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,
  codelistType = "index event"
)

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, codelist_with_details, or a concept_set. See newCodelist(), newCodelistWithDetails(), newConceptSetExpression() functions for more details. If set to NULL, the codelist associated with the cohort will be used.
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).
codelistType: The reason for the codelist. Can be "index event", "inclusion criteria", or "exit criteria". Only apply when x is NULL and using codes associated with a cohort.

Value

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

Examples

if (FALSE) { # \dontrun{
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)
} # }