R Observatory: Metrics for metamorphr version 0.4.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

metamorphr

0.4.1Package record

Tidy and Streamlined Metabolomics Data Workflows

0packages depend

2.8Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Yannik SchermerCRAN page ↗GitHub ↗Website ↗Issues ↗

Facilitate tasks typically encountered during metabolomics data analysis including data import, filtering, missing value imputation (Stacklies et al. (2007) doi:10.1093/bioinformatics/btm069, Stekhoven et al. (2012) doi:10.1093/bioinformatics/btr597, Tibshirani et al. (2017) doi:10.18129/B9.BIOC.IMPUTE, Troyanskaya et al. (2001) doi:10.1093/bioinformatics/17.6.520), normalization (Bolstad et al. (2003) doi:10.1093/bioinformatics/19.2.185, Dieterle et al. (2006) doi:10.1021/ac051632c, Zhao et al. (2020) doi:10.1038/s41598-020-72664-6) transformation, centering and scaling (Van Den Berg et al. (2006) doi:10.1186/1471-2164-7-142) as well as statistical tests and plotting. 'metamorphr' introduces a tidy (Wickham et al. (2019) doi:10.21105/joss.01686) format for metabolomics data and is designed to make it easier to build elaborate analysis workflows and to integrate them with 'tidyverse' packages including 'dplyr' and 'ggplot2'.

Changes in 0.4.1

Fixes

Fixed critical bug in read_featuretable where empty metadata columns caused issues if metadata_cols were supplied as numerics.

From NEWS.md in the release

Install

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

install.packages("metamorphr", 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("yasche/metamorphr")

Development version from yasche/metamorphr. 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-metamorphr

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

13OK

CRAN check page ↗

Slowest check: 5.6 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 ERROR2026-06-08
OK12 OK2026-04-25

Show 1 earlier changeHide 1 earlier change

NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.4.1

READMEYes · 178 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 0.4.1Citation fileNoWebsiteYes · pkgdown

Description cites a JOSS paper

Help pages: 67 (2 internal)includes a package overview page
Examples that run: 100%61 run in a plain check
Exported functions with examples: 98%
Documented parameters: 99%
Return-value docs: 100%
Help pages citing references: 46%

Vignettes (2)

How these are measured

Downloads

2.8K

CRAN downloads in the past year

Rank #17,629 · ~8/day · ~230/mo

Releases R versions

Daily download trend is not available in this view yet.

30430 days

72890 days

2.8K1 year

Compare downloads with other packages →

Also on80 r2u

How downloads are counted

Repository

yasche/metamorphr ↗Account: yasche

1Stars

0Forks

0Open issues

0Open PRs

5Releases

360Commits

1Commit identities

360 commits · Last activity 2026-09-27 · Default branch at 0.4.1.9000, ahead of CRAN 0.4.1 (checked 2026-10-18)

Responsiveness

How these are sampled

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

Stars over time

2025-09-04 · 12026-07-07 · 1

How these are measured

PracticesBeta

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

Checks run against github.com/yasche/metamorphr 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

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-09-27 · The repository has a site deploy workflow

pkgdown site last built 2026-09-27

Coverage (1)

Coverage reporting

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 2 practices

CRAN release process (2)

cran-comments.mdrevdep/

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

22 external dependencies (excludes base and recommended)

Installing metamorphr adds 54 packages (27 with compiled code, 37 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, Rcpp 1.8 MB. 2 more not on CRAN are not measured.

Depends (1)

R >= 3.5

Imports (19)

broom crayon dplyr ggplot2 impute lifecycle magrittr missForest pcaMethods purrr readr rlangstatsstringi tibble tidyrutilsvctrs withr

LinkingTo (0)

none

Suggests (5)

knitr qsmooth rmarkdown stringr 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 (1)

Yannik Schermer

Releases (5)

Pick two releases to compare their code metrics.

0.4.1Latest
record
2026-06-10 · current release · diff ↗
0.4.0
record
2026-06-09 · diff ↗ ·
added 4 exports
convert_from_matrix, convert_from_wide, read_featuretable_mzmine, remove_empty_cols
R
R 4.6.0 released · 2026-04-24
0.3.0
record
2026-03-04 · diff ↗ ·
added 2 exports
msn_calc_nl, msn_scale
0.2.0
record
2025-10-09 · diff ↗ ·
added 4 exports
calc_km, calc_kmd, calc_nominal_km, formula_to_mass
0.1.1
record
2025-09-01
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-09-01
Total releases: 5 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5
Bundled data: 12 KB / 4 files
Download size: 509 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("metamorphr")

Format

Schermer, Y. (2026). metamorphr: Tidy and Streamlined Metabolomics Data Workflows (Version 0.4.1) [Computer software]. https://doi.org/10.32614/CRAN.package.metamorphr

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 metamorphr version 0.4.1 [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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