R Observatory: Metrics for metacoder version 0.3.9

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

metacoder

0.3.9

Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data

1packages depend

5Kdownloads / year

66.1%test coverage

8/13checks pass

Overview

About

Maintained by Zachary FosterFirst published 2026-04-1115 releasesCRAN page ↗GitHub ↗

Reads, plots, and manipulates large taxonomic data sets, like those generated from modern high-throughput sequencing, such as metabarcoding (i.e. amplification metagenomics, 16S metagenomics, etc). It provides a tree-based visualization called "heat trees" used to depict statistics for every taxon in a taxonomy using color and size. It also provides various functions to do common tasks in microbiome bioinformatics on data in the 'taxmap' format defined by the 'taxa' package. The 'metacoder' package is described in the publication by Foster et al. (2017) doi:10.1371/journal.pcbi.1005404.

Install

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

install.packages("metacoder", 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("grunwaldlab/metacoder")

Development version from grunwaldlab/metacoder. 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-metacoder

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

# 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-metacoder

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

Health

CRAN checks

5NOTE8OK

Failing flavors

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

Slowest check: 6.4 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.34

66.1%

Coverage · measured lines

99%

Documentation · exports

24

Dependencies · direct

Check history

NOTE2026-06-18
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-02
10 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
10 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-12
6 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 706 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 86%
Documented parameters: 99%
Return-value docs: 72%
References docs: 0%

Downloads

5K

CRAN downloads in the past year

Rank #3,515 · ~14/day · ~418/mo

Releases R versions

Daily download trend is not available in this view yet.

65030 days

2.8K90 days

5K1 year

Compare downloads with other packages →

Also on397 r2u17 autocran2.5K bioconda93 c2d4u

Repository

GitHub ↗ grunwaldlab/metacoder

146Stars

30Forks

43Open issues

0Open PRs

11Releases

1,115Commits

10Contributors

taxonomymetabarcodingtreesrcommunity-diversitypcrhierarchicalcran

1,115 commits · Last activity 2026-07-17 · +1.4% stars, 30d

Stars over time

2025-08-04 · 1432026-08-08 · 146

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/grunwaldlab/metacoder on 2026-08-16.

Continuous integration (1)

GitHub Actions

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

30 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.0.2

Imports (24)

stringr ggplot2 igraphgridtaxize seqinr RCurl apestatsgrDevicesutilslazyeval dplyr magrittr readr rlang ggfittext vegan cowplot GA Rcpp crayon tibble R6

LinkingTo (1)

Rcpp

Suggests (9)

knitr rmarkdown testthat BiocManager phyloseq phylotate traits biomformat DESeq2

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

demulticoder

Code & Tests

Datasets

People & History

People (5)

Maintainer (1)

Zachary Foster

Author, Maintainer

Authors (1)

Zachary Foster

Author, Maintainer

Contributors (3)

Scott Chamberlain

Contributor · added in 0.3.8

Rob Gilmore

Contributor · added in 0.2.1

Kamil Slowikowski

Contributor · added in 0.3.8

Other (1)

Niklaus Grunwald

Thesis advisor

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
0.3.9Latest
2026-04-11 · current release · diff ↗
unarchivedReturned to CRAN
2026-04-11
archivedRemoved from CRAN
2025-10-18
issues were not corrected despite reminders
R
R 4.5.0 released · 2025-04-11
0.3.8
2025-02-11 · diff ↗
unarchivedReturned to CRAN
2025-02-11
archivedRemoved from CRAN
2024-10-01
issues were not corrected in time
R
R 4.4.0 released · 2024-04-24
0.3.7
2024-02-20 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.3.6
2023-04-04 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.3.5
2021-06-23 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.3.4
2020-04-29 · diff ↗

Show 16 earlier events

R
R 4.0.0 released · 2020-04-24
0.3.3
2019-07-18 · diff ↗
R
R 3.6.0 released · 2019-04-26
0.3.2
2019-04-08 · diff ↗
unarchivedReturned to CRAN
2019-01-05
0.3.1
2019-01-04 · diff ↗
0.3.0.1
2018-11-19 · diff ↗
orphanedOrphaned by its maintainer
2018-11-19
maintainer did not respond to request for correction
0.3.0
2018-08-28 · diff ↗
0.2.1
2018-05-02 · diff ↗
R
R 3.5.0 released · 2018-04-23
0.2.0
2018-01-05 · diff ↗
0.1.3
2017-05-23 · diff ↗
R
R 3.4.0 released · 2017-04-21
0.1.2
2016-08-27
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2026-04-11
Total releases: 15 / 1 yrs
License: GPL-2 | GPL-3 OSI
Minimum R: ≥ 3.0.2
Bundled data: 209 KB / 4 files
Download size: 852 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Phylogenetics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("metacoder")

Format

Foster, Z., Chamberlain, S., Gilmore, R., Grunwald, N., & Slowikowski, K. (2026). metacoder: Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data (Version 0.3.9) [Computer software]. https://doi.org/10.32614/CRAN.package.metacoder

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 metacoder version 0.3.9 [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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