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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.

combine_query_boolean.aurum.Rd

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")
#> 
  |                                                                            
  |                                                                      |   0%
#> Adding /home/runner/work/_temp/Library/rcprd/aurum_data/aurum_allpatid_set1_extract_observation_001.txt 2024-11-14 15:23:40.70908
#> 
  |                                                                            
  |=======================                                               |  33%
#> Adding /home/runner/work/_temp/Library/rcprd/aurum_data/aurum_allpatid_set1_extract_observation_002.txt 2024-11-14 15:23:40.721632
#> 
  |                                                                            
  |===============================================                       |  67%
#> Adding /home/runner/work/_temp/Library/rcprd/aurum_data/aurum_allpatid_set1_extract_observation_003.txt 2024-11-14 15:23:40.732832
#> 
  |                                                                            
  |======================================================================| 100%

## 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)
#>  [1] 0 0 0 0 0 0 0 0 0 0 0 0

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