validate_clinical_codes: Validate a clinical codes data frame

In rmgpanw/ukbwranglr: Exploring UKB Data

Validate a clinical codes data frame

Description

Checks whether a data frame of clinical codes is correctly formatted for use with extract_phenotypes.

Usage

validate_clinical_codes(clinical_codes, allow_overlapping_categories = FALSE)

Arguments

clinical_codes	A data frame. See example_clinical_codes for an example.
allow_overlapping_categories	If TRUE, will pass with a warning if any codes are duplicated between disease categories. If FALSE, an error will be raised. Default value is FALSE.

Details

Checks that:

• Expected column names are present

• All columns are of type character

• No missing values are present in any column

• No disease categories overlap with each other i.e. each disease (for each author) contains a unique set of clinical codes. Overlapping disease categories may optionally be permitted by setting allow_overlapping_categories to TRUE

Note that currently this does not check whether the clinical codes themselves are valid (i.e. whether a clinical code exists for a given coding system).

Value

Returns invisibly TRUE if all checks pass.

Examples

validate_clinical_codes(example_clinical_codes())

rmgpanw/ukbwranglr documentation built on April 30, 2024, 7:47 a.m.