CodelistGenerator (version 4.0.0)

summariseCohortCodeUse: Summarise code use among a cohort in the cdm reference

Description

Summarise code use among a cohort in the cdm reference

Usage

summariseCohortCodeUse(
  cdm,
  cohortTable,
  x = NULL,
  cohortId = NULL,
  timing = "any",
  countBy = c("record", "person"),
  byConcept = TRUE,
  byYear = FALSE,
  bySex = FALSE,
  ageGroup = NULL,
  useSourceCodes = FALSE
)

Value

A tibble with results overall and, if specified, by strata

Arguments

cdm

A cdm reference to an OMOP CDM dataset. If data is held within a database, the vocabulary tables should be in the same schema as the clinical tables (person, observation period, and so on).

cohortTable

A cohort table from the cdm reference.

x

A codelist or cohort table name.

cohortId

A vector of cohort IDs to include

timing

When to assess the code use relative cohort dates. This can be "any"(code use any time by individuals in the cohort) or "entry" (code use on individuals' cohort start date).

countBy

Either "record" for record-level counts or "person" for person-level counts.

byConcept

TRUE or FALSE. If TRUE code use will be summarised by concept.

byYear

TRUE or FALSE. If TRUE code use will be summarised by year.

bySex

TRUE or FALSE. If TRUE code use will be summarised by sex.

ageGroup

If not NULL, a list of ageGroup vectors of length two.

useSourceCodes

Whether the codelist provided contains source codes (TRUE) or standard codes (FALSE).

Examples

if (FALSE) {
library(CodelistGenerator)
library(duckdb)
library(DBI)
library(CDMConnector)
con <- dbConnect(duckdb(),
                 dbdir = eunomiaDir())
cdm <- cdmFromCon(con,
                 cdmSchema = "main",
                 writeSchema = "main")
cdm <- generateConceptCohortSet(cdm = cdm,
                  conceptSet = list(a = 260139,
                                    b = 1127433),
                  name = "cohorts",
                  end = "observation_period_end_date",
                  overwrite = TRUE)

results_cohort_mult <-
summariseCohortCodeUse(omopgenerics::newCodelist(list(cs = c(260139,19133873))),
                      cdm = cdm,
                      cohortTable = "cohorts",
                      timing = "entry")

results_cohort_mult
CDMConnector::cdmDisconnect(cdm)
}