label_ukb_main: Label a UK Biobank main dataset

In rmgpanw/ukbwranglr: Exploring UKB Data

Label a UK Biobank main dataset

Description

Applies variable labels and factor labels to coded values in a UK Biobank main dataset.

Usage

label_ukb_main(
  ukb_main,
  data_dict,
  ukb_codings = get_ukb_codings(),
  colnames_col = "descriptive_colnames",
  max_n_labels = 30
)

Arguments

ukb_main	A UK Biobank main dataset (data frame)
data_dict	A data dictionary specific to the UKB main dataset file, generated by make_data_dict. This can be filtered for a subset of columns to be labelled.
ukb_codings	The UKB codings file (available online at the UK Biobank data showcase. This should be a data frame where all columns are of type character.
colnames_col	The name of the column in data_dict that contains column names matching those in ukb_main.
max_n_labels	Coded variables with associated value labels less than or equal to this threshold will be labelled as factors. If NULL, then all value labels will be applied. Default value is 30.

Value

A data frame.

Examples

## Not run: 
# get dummy UKB data dictionary and codings
dummy_ukb_data_dict <- get_ukb_dummy("dummy_Data_Dictionary_Showcase.tsv")
dummy_ukb_codings <- get_ukb_dummy("dummy_Codings.tsv")

# file path to dummy UKB main dataset
dummy_ukb_main_path <- get_ukb_dummy("dummy_ukb_main.tsv", path_only = TRUE)

# to read only a subset of variables, create a data dictionary and filter
# for selected variables, then supply to `read_ukb()`
data_dict_selected <- make_data_dict(
  ukb_main = dummy_ukb_main_path,
  ukb_data_dict = dummy_ukb_data_dict
) %>%
  dplyr::filter(FieldID %in% c("eid", "31", "34", "21001"))

# read ukb_main as is, and label afterwards
read_ukb(
  path = dummy_ukb_main_path,
  data_dict = data_dict_selected,
  ukb_data_dict = dummy_ukb_data_dict,
  ukb_codings = dummy_ukb_codings,
  descriptive_colnames = TRUE,
  label = FALSE
) %>%
  label_ukb_main(
    data_dict = data_dict_selected,
    ukb_codings = dummy_ukb_codings,
    colnames_col = "descriptive_colnames"
  )

## End(Not run)

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