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

In oxford-pharmacoepi/CodelistGenerator: Identify Relevant Clinical Codes and Evaluate Their Use

Summarise code use among a cohort in the cdm reference

Description

Summarise code use among a cohort in the cdm reference

Usage

summariseCohortCodeUse(
  x,
  cdm,
  cohortTable,
  cohortId = NULL,
  timing = "any",
  countBy = c("record", "person"),
  byConcept = TRUE,
  byYear = FALSE,
  bySex = FALSE,
  ageGroup = NULL,
  minCellCount = 5
)

Arguments

x	Vector of concept IDs
cdm	cdm_reference via CDMConnector::cdm_from_con()
cohortTable	A cohort table from the cdm reference.
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
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.
minCellCount	The minimum number of counts to reported, below which results will be suppressed. If 0, all results will be reported.

Value

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

Examples

## Not run: 
con <- DBI::dbConnect(duckdb::duckdb(),
                      dbdir = CDMConnector::eunomia_dir())
cdm <- CDMConnector::cdm_from_con(con,
                                  cdm_schem = "main",
                                  write_schema = "main")
cdm <- CDMConnector::generateConceptCohortSet(cdm = cdm,
conceptSet = list(a = 260139,
                  b = 1127433),
                  name = "cohorts",
                  end = "observation_period_end_date",
                  overwrite = TRUE)

results_cohort_mult <-
summariseCohortCodeUse(list(cs = c(260139,19133873)),
                      cdm = cdm,
                      cohortTable = "cohorts",
                      timing = "entry",
                      minCellCount = 0)

results_cohort_mult
CDMConnector::cdmDisconnect(cdm)

## End(Not run)

oxford-pharmacoepi/CodelistGenerator documentation built on April 12, 2024, 9:30 a.m.