get_incidence_prevalence: Get data for phenotype incidence and prevalence

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

Get data for phenotype incidence and prevalence

Description

Given a data.table with all events for a phenotype and reference dates per individual, compute the time to event data for each individual. If no reference date is given then the date of first available event will be taken as reference date for each individual. ...

Usage

get_incidence_prevalence(
  all_event_dt,
  df.data.settings,
  df_reference_date = NULL,
  include_secondary_recurrence = FALSE,
  window_ref_days_include = 0,
  window_fu_days_mask = 0,
  verbose = TRUE
)

Arguments

all_event_dt	data table containing all events
df.data.settings	data frame containing data settings
window_ref_days_include	number of days around the reference date (visit) that should be used to indicates if individuals had the event on the reference date. Relevant if you want to know if participant took medication on the visit
window_fu_days_mask	number of days that future events should not be counted
reference_date	reference dates for each individuals in the whole cohort as a named vector

Value

a data table with individual with time to event information

Examples

all_event_dt <- get_all_events(dfDefinitions_processed_expanded[1,],lst.data,df.data.settings)
get_incidence_prevalence(all_event_dt,df.data.settings, reference_date = setNames(as.Date(as.character(dfukb$f.53.0.0),format="%Y-%m-%d"),dfukb$identifier))

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