https://github.com/rmgpanw/ukbwranglr

An R package for UK Biobank data wrangling.
https://github.com/rmgpanw/ukbwranglr

package r uk-biobank

Last synced: 4 months ago
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An R package for UK Biobank data wrangling.

• Host: GitHub
• URL: https://github.com/rmgpanw/ukbwranglr
• Owner: rmgpanw
• License: other
• Created: 2020-10-30T14:13:05.000Z (over 3 years ago)
• Default Branch: main
• Last Pushed: 2023-03-29T11:30:33.000Z (over 1 year ago)
• Last Synced: 2024-01-17T01:07:47.720Z (6 months ago)
• Topics: package, r, uk-biobank
• Language: R
• Homepage: https://rmgpanw.github.io/ukbwranglr/
• Size: 4.19 MB
• Stars: 12
• Watchers: 2
• Forks: 0
• Open Issues: 2
• Metadata Files:
  • Readme: README.Rmd
  • Contributing: .github/CONTRIBUTING.md
  • License: LICENSE

Lists

• awesome-uk-biobank - ukbwranglr

README

        
---

output: 

  github_document

---

```{r, include = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  comment = "#>",

  fig.path = "man/figures/README-",

  out.width = "100%"

)

# copy and paste this next to '# ukbwranglr' below to include hex badge

# 

```

# ukbwranglr

[![R build status](https://github.com/rmgpanw/ukbwranglr/workflows/R-CMD-check/badge.svg)](https://github.com/rmgpanw/ukbwranglr/actions) [![Codecov test coverage](https://codecov.io/gh/rmgpanw/ukbwranglr/branch/main/graph/badge.svg)](https://codecov.io/gh/rmgpanw/ukbwranglr?branch=main) [![pkgdown](https://github.com/rmgpanw/ukbwranglr/workflows/pkgdown/badge.svg)](https://github.com/rmgpanw/ukbwranglr/actions) [![Launch RStudio Cloud](https://img.shields.io/badge/RStudio-Cloud-blue)](https://rstudio.cloud/project/2528744) [![DOI](https://zenodo.org/badge/308650225.svg)](https://zenodo.org/badge/latestdoi/308650225) [![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)

# Overview

The goal of ukbwranglr is to facilitate analysing UK Biobank data, including:

1.  Reading a selection of UK Biobank variables into R.

2.  Summarising repeated continuous variable measurements.[^1]

3.  Extracting phenotypic outcomes of interest from clinical events data.[^2]

[^1]: For example, calculating a mean/minimum/maximum body mass index (BMI) from repeated BMI measurements.

[^2]: For example, identifying participants with a diagnosis of hypertension from linked primary and secondary health care records.

# Installation

You can install the development version of ukbwranglr with:

```{r eval=FALSE}

# install.packages("devtools")

devtools::install_github("rmgpanw/ukbwranglr")

```

# Basic workflow

The basic workflow is as follows:

1.  Create a data dictionary for your main UK Biobank dataset with `make_data_dict()`.

2.  Read selected variables into R with `read_ukb()`.

3.  Summarise continuous variables with `summarise_numerical_variables()`.

4.  Tidy clinical events data with `tidy_clinical_events()` or `make_clinical_events_db()`, and extract outcomes of interest with `extract_phenotypes()`.

5.  Analyse.

Please see `vignette('ukbwranglr')` for further details.