R Observatory: Metrics for MiscMetabar version 0.16.8

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

MiscMetabar

0.16.8Package record

Miscellaneous Functions for Metabarcoding Analysis

0packages depend

6.2Kdownloads / year

–test coverage

7/13flavors OK

Overview

About

Maintained by Adrien TaudièreCRAN page ↗GitHub ↗Website ↗Issues ↗

Facilitate the description, transformation, exploration, and reproducibility of metabarcoding analyses. 'MiscMetabar' is mainly built on top of the 'phyloseq', 'dada2' and 'targets' 'R' packages. It helps to build reproducible and robust bioinformatics pipelines in 'R'. 'MiscMetabar' makes ecological analysis of alpha and beta-diversity easier, more reproducible and more powerful by integrating a large number of tools. Important features are described in Taudière A. (2023) doi:10.21105/joss.06038.

Changes in 0.16.8

accu_plot(), dist_pos_control(), hill_curves_pq() and tsne_pq() no longer error under recent R-devel: the otu_table is now coerced to a base matrix before being passed to vegan functions (renyi(), renyiaccum(), specaccum(), vegdist()), which previously triggered an assignment of an object of class "numeric" is not valid for @'.Data' error because plain as.matrix() does not strip the S4 otu_table class.
Rarefaction across the package is now performed by an internal R-version-robust reimplementation rather than phyloseq::rarefy_even_depth(), whose replace = FALSE code path errors with invalid 'length.out' value under recent R-devel (phyloseq issue #1753). The reimplementation is bit-identical to phyloseq::rarefy_even_depth() for the same seed, depth and replace value (and is more correct in the degenerate case where a retained sample has a single read). This affects rarefy_pq(), adonis_pq(), adonis_rarperm_pq(), hill_test_rarperm_pq(), hill_pq(), biplot_pq(), ggvenn_pq(), upset_pq(), ggaluv_pq() and ggscatt_pq().
rarefy_pq() gains a replace argument (default FALSE, sampling without replacement) and accepts seed = FALSE to leave the random number generator untouched, mirroring phyloseq::rarefy_even_depth().
Further check-time reductions for CRAN compliance: extra examples \dontrun{} (kept for documentation, not run during checks).
Added file-level skip_on_cran() to some heavy test files.
Example speed-ups for some functions.
Fix several bugs when using Windows paths by quoting system call arguments with shQuote()

From NEWS.md in the release

Install

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

install.packages("MiscMetabar", 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("adrientaudiere/MiscMetabar")

Development version from adrientaudiere/MiscMetabar. 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-miscmetabar

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

Health

CRAN checks

1ERROR5NOTE7OK

Check messages

ERRORpackage dependenciesr-oldrel-macos-arm64

Package required but not available: ‘dada2’

Packages suggested but not available for checking:
  'ALDEx2', 'ANCOMBC', 'DECIPHER', 'lefser', 'mia', 'metagenomeSeq'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

NOTEdependencies in R coder-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

r-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

Base package in Suggests/Enhances imported in NAMESPACE:
  ‘grDevices’

r-devel-windows-x86_64

Base package in Suggests/Enhances imported in NAMESPACE:
  'grDevices'

Additional issues

donttest

CRAN check page ↗

Slowest check: 16.1 min · r-oldrel-windows-x86_64

Status changes

ERROR7 OK, 5 NOTE, 1 ERRORNow
ERROR9 OK, 3 WARNING, 1 ERROR2026-05-03
WARNING11 OK, 1 NOTE, 2 WARNING2026-04-24
ERROR10 OK, 1 NOTE, 2 WARNING, 1 ERROR2026-04-23
NOTE13 OK, 1 NOTE2026-03-30
ERROR12 OK, 1 NOTE, 1 ERROR2026-03-28

Show 6 earlier changesHide 6 earlier changes

NOTE13 OK, 1 NOTE2026-03-27
ERROR12 OK, 1 NOTE, 1 ERROR2026-03-26
NOTE13 OK, 1 NOTE2026-03-16
ERROR12 OK, 1 NOTE, 1 ERROR2026-03-13
NOTE13 OK, 1 NOTE2026-03-12
ERROR12 OK, 1 NOTE, 1 ERROR2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.16.8

READMEYes · 838 wordsVignettesYes · 1 · dynamicNEWSYes · 67% structured · mentions 0.16.8Citation fileNoWebsiteYes · pkgdown

The repository also keeps web-only articles.

Description cites a JOSS paper

Help pages: 180includes a package overview page
Examples that run: 59%101 run in a plain check (27 of them under a condition) · 39 only when donttest examples are enabled (R CMD check --as-cran) · 30 never run
Exported functions with examples: 98%
Documented parameters: 98%
Return-value docs: 99%
Help pages citing references: 9%

Vignettes (1)

Introduction HTML

How these are measured

Downloads

6.2K

CRAN downloads in the past year

Rank #5,346 · ~17/day · ~514/mo

Releases R versions

Daily download trend is not available in this view yet.

61230 days

1.5K90 days

6.2K1 year

Compare downloads with other packages →

Also on117 r2u

How downloads are counted

Repository

adrientaudiere/miscmetabar ↗Account: adrientaudiere

21Stars

2Forks

0Open issues

1Open PRs

31Releases

920Commits

6Commit identities

ecologymetabarcodingngs-analysispackagerampliconamplicon-sequencingbiodiversity-informatics

License file reads as AGPL-3.0 · 920 commits · Last activity 2026-07-07 · 0% stars, 30d · Default branch at 0.17.0.9000, ahead of CRAN 0.16.8 (checked 2026-10-18)

Responsiveness

How these are sampled

PRs merged (all time): 93%
Median days to close, 50 most recently updated closed issues: 4
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-07-09 · 172026-07-07 · 21

How these are measured

PracticesBeta

15 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/adrientaudiere/miscmetabar on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Governance and community (3)

Code of conductContributing guideIssue templates

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-07-07 · The repository has a site deploy workflow

pkgdown site last built 2024-04-28, before release 0.16.8 (2026-06-08)

Coverage (1)

Coverage reporting

Show all practicesHide 2 practices

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (3)

lintrVS CodeRStudio project

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

GitHub Copilotfirst seen 2025-09-12
Pull request: opened by its own account
Commits: 19 by its own account
Claude Codefirst seen 2026-02-05
Seen in the repository: .claude, CLAUDE.md
Named in .Rbuildignore: .claude, CLAUDE.md
Commits: at least 18 crediting it in the message

Models named in its commits

Claude Sonnet 4.612 commits · Feb to Jun 2026
Claude Opus 4.65 commits · Feb 2026
Claude Opus 4.81 commit · Jun 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

79 external dependencies (excludes base and recommended)

Installing MiscMetabar adds 74 packages (43 with compiled code, 61 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, igraph 4.8 MB. 4 more not on CRAN are not measured.

Depends (4)

R >= 4.1.0phyloseq ggplot2 dplyr

Imports (10)

ape Biostrings cli dada2 divent lifecycle purrr rlangstatsXVector

LinkingTo (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Adrien Taudière

Releases (11)

Pick two releases to compare their code metrics.

unarchivedReturned to CRAN
2026-06-08
0.16.8Latest
record
2026-06-08 · current release · diff ↗ ·
added 27 exports
aldex_pq, assign_mmseqs2, css_pq, divent_hill_matrix_pq, find_mmseqs2, find_vsearch, gmpr_pq, hill_acc_pq, hill_bar_pq, install_mmseqs2, install_vsearch, is_mmseqs2_installed, lefser_pq, mcknight_residuals_pq, mmseqs2_clustering, plot_ordination_pq, profile_hill_pq, rarefy_even_depth_pq, rarefy_pq, reorder_distinct_colors, ridges_sam_pq, srs_pq, tmm_pq, transform_pq, unwanted_tax_patterns, verify_tax_table, vst_pq
archivedRemoved from CRAN
2026-05-19
issues were not corrected in time
R
R 4.6.0 released · 2026-04-24
0.14.4
record
2025-09-30 · diff ↗ ·
added 1 export
plot_seq_ratio_pq
unarchivedReturned to CRAN
2025-06-21
0.14.3
record
2025-06-21 · diff ↗ ·
added 1 export
filt_taxa_wo_NA
archivedRemoved from CRAN
2025-06-20
issues were not corrected in time
R
R 4.5.0 released · 2025-04-11
unarchivedReturned to CRAN
2025-03-20
0.14.2
record
2025-03-20 · diff ↗
archivedRemoved from CRAN
2025-02-20
policy violation On Internet access Even after update
0.14.1
record
2025-02-19 · diff ↗ ·
added 6 exports
assign_blastn, assign_dada2, format2dada2, format2dada2_species, format2sintax, resolve_vector_ranks
0.12.1
record
2025-01-29 · diff ↗ ·
added 13 exports
assign_idtaxa, assign_sintax, assign_vsearch_lca, filt_taxa_pq, hill_curves_pq, learn_idtaxa, no_legend, plot_complexity_pq, plot_refseq_extremity_pq, plot_refseq_pq, sam_data_matching_names, tbl_sum_taxtable, umap_pq
0.10.1
record
2024-10-07 · diff ↗ ·
removed 2 exports
heat_tree_pq, physeq_heat_tree
0.9.3
record
2024-09-09 · diff ↗ ·
added 2 exports
filter_taxa_blast, postcluster_pq

Show 5 earlier eventsHide 5 earlier events

0.9.1
record
2024-04-28 · diff ↗ ·
added 21 exports
accu_plot_balanced_modality, adonis_rarperm_pq, distri_1_taxa, fac2col, formattable_pq, ggaluv_pq, ggscatt_pq, glmutli_pq, hill_test_rarperm_pq, normalize_prop_pq, plot_ancombc_pq, plot_var_part_pq, psmelt_samples_pq, rarefy_sample_count_by_modality, signif_ancombc, taxa_as_columns, taxa_as_rows, taxa_only_in_one_level, transp, var_par_pq, var_par_rarperm_pq
R
R 4.4.0 released · 2024-04-24
0.7.10
record
2024-03-08 · diff ↗ ·
added 2 exports
is_krona_installed, is_mumu_installed
0.7.9
record
2024-02-17
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2024-02-17
Total releases: 11 / 2 yrs
License: AGPL-3 OSI
Minimum R: ≥ 4.1.0
Bundled data: 399 KB / 4 files
Download size: 4.1 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("MiscMetabar")

Format

Taudière, A. (2026). MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis (Version 0.16.8) [Computer software]. https://doi.org/10.32614/CRAN.package.MiscMetabar

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 MiscMetabar version 0.16.8 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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