R Observatory: Metrics for demulticoder version 0.1.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

demulticoder

0.1.2Package record

Simultaneous Analysis of Multiplexed Metabarcodes

0packages depend

5.5Kdownloads / year

2.7%test coverage

13/13flavors OK

Overview

About

Maintained by Martha A. SudermannCRAN page ↗GitHub ↗Website ↗Issues ↗

A comprehensive set of wrapper functions for the analysis of multiplex metabarcode data. It includes robust wrappers for 'Cutadapt' and 'DADA2' to trim primers, filter reads, perform amplicon sequence variant (ASV) inference, and assign taxonomy. The package can handle single metabarcode datasets, datasets with two pooled metabarcodes, or multiple datasets simultaneously. The final output is a matrix per metabarcode, containing both ASV abundance data and associated taxonomic assignments. An optional function converts these matrices into 'phyloseq' and 'taxmap' objects. For more information on 'DADA2', including information on how DADA2 infers samples sequences, see Callahan et al. (2016) doi:10.1038/nmeth.3869. For more details on the demulticoder R package see Sudermann et al. (2025) doi:10.1094/PHYTO-02-25-0043-FI.

Install

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

install.packages("demulticoder", 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/demulticoder")

Development version from grunwaldlab/demulticoder. 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-demulticoder

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-demulticoder

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-demulticoder

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

Additional issues

donttest

CRAN check page ↗

Slowest check: 1.9 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.2

READMEYes · 519 wordsVignettesNoNEWSYes · 67% structured · does not mention 0.1.2Citation fileNoWebsiteYes · pkgdown

The repository also keeps web-only articles.

Help pages: 40 (35 internal)
Examples that run: 0%5 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

5.5K

CRAN downloads in the past year

Rank #8,220 · ~15/day · ~461/mo

Releases R versions

Daily download trend is not available in this view yet.

35030 days

1.1K90 days

5.5K1 year

Compare downloads with other packages →

Also on87 r2u7 autocran

How downloads are counted

Repository

grunwaldlab/demulticoder ↗Organization: grunwaldlab

1Stars

0Forks

2Open issues

0Open PRs

0Releases

615Commits

51Commit identities

615 commits · Last activity 2025-06-13

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-04-30 · 12026-07-07 · 1

How these are measured

PracticesBeta

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

Checks run against github.com/grunwaldlab/demulticoder on 2026-10-21.

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2025-06-13

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Installing demulticoder adds 45 packages (22 with compiled code, 32 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, isoband 1.5 MB.

Depends (1)

R >= 3.0.2

Imports (9)

furrr purrr readr stringr tidyr dplyr ggplot2 tibbleutils

LinkingTo (0)

none

Suggests (9)

BiocManager Biostrings dada2 metacoder ShortRead phyloseq rmarkdown RcppParallel testthat

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 (6)

Author

Author

Author, Copyright holder

Jeff H. Chang

Author

Hung Phan

Author

Releases (1)

R
R 4.6.0 released · 2026-04-24
0.1.2Latest
record
2025-05-05 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-05-05
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.0.2
Download size: 1.5 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("demulticoder")

Format

Sudermann, M. A., Dawson, S., Foster, Z. S. L., Grünwald, N., H. Chang, J., & Phan, H. (2025). demulticoder: Simultaneous Analysis of Multiplexed Metabarcodes (Version 0.1.2) [Computer software]. https://doi.org/10.32614/CRAN.package.demulticoder

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 demulticoder version 0.1.2 [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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