Changelog

Source: NEWS.md

ukbflow 0.3.3

CRAN release: 2026-04-07

Released: April 2026

Bug Fixes

• grs_validate() — added skip_if_not_installed("pROC") guard to all logistic-path tests so the suite passes cleanly when pROC is absent

Improvements

• Removed hardcoded default paths across all modules; examples refactored to use ops_toy() data where possible — runnable examples unwrapped, long-running examples (>5s) wrapped in \donttest{}, network-dependent examples remain in \dontrun{}
• VignetteBuilder field corrected in DESCRIPTION

CI

• R CMD check split into four targeted workflows: dev (3 jobs), main (6 jobs), release (8 jobs, --as-cran), and weekly (scheduled every Saturday 21:00 CST, full CRAN-like matrix)
• Added _R_CHECK_DEPENDS_ONLY_ matrix to verify Suggests packages are correctly declared

Documentation

• Rd files regenerated across all modules after example and parameter updates

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ukbflow 0.3.2

Released: March 26, 2026

Bug Fixes

• ops_snapshot() — removed Unicode character Δ from documentation to fix LaTeX PDF manual build on CRAN
• test-plot.R — added skip_on_cran() to plot_tableone() rendering tests that caused a 20-minute hang on Windows CRAN

Improvements

• plot_forest() and plot_tableone() examples are now fully runnable (removed \dontrun{} wrapper; save = FALSE throughout)

Documentation

• README.md — updated Codecov badge URL; fixed CONTRIBUTING.md and README_zh.md links to full GitHub URLs
• Added inst/WORDLIST with Biobank to suppress false-positive spelling NOTE on CRAN

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ukbflow 0.3.1

Released: March 25, 2026

Bug Fixes

• derive_followup() — coerce date columns to IDate before pmin() to avoid type mismatch
• install.Rmd — corrected vignette cross-references

Improvements

• All modules hardened with consistent .assert_*() input validation helpers
• All cli::cli_abort() calls now use call = NULL for cleaner error messages
• plot_tableone() — auto-coerce data.table input to data.frame

Documentation

• Man pages updated across all modules (auth, fetch, extract, job, decode, derive, ops, grs, assoc, plot)
• All vignettes reviewed and corrected (output format, param contracts, example accuracy)
• get-started.Rmd and README updated for accuracy
• pkgdown reference index and vignette menu completed

Tests

• Test suites overhauled for all modules: added input validation coverage, integration-style stubs, and edge cases

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ukbflow 0.3.0

Released: March 13, 2026

New Features

Operations (ops_*)

• ops_withdraw() — exclude UKB withdrawn participants from a cohort data.table by EID

Snapshot — Column Tracking

• ops_snapshot() gains column-tracking helpers: cols(), diff(), remove(), and set_safe_cols()

Visualisation Enhancements

• plot_tableone() — new png_scale, pdf_width, and pdf_height parameters for fine-grained output control

Bug Fixes

• fetch_file() — enforce RAP-only guard; updated tests
• grs_score() — fix -icmd argument format; skip script upload if file already exists on RAP
• GRS pipeline — updated chr split threshold: chromosomes 1–16 use large instances, 17–22 use standard

Documentation

• Added roxygen2 documentation for ops_withdraw()
• Unit tests added for ops_withdraw()

Internal

• Added broom to DESCRIPTION Imports and ops_setup() dependency check
• Updated package logo (new hex sticker design)
• Integration tests requiring RAP environment are now skipped in local CI

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ukbflow 0.2.0

Released: March 10, 2026

New Features

Operations (ops_*)

• ops_setup() — check and report the local environment (R, dx-toolkit, dxpy) health
• ops_toy() — generate synthetic UKB-style cohort or forest-plot data for testing and demos; includes GRS columns and cancer self-report fields
• ops_na() — summarise missing-value rates per column with threshold-based filtering and cli progress feedback
• ops_snapshot() — record and display a history of dataset row/column counts across pipeline steps

Bug Fixes

• All cli::cli_abort() calls now pass call = NULL to suppress internal call-stack noise in error messages
• ops_toy(): added cancer self-report fields (p20001, p20006) and corrected sr_codes → text label mapping

Documentation

• New vignette: Smoking and Lung Cancer — End-to-End Analysis (vignette("smoking_lung_cancer"))
• New vignette: ops_ Series* covering setup, toy data, NA summary, and snapshots
• pkgdown site now auto-deploys via GitHub Actions (CI-managed docs/)

Internal

• Resolved R CMD check NOTEs: added importFrom(stats, rnorm, runif), importFrom(utils, object.size), and pct_na to globalVariables()
• Added builds/ to .Rbuildignore

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ukbflow 0.1.0

Released: March 6, 2026

Initial release of ukbflow — a RAP-native R workflow for UK Biobank analysis.

New Features

Connection

• auth_login() — authenticate to RAP via dx-toolkit token
• auth_logout() — revoke current session
• auth_status() — check current login state
• auth_list_projects() — list accessible RAP projects
• auth_select_project() — set active RAP project

Data Access

• fetch_ls() / fetch_tree() — browse RAP project file structure
• fetch_file() — download files from RAP to local
• fetch_url() — generate pre-signed download URLs
• fetch_metadata() — retrieve UKB field metadata (field.tsv, encoding.tsv)
• fetch_field() — retrieve UKB field-level metadata for specific field IDs
• extract_ls() — list available UKB datasets on RAP
• extract_pheno() — synchronously extract phenotype fields from a RAP dataset
• extract_batch() — submit a DNAnexus table-exporter job to extract phenotype fields
• job_wait() — poll job status until completion
• job_status() / job_ls() / job_path() / job_result() — monitor and locate RAP jobs

Data Processing

• decode_values() — convert integer codes to human-readable labels
• decode_names() — rename p{field}_i{instance}_a{array} columns to descriptive names
• derive_missing() — recode UKB informative-missing labels to NA
• derive_covariate() — standardise common covariates (age, BMI, TDI, etc.)
• derive_cut() — create ordered factor variables from numeric cutpoints
• derive_hes() — derive disease phenotypes from Hospital Episode Statistics (ICD-10)
• derive_cancer_registry() — derive cancer phenotypes from UK cancer registry (ICD-10)
• derive_death_registry() — derive phenotypes from death registry (primary + secondary causes)
• derive_first_occurrence() — derive phenotypes from UKB First Occurrence fields
• derive_selfreport() — derive disease phenotypes from self-reported illness codes
• derive_icd10() — merge multi-source ICD-10 case definitions across all registers
• derive_case() — merge arbitrary multi-source case definitions
• derive_followup() — compute follow-up time with competing event support
• derive_timing() — classify prevalent vs. incident cases
• derive_age() — compute age at event

Association Analysis

• assoc_linear() — linear regression with automatic three-model framework
• assoc_logistic() — logistic regression with automatic three-model framework
• assoc_coxph() — Cox proportional hazards with automatic three-model framework
• assoc_coxph_zph() — test proportional hazards assumption
• assoc_competing() — Fine-Gray competing risks regression
• assoc_subgroup() — subgroup analysis with interaction likelihood-ratio test
• assoc_trend() — dose-response trend analysis across ordered categories
• assoc_lag() — landmark / lag-time sensitivity analysis

Genomic Risk Score (GRS)

• grs_check() — validate and reformat a GWAS summary statistics weight file
• grs_bgen2pgen() — submit parallel BGEN → PGEN conversion jobs on RAP
• grs_score() — submit distributed plink2 GRS scoring jobs on RAP
• grs_standardize() — standardise GRS columns to mean = 0, SD = 1
• grs_validate() — validate GRS distribution and association with known risk factors

Visualization

• plot_forest() — publication-ready forest plots with customisable CI columns and p-value formatting
• plot_tableone() — Table 1 baseline characteristics figure