ukb_context {ukbtools}

Demographics of a UKB sample subset

Description

Describes a subset of the UKB sample, relative to a reference subsample, on the UKB primary demographics (sex, age, ethnicity, Townsend deprivation) and assessment centre and current employment status. The "subset" and "reference" samples are defined either by a variable of interest (nonmiss.var - those with data form the "subset" of interest and samples with missing data are the "reference" sample), or a logical vector (subset.var - where TRUE values define the "subset" and FALSE the "reference" samples) . This function is intended as an exploratory data analysis and quality control tool.

Usage

ukb_context(data, nonmiss.var = NULL, subset.var = NULL,
  bar.position = "fill", sex.var = "^sex.*0_0",
  age.var = "^age_when_attended_assessment_centre.*0_0",
  socioeconomic.var = "^townsend_deprivation_index_at_recruitment.*0_0",
  ethnicity.var = "^ethnic_background.*0_0",
  employment.var = "^current_employment_status.*0_0",
  centre.var = "^uk_biobank_assessment_centre.*0_0")

Arguments

data

A UKB dataset constructed with ukb_df.

nonmiss.var

The variable of interest which defines the "subset" (samples with data) and "reference" (samples without data, i.e., NA) samples.

subset.var

A logical vector defining a "subset" (TRUE) and "reference" subset (FALSE). Length must equal the number of rows in your data.

bar.position

This argument is passed to the position in geom_bar. The default value is "fill" which shows reference and subset of interest as proportions of the full dataset. Useful alternatives are "stack" for counts and "dodge" for side-by-side bars.

sex.var

The variable to be used for sex. Default value is the regular expression "^sex.*0_0".

age.var

The variable to be use for age. Default value is the regular expression "^age_when_attended_assessment_centre.*0_0".

socioeconomic.var

The variable to be used for socioeconomic status. Default value is deprivation at baseline, the regular expression "^townsend_deprivation_index_at_recruitment.*0_0".

ethnicity.var

The variable to be used for ethnicity. Default value is the regular expression "^ethnic_background.*0_0".

employment.var

The variable to be used for employment status. Default value is employment status at baseline "^current_employment_status.*0_0".

centre.var

The variable to be used for assessment centre. Default value is the regular expression "^uk_biobank_assessment_centre.*0_0".

See Also

ukb_df

Examples

## Not run: 
# Compare those with data to those without
ukb_context(my_ukb_data, nonmiss.var = "my_variable_of_interest")

# Define a subset of interest as a logical vector
subgroup_of_interest <- (my_ukb_data$bmi > 40 & my_ukb_data$age < 50)
ukb_context(my_ukb_data, subset.var = subgroup_of_interest)

## End(Not run)