summariseCohortCodeUse: Summarise code use among a cohort in the cdm reference
In CodelistGenerator: Identify Relevant Clinical Codes and Evaluate Their Use

summariseCohortCodeUse

R Documentation

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 = lifecycle::deprecated()
)

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`	`⁠\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}}⁠`

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")

results_cohort_mult
CDMConnector::cdmDisconnect(cdm)

## End(Not run)

CodelistGenerator documentation built on Oct. 17, 2024, 5:09 p.m.