R Observatory: Metrics for ukbnmr version 3.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ukbnmr

3.4Package record

Removal of Unwanted Technical Variation from UK Biobank NMR Metabolomics Biomarker Data

0packages depend

5Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Scott C RitchieCRAN page ↗GitHub ↗Issues ↗

A suite of utilities for working with the UK Biobank https://www.ukbiobank.ac.uk/ Nuclear Magnetic Resonance spectroscopy (NMR) metabolomics data https://biobank.ndph.ox.ac.uk/showcase/label.cgi?id=220. Includes functions for extracting biomarkers from decoded UK Biobank field data, removing unwanted technical variation from biomarker concentrations, computing an extended set of lipid, fatty acid, and cholesterol fractions, and for re-deriving composite biomarkers and ratios after adjusting data for unwanted biological variation. For further details on methods see Ritchie SC et al. Sci Data (2023) doi:10.1038/s41597-023-01949-y.

Changes in 3.4

Added lipoprotein fatty acid contents to the extended set of biomarkers computed by the ukbnmr package based on the formula published by Belkadi *et al.* 2026 (doi: 10.1021/acs.jproteome.6c00107). These can be computed directly by the new compute_lipoprotein_fatty_acids() function, and are returned with the extended set of biomarkers computed by the recompute_derived_biomarkers() and remove_technical_variation() functions.
Updated outdated documentation that referred to the tools used for legacy UK Biobank datasets for data extraction that are no longer relevant now that analyses must take place on the UK Biobank Research Analysis Platform.

From NEWS.md in the release

Install

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

install.packages("ukbnmr", 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("sritchie73/ukbnmr")

Development version from sritchie73/ukbnmr. 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-ukbnmr

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-ukbnmr

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-ukbnmr

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

CRAN check page ↗

Slowest check: 1.7 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
NOTE12 OK, 1 NOTE2026-06-08
OK14 OK2026-04-14

Show 2 earlier changesHide 2 earlier changes

NOTE13 OK, 1 NOTE2026-04-12
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 3.4

README· In the repository, left out of the releaseVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 3.4Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 14includes a package overview page
Examples that run: 100%10 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 14%

Vignettes (1)

Guide to using the ukbnmr package HTML

How these are measured

Downloads

5K

CRAN downloads in the past year

Rank #10,781 · ~14/day · ~418/mo

Releases R versions

Daily download trend is not available in this view yet.

34830 days

95990 days

5K1 year

Compare downloads with other packages →

Also on113 r2u3 autocran1.3K conda_forge

How downloads are counted

Repository

sritchie73/ukbnmr ↗Account: sritchie73

66Stars

6Forks

0Open issues

0Open PRs

14Releases

190Commits

3Commit identities

190 commits · Last activity 2026-07-07 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 17
Median days to close, 50 most recently updated closed PRs: 12

Stars over time

2025-10-10 · 422026-07-20 · 66

How these are measured

PracticesBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/sritchie73/ukbnmr on 2026-10-11.

Reproducibility and dev environment (1)

data-raw/

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

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Installing ukbnmr adds 7 packages (5 with compiled code, 7.0 MB of source tarballs). Heaviest: data.table 5.7 MB, lubridate 420 KB, cpp11 298 KB.

Depends (1)

R >= 2.10

Imports (4)

data.table bit64 lubridateMASS

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

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)

Scott C Ritchie

Author, Maintainer since 1.4 (2023)

Listed in earlier versions (1)

Ritchie

no longer listed · 1.4 to 3.4

Releases (9)

Pick two releases to compare their code metrics.

3.4Latest
record
2026-07-07 · current release · diff ↗ ·
added 2 exports
compute_lipoprotein_fatty_acids, compute_lipoprotein_fatty_acids_flags
R
R 4.6.0 released · 2026-04-24
3.3.2
record
2026-04-12 · diff ↗
3.3.1
record
2025-11-30 · diff ↗
3.3.0
record
2025-11-28 · diff ↗
R
R 4.5.0 released · 2025-04-11
3.2.0
record
2024-11-14 · diff ↗ ·
removed 2 exports
compute_nightingale_ratio_qc_flags, compute_nightingale_ratios
R
R 4.4.0 released · 2024-04-24
2.2
record
2023-08-23 · diff ↗
2.1.3
record
2023-08-21 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.5
record
2023-01-31 · diff ↗
1.4
record
2023-01-09
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2023-01-09
Total releases: 9 / 3 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 2.10
Bundled data: 12 KB / 3 files
Download size: 3.6 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("ukbnmr")

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

It points to 10.1038/s41597-023-01949-y, 10.1021/acs.jproteome.6c00107.

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 ukbnmr version 3.4 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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