R Observatory: Metrics for metacoder version 0.3.9

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

metacoder

0.3.9Package record

Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data

0packages dependsuggested by 1

6.4Kdownloads / year

66.1%test coverage

8/13flavors OK

Overview

About

Maintained by Zachary FosterCRAN page ↗GitHub ↗Website ↗Issues ↗

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.

Changes in 0.3.9

Maintenance release to fix CRAN check issues.

From NEWS.md in the release

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. 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

# 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). 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

5NOTE8OK

Check messages

NOTER code for possible problemsr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64

Found calls to structure() using deprecated special names:
  metacoder/tests/testthat/test--taxmap_parsers.R (.Names: 1)
'.Names' should be changed to 'names'.

NOTERd contentsr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Rd files without \usage:
  ‘all_names.Rd’ ‘arrange_obs.Rd’ ‘arrange_taxa.Rd’ ‘branches.Rd’
  ‘classifications.Rd’ ‘filter_obs.Rd’ ‘filter_taxa.Rd’ ‘get_data.Rd’
  ‘get_data_frame.Rd’ ‘get_dataset.Rd’ ‘id_classifications.Rd’
  ‘internodes.Rd’ ‘is_branch.Rd’ ‘is_internode.Rd’ ‘is_leaf.Rd’
  ‘is_root.Rd’ ‘is_stem.Rd’ ‘leaves.Rd’ ‘leaves_apply.Rd’ ‘map_data.Rd’
  ‘map_data_.Rd’ ‘mutate_obs.Rd’ ‘n_leaves.Rd’ ‘n_leaves_1.Rd’
  ‘n_obs.Rd’ ‘n_obs_1.Rd’ ‘n_subtaxa.Rd’ ‘n_subtaxa_1.Rd’
  ‘n_supertaxa.Rd’ ‘n_supertaxa_1.Rd’ ‘obs.Rd’ ‘obs_apply.Rd’
  ‘print_tree.Rd’ ‘remove_redundant_names.Rd’ ‘replace_taxon_ids.Rd’
  ‘roots.Rd’ ‘sample_frac_obs.Rd’ ‘sample_frac_taxa.Rd’
  ‘sample_n_obs.Rd’ ‘sample_n_taxa.Rd’ ‘select_obs.Rd’ ‘stems.Rd’
  ‘subtaxa.Rd’ ‘subtaxa_apply.Rd’ ‘supertaxa.Rd’ ‘supertaxa_apply.Rd’
  ‘taxon_ids.Rd’ ‘taxon_indexes.Rd’ ‘taxon_names.Rd’ ‘taxon_ranks.Rd’
  ‘taxonomy_table.Rd’ ‘transmute_obs.Rd’
\arguments should not be documented without \usage.

NOTEdependencies in R coder-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Namespace in Imports field not imported from:
  ‘R6’
All declared Imports should be used.

Additional issues

donttest

CRAN check page ↗

Slowest check: 6.3 min · r-oldrel-windows-x86_64

Status changes

NOTE8 OK, 5 NOTENow
NOTE11 OK, 2 NOTE2026-06-18
ERROR10 OK, 2 NOTE, 1 ERROR2026-06-02
NOTE12 OK, 2 NOTE2026-04-22
ERROR10 OK, 2 NOTE, 1 ERROR2026-04-18
NOTE6 OK, 1 NOTE2026-04-12

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.3.9

READMEYes · 706 wordsVignettesYes · 1 · staticNEWSYes · 100% structured · mentions 0.3.9Citation fileYes · cites a publicationWebsiteYes

Help pages: 238 (111 internal)
Examples that run: 86%83 run in a plain check · 13 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 76%
Documented parameters: 99%
Return-value docs: 72%
Help pages citing references: 0%

Vignettes (1)

Documentation for metacoder HTML

How these are measured

Downloads

6.4K

CRAN downloads in the past year

Rank #3,831 · ~17/day · ~532/mo

Releases R versions

Daily download trend is not available in this view yet.

78330 days

2.4K90 days

6.4K1 year

Compare downloads with other packages →

Also on470 r2u2 autocran2.6K bioconda176 c2d4u

How downloads are counted

Repository

grunwaldlab/metacoder ↗Organization: grunwaldlab

149Stars

30Forks

43Open issues

0Open PRs

11Releases

1,115Commits

10Commit identities

taxonomymetabarcodingtreesrcommunity-diversitypcrhierarchicalcran

1,115 commits · Last activity 2026-07-17 · +0.7% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 3,109
Median days to close, 50 most recently updated closed PRs: 2

Stars over time

2025-09-04 · 1442026-09-24 · 149

How these are measured

PracticesBeta

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

Checks run against github.com/grunwaldlab/metacoder on 2026-10-11.

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 (2)

README.Rmd

GitHub Pages site last deployed 2016-10-31

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen 2026-07-09
Commits: at least 1 crediting it in the message

From outside contributors

Claude Code
Pull requests: 1 from outside contributors, first on 2026-07-09, 1 from forks

Models named in its commits

Claude Opus 4.81 commit · Jul 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

30 external dependencies (excludes base and recommended)

Installing metacoder adds 95 packages (53 with compiled code, 80 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

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

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

demulticoder

How these are counted

Code & Tests

Datasets

People & History

People (5)

Zachary Foster

Author, Maintainer since 0.1.2 (2016)

Scott Chamberlain

Contributor · added in 0.3.8

Rob Gilmore

Contributor · added in 0.2.1

Kamil Slowikowski

Contributor · added in 0.3.8

Niklaus Grunwald

Thesis advisor

Releases (15)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
unarchivedReturned to CRAN
2026-04-11
0.3.9Latest
record
2026-04-11 · current release · diff ↗ ·
added 1 export
primersearch_is_installed
archivedRemoved from CRAN
2025-10-18
issues were not corrected despite reminders
R
R 4.5.0 released · 2025-04-11
unarchivedReturned to CRAN
2025-02-11
0.3.8
record
2025-02-11 · diff ↗
archivedRemoved from CRAN
2024-10-01
issues were not corrected in time
R
R 4.4.0 released · 2024-04-24
0.3.7
record
2024-02-20 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.3.6
record
2023-04-04 · diff ↗ ·
added 1 export
calc_diff_abund_deseq2
R
R 4.2.0 released · 2022-04-22
0.3.5
record
2021-06-23 · diff ↗ ·
added 71 exports
all_names, arrange_obs, arrange_taxa, branches, classifications, database_list, extract_tax_data, filter_obs, filter_taxa, get_data, get_data_frame, get_dataset, hierarchies, hierarchy, id_classifications, ids, internodes, is_branch, is_internode, is_leaf, is_root, is_stem, leaves, leaves_apply, lookup_tax_data, map_data, map_data_, mutate_obs, n_leaves, n_leaves_1 and 41 more
R
R 4.1.0 released · 2021-05-18
0.3.4
record
2020-04-29 · diff ↗ ·
added 1 export
ambiguous_synonyms

Show 16 earlier eventsHide 16 earlier events

R
R 4.0.0 released · 2020-04-24
0.3.3
record
2019-07-18 · diff ↗
R
R 3.6.0 released · 2019-04-26
0.3.2
record
2019-04-08 · diff ↗
unarchivedReturned to CRAN
2019-01-05
0.3.1
record
2019-01-04 · diff ↗ ·
added 3 exports
make_dada2_asv_table, make_dada2_tax_table, parse_dada2
orphanedOrphaned by its maintainer
2018-11-19
maintainer did not respond to request for correction
0.3.0.1
record
2018-11-19 · diff ↗
0.3.0
record
2018-08-28 · diff ↗ ·
added 5 exports
as_phyloseq, calc_prop_samples, counts_to_presence, parse_ubiome, primersearch_raw
0.2.1
record
2018-05-02 · diff ↗ ·
added 4 exports
calc_group_mean, calc_group_median, calc_group_rsd, calc_group_stat
R
R 3.5.0 released · 2018-04-23
0.2.0
record
2018-01-05 · diff ↗ ·
removed 39 exports
arrange_obs, arrange_taxa, drawDetails.resizingTextGrob, extract_taxonomy, filter_obs, filter_taxa, hierarchies, mutate_obs, mutate_taxa, n_obs, n_obs_1, n_subtaxa, n_subtaxa_1, n_supertaxa, obs, obs_data, obs_data_colnames, parse_hmp_qiime, parse_mothur_summary, parse_taxonomy_table, postDrawDetails.resizingTextGrob, preDrawDetails.resizingTextGrob, remove_redundant_names, resizingTextGrob, roots, sample_frac_obs, sample_frac_taxa, sample_n_obs, sample_n_taxa, select_obs and 9 more

added 28 exports
calc_n_samples, calc_obs_props, calc_taxon_abund, compare_groups, complement, filter_ambiguous_taxa, heat_tree_matrix, is_ambiguous, ncbi_taxon_sample, parse_greengenes, parse_mothur_tax_summary, parse_mothur_taxonomy, parse_newick, parse_phylo, parse_phyloseq, parse_qiime_biom, parse_rdp, parse_silva_fasta, parse_unite_general, rarefy_obs, rev_comp, reverse, write_greengenes, write_mothur_taxonomy, write_rdp, write_silva_fasta, write_unite_general, zero_low_counts
0.1.3
record
2017-05-23 · diff ↗
R
R 3.4.0 released · 2017-04-21
0.1.2
record
2016-08-27
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2016-08-27
Total releases: 15 / 10 yrs
License: GPL-2 | GPL-3 OSI
Minimum R: ≥ 3.0.2
Bundled data: 209 KB / 4 files
Download size: 852 KB

Appears in task views

Phylogenetics

Cite

Cite this package

Run in R for the authors' entry:

citation("metacoder")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1371/journal.pcbi.1005404.

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 v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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