R Observatory: Metrics for UKBAnalytica version 1.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

UKBAnalytica

1.0.0Package record

UK Biobank Data Processing and Survival Analysis Toolkit

0packages depend

1.1Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Nan HeCRAN page ↗GitHub ↗Website ↗Issues ↗

Provides an integrated workflow for UK Biobank Research Analysis Platform (RAP) hosted and RAP-generated analysis tables. The package supports RAP phenotype extraction planning, predefined variable sets and disease definitions, standardized baseline preprocessing, multi-source endpoint ascertainment, prevalent and incident case classification, survival-ready cohort construction, regression, multiple imputation, propensity score analysis, mediation analysis, subgroup and sensitivity analyses, machine learning, proteomics enrichment and protein-protein interaction analysis, and publication-oriented visualization. The package workflow is described in He et al. (2026) doi:10.64898/2026.06.19.26356057.

Changes in 1.0.0

Official release

Released UKBAnalytica 1.0.0 as an integrated RAP-oriented workflow package for UK Biobank epidemiological analyses.
Expanded the package description to reflect the current end-to-end scope, including RAP extraction planning, predefined variables and diseases, cohort construction, statistical modeling, machine learning, proteomics analysis, and publication-oriented visualization.

Workflow coverage

Consolidated predefined disease definitions and baseline variable mappings for rapid phenotype and covariate setup.
Standardized the analysis flow from RAP data extraction and preprocessing to multi-source endpoint definition, prevalent/incident classification, survival-ready cohort generation, and downstream analyses.
Added high-level machine-learning interfaces for single-model workflows and comparison across feature sets or algorithms, with ROC, threshold selection, calibration, SHAP interpretation, and validation-set evaluation helpers.
Extended proteomics utilities for volcano plots, Gene Ontology enrichment, STRING-based PPI retrieval, topology metrics, fast-greedy community detection, and cluster-level enrichment analysis.
Refined visualization helpers for forest plots, volcano plots, calibration and decision-curve analysis, ROC comparison, SHAP summaries, enrichment plots, and manuscript-ready figure export.

Recent updates

Added ukb_time_skeleton() to create a reusable follow-up time skeleton with baseline date, death date, loss-to-follow-up date, administrative censoring, follow-up end reason, and valid follow-up indicators.
Added optional time_skeleton support to build_survival_dataset() while preserving the default survival workflow.

Show all changes in 1.0.0Hide the rest of the changes in 1.0.0

Added RAP-protected dictionary utilities, including ukb_download_rap_dictionary(), ukb_query_dictionary(), and ukb_validate_columns(), for official RAP dictionary lookup, Chinese/English field search, and column validation.
Added the built-in ukb_dictionary_zh metadata dataset for Chinese UKB field-path lookup.
Extended run_regression() with covariate_sets for nested epidemiological models such as crude, partially adjusted, and fully adjusted analyses.
Added lightweight publication-style plotting helpers for heatmaps, stacked bars, violin plots, and scatter plots.
Excluded local tests/ from package builds and remote tracking.

From NEWS.md in the release

Install

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

install.packages("UKBAnalytica", 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("Hinna0818/UKBAnalytica")

Development version from Hinna0818/UKBAnalytica. 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-ukbanalytica

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-UKBAnalytica

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-UKBAnalytica

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: 7.6 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK7 OK2026-07-01

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.0

README· In the repository, left out of the releaseVignettesNoNEWSYes · 100% structured · mentions 1.0.0Citation fileNoWebsiteYes

Help pages: 244 (40 internal)includes a package overview page
Examples that run: 100%29 run in a plain check
Exported functions with examples: 15%
Documented parameters: 99%
Return-value docs: 100%
Help pages citing references: 2%

How these are measured

Downloads

1.1K

CRAN downloads in the past year

Rank #15,022 · ~3/day · ~96/mo

Releases R versions

Daily download trend is not available in this view yet.

24630 days

81190 days

1.1K1 year

Compare downloads with other packages →

Also on28 r2u5 autocran

How downloads are counted

Repository

hinna0818/ukbanalytica ↗Account: Hinna0818

35Stars

0Forks

1Open issues

0Open PRs

0Releases

122Commits

1Commit identities

122 commits · Last activity 2026-08-07 · 0% stars, 30d · Default branch at 1.1.0, ahead of CRAN 1.0.0 (checked 2026-10-21)

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 1
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2026-04-19 · 132026-07-26 · 35

How these are measured

PracticesBeta

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

Checks run against github.com/hinna0818/ukbanalytica on 2026-10-21.

Continuous integration (1)

GitHub Actions

Docs source (2)

GitHub Pages site last deployed 2026-08-01 · The repository has a site deploy workflow

Reproducibility and dev environment (1)

Makefile

For agents and models (1)

Agent skills

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

Dependencies

Declared dependencies

31 external dependencies (excludes base and recommended)

Installing UKBAnalytica adds 80 packages (45 with compiled code, 70 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 4.0

Imports (16)

data.table stringi ggplot2 rlang scalessurvivalpROC tableone mice mitools sandwich lmtestMASSmgcvxml2 igraph

LinkingTo (0)

none

Suggests (20)

testthat rms gbm cobalt survminer MatchIt regmedint ranger xgboost glmnet e1071nnetrpartBoruta rBayesianOptimization randomForestSRC clusterProfiler AnnotationDbi org.Hs.eg.db qs2

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)

Nan He

Author, Maintainer since 1.0.0 (2026)

Releases (1)

1.0.0Latest
record
2026-06-30 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-06-30
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.0
Bundled data: 136 KB / 1 file
Download size: 1.0 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("UKBAnalytica")

Format

He, N. (2026). UKBAnalytica: UK Biobank Data Processing and Survival Analysis Toolkit (Version 1.0.0) [Computer software]. https://doi.org/10.32614/CRAN.package.UKBAnalytica

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 UKBAnalytica version 1.0.0 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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