README.md

In philipdarke/ukbbhelpr: Helper functions for UK Biobank data

ukbbhelpr

A collection of helper functions for working with UK Biobank data, focussing on the linked primary care EHR data.

Installation

Install from GitHub using:

devtools::install_github("philipdarke/ukbbhelpr", dependencies = TRUE)

Reference

The main functionality is summarised below. See the manual for more details.

Functions for use with data collected at UK Biobank assessment centre visits start visit_. Functions for use with primary care EHR data start ehr_.

ehr_extract(ehr_data, read_codes)

Extracts observations/test results from linked EHR data (ehr_data) from records matching the provided read_codes. Data is extracted from the value1 field with the exception of data provider 2 where values are extracted from value2 if value1 is empty. Units are taken from value3 for data provider 2 (otherwise units are unavailable). NA, zero and duplicate values are dropped.

visit_extract(visit_data, field)

Extracts all instances/arrays of a UK Biobank field(s) from visit_data. See https://biobank.ndph.ox.ac.uk/showcase/ to identify field codes.

visit_conditions(visit_data)

Extracts self-reported non-cancer medical history from visit_data in a "long" format that is easier to work with than "wide" as provided by UK Biobank.

visit_cancer(visit_data)

Extracts self-reported cancer history from visit_data in a "long" format that is easier to work with than "wide" as provided by UK Biobank.

visit_family_history(visit_data, fields, condition)

Determines presence of a specified condition in the self-reported family history data (visit_data). If multiple history fields are provided (e.g. history of mother and father), presence of the condition in any field determines a positive family history.

Licence

Made available under the MIT Licence.

philipdarke/ukbbhelpr documentation built on Dec. 22, 2021, 7:49 a.m.