tibble tsne uwot

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

strollur

Code & Tests

People & History

People (2)

Maintainer (1)

Daniel P. Smith

Author, Maintainer

Authors (1)

Daniel P. Smith

Author, Maintainer

Alkek Center for Metagenomics and Microbiome Research

Funders (1)

Alkek Center for Metagenomics and Microbiome Research

Package Timeline

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

3.1.0Latest
2026-05-08 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
2.2.1
2025-06-27 · diff ↗
R
R 4.5.0 released · 2025-04-11
2.2.0
2025-04-04 · diff ↗
2.1.2
2025-03-18 · diff ↗
2.1.1
2025-03-10 · diff ↗
2.0.13
2025-01-24 · diff ↗
2.0.10
2025-01-19 · diff ↗
2.0.7
2025-01-11 · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
1.0.3
2021-11-05 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.0.2
2020-05-29 · diff ↗

Show 2 earlier events

1.0.0
2020-05-26
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-05-26
Total releases: 11 / 6 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.3.0
Download size: 1.0 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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