combine_query_boolean.aurum: Combine a CPRD aurum database query with a cohort returning a...

In rcprd: Extraction and Management of Clinical Practice Research Datalink Data

Combine a CPRD aurum database query with a cohort returning a 0/1 vector depending on whether each individual has a recorded code of interest.

Description

An S3 method that can be used on database queries from Aurum extracts. Combine a database query with a cohort returning a 0/1 vector depending on whether each individual has a recorded code of interest. cohort must contain variables patid and indexdt. The database query will be merged with the cohort by variable patid. If an individual has at least numobs observations between time_prev days prior to indexdt, and time_post days after indexdt, a 1 will be returned, 0 otherwise. The type of query must be specified for appropriate data manipulation.

Usage

## S3 method for class 'aurum'
combine_query_boolean(
  db_query,
  cohort,
  query_type,
  time_prev = Inf,
  time_post = 0,
  numobs = 1
)

Arguments

db_query	Output from database query (ideally obtained through db_query).
cohort	Cohort to combine with the database query.
query_type	Type of query
time_prev	Number of days prior to index date to look for codes.
time_post	Number of days after index date to look for codes.
numobs	Number of observations required to be observed in specified time window to return a 1.

Value

A 0/1 vector.

Examples

## Create connection to a temporary database
aurum_extract <- connect_database(file.path(tempdir(), "temp.sqlite"))

## Add observation data from all observation files in specified directory
cprd_extract(db = aurum_extract,
filepath = system.file("aurum_data", package = "rcprd"),
filetype = "observation")

## Query database for a specific medcode
db_query <- db_query(db_open = aurum_extract,
tab ="observation",
codelist_vector = "187341000000114")

## Define cohort
pat<-extract_cohort(filepath = system.file("aurum_data", package = "rcprd"))

### Add an index date to pat
pat$indexdt <- as.Date("01/01/2020", format = "%d/%m/%Y")

## Combine query with cohort retaining most recent three records
combine_query_boolean(cohort = pat,
db_query = db_query,
query_type = "med",
numobs = 3)

## clean up
RSQLite::dbDisconnect(aurum_extract)
unlink(file.path(tempdir(), "temp.sqlite"))

rcprd documentation built on April 12, 2025, 1:57 a.m.