expand_dfDefinitions_processed2: Expand the illness/medication codes in definition table to...

In niekverw/ukbpheno: Extraction and processing UK Biobank data to generate health outcome phenotypes

Expand the illness/medication codes in definition table to include codes that belong to this code

Description

Explicitly fill in codes covered by the parent codes stated in the definition table. This differs from expand_dfDefinitions_processed() in the dictionaries taken - it reads the code dictionaries stated in lst.data.setting and expand to available codes accordingly. Codes not present will be removed.

Usage

expand_dfDefinitions_processed2(
  dfDefinitions_processed,
  lst.data.settings,
  code_map_dir
)

Arguments

dfDefinitions_processed	definition table as dataframe
lst.data.settings	data.setting as dataframe, it includes settings that should be used, e.g. if ICD10 should be looked up case sensitive or not (incase of READ cases are important, dotts should also NOT be interpreted)
code_map_dir	the directory storing the coding files

Value

definition table as dataframe

niekverw/ukbpheno documentation built on Oct. 30, 2023, 9:17 p.m.