R Observatory: Metrics for rbiom version 3.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

rbiom

3.1.0Package record

Integrated Analysis and Visualization of Microbiome Data

1packages depend

75.2Kdownloads / year

91.9%test coverage

13/13flavors OK

Overview

About

Maintained by Daniel P. SmithCRAN page ↗GitHub ↗Website ↗Issues ↗Declared funder: Alkek Center for Metagenomics and Microbiome Research

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. 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-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). 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: 7.3 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-07
OK13 OK2026-04-28

Show 4 earlier changesHide 4 earlier changes

ERROR11 OK, 1 ERROR2026-04-27
OK14 OK2026-04-11
ERROR13 OK, 1 ERROR2026-04-10
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 3.1.0

READMEYes · 179 wordsVignettes· In the repository, left out of the releaseNEWS· In the repository, left out of the releaseCitation fileNoWebsiteYes · pkgdown

The repository also keeps web-only articles.

Help pages: 74 (15 internal)includes a package overview page
Examples that run: 98%57 run in a plain check · 1 never run
Exported functions with examples: 75%
Documented parameters: not tracked
Return-value docs: 0%
Help pages citing references: 0%

How these are measured

Downloads

75.2K

CRAN downloads in the past year

Rank #2,770 · ~206/day · ~6.3K/mo

Releases R versions

Daily download trend is not available in this view yet.

1.7K30 days

5.4K90 days

75.2K1 year

Compare downloads with other packages →

Also on636 r2u6 autocran23K conda_forge

How downloads are counted

Repository

cmmr/rbiom ↗Organization: cmmr

19Stars

1Forks

3Open issues

0Open PRs

6Releases

427Commits

2Commit identities

427 commits · Last activity 2026-10-08 · 0% stars, 30d · Default branch at 3.1.1, ahead of CRAN 3.1.0 (checked 2026-10-22)

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 2
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-07-07 · 182026-07-07 · 19

How these are measured

PracticesBeta

8 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/cmmr/rbiom on 2026-10-22.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-10-08 · The repository has a site deploy workflow

pkgdown site last built 2026-10-08

Coverage (1)

Coverage reporting

Lint, format, editor (1)

lintr

How this is detected·Detection ruleset v4 (2026-10-20)

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen 2026-04-23
Named in .Rbuildignore: .claude
Commits: at least 2 crediting it in the message

Models named in its commits

Claude Opus 52 commits · Sep 2026

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

36 external dependencies (excludes base and recommended)

Installing rbiom adds 69 packages (36 with compiled code, 54 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, vipor 4.5 MB.

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

1indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

strollur

How these are counted

Code & Tests

People & History

People (2)

Daniel P. Smith

Author, Maintainer since 1.0.0 (2020)

Alkek Center for Metagenomics and Microbiome Research

Copyright holder, Funder · added in 2.0.7

Releases (11)

Pick two releases to compare their code metrics.

3.1.0Latest
record
2026-05-08 · current release · diff ↗ ·
removed 51 exports
`taxa_max`, `alpha.div`, `as.percent`, `beta.div`, `comments`, `comments<-`, `counts`, `counts<-`, `depth`, `depths_barplot`, `has.phylogeny`, `has.sequences`, `id`, `id<-`, `info`, `is.rarefied`, `metadata`, `metadata<-`, `nsamples`, `ntaxa`, `phylogeny`, `phylogeny<-`, `read.biom`, `read.fasta`, `read.tree`, `repair`, `sample.names`, `sample.names<-`, `sample_subset`, `sample.sums` and 21 more

added 18 exports
`adiv_vector`, `biom_inflate`, `biom_relativize`, `biom_rescale`, `convert_to_animalcules`, `convert_to_biomformat`, `suggest_inflate_depths`, `suggest_rarefy_depth`, babies, gems, hmp50, `mtx_rarefy`, `mtx_percent`, `mtx_rescale`, ggsave, list_metrics, match_metric, n_cpus
R
R 4.6.0 released · 2026-04-24
2.2.1
record
2025-06-27 · diff ↗
R
R 4.5.0 released · 2025-04-11
2.2.0
record
2025-04-04 · diff ↗
2.1.2
record
2025-03-18 · diff ↗
2.1.1
record
2025-03-10 · diff ↗ ·
added 3 exports
`convert_to_phyloseq`, `write_mothur`, `write_qiime2`
2.0.13
record
2025-01-24 · diff ↗ ·
added 2 exports
`convert_to_SE`, `convert_to_TSE`
2.0.10
record
2025-01-19 · diff ↗ ·
added 1 export
availableCores
2.0.7
record
2025-01-11 · diff ↗ ·
removed 25 exports
alpha.div, beta.div, counts, info, nsamples, ntaxa, metadata, phylogeny, rarefy, read.biom, read.fasta, read.tree, sample.names, sequences, subtree, taxonomy, taxa.names, taxa.ranks, taxa.rollup, tips, unifrac, write.biom, write.fasta, write.tree, write.xlsx

added 126 exports
`adiv_boxplot`, `adiv_corrplot`, `adiv_matrix`, `adiv_stats`, `adiv_table`, `as_rbiom`, `bdiv_boxplot`, `bdiv_clusters`, `bdiv_corrplot`, `bdiv_distmat`, `bdiv_heatmap`, `bdiv_matrix`, `bdiv_ord_plot`, `bdiv_ord_table`, `bdiv_stats`, `bdiv_table`, `bdply`, `biom_merge`, `blply`, `distmat_ord_table`, `distmat_stats`, `plot_heatmap`, `rare_corrplot`, `rare_multiplot`, `rare_stacked`, `rarefy`, `rarefy_cols`, `read_biom`, `read_fasta`, `read_tree` and 96 more
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
record
2021-11-05 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.0.2
record
2020-05-29 · diff ↗

Show 2 earlier eventsHide 2 earlier events

1.0.0
record
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 · relicensed from AGPL-3 in 2.0.7
Minimum R: ≥ 4.3.0
Download size: 1.0 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("rbiom")

Format

Smith, D. P., & Alkek Center for Metagenomics and Microbiome Research. (2026). rbiom: Integrated Analysis and Visualization of Microbiome Data (Version 3.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.rbiom

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 rbiom version 3.1.0 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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