tableCohortCodeUse: Format the result of summariseCohortCodeUse into a visual...

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

Format the result of summariseCohortCodeUse into a visual table.

Description

Usage

tableCohortCodeUse(
  result,
  type = "gt",
  header = c("cdm_name", "estimate"),
  splitStrata = TRUE,
  conceptId = TRUE,
  sourceConcept = TRUE,
  timing = FALSE,
  groupColumns = NULL,
  excludeColumns = c("result_id", "estimate_type", "additional_name", "additional_level"),
  .options = list()
)

Arguments

result	A summarised result with results of the type "cohort_code_use".
type	Type of desired formatted table, possibilities: "gt", "flextable", "tibble".
header	A vector containing which elements should go into the header in order. Allowed are: cdm_name, group, strata, additional, variable, estimate, settings.
splitStrata	If TRUE strata will be split.
conceptId	If TRUE concept ids will be displayed.
sourceConcept	If TRUE source concepts will be displayed.
timing	If TRUE the timing setting will be displayed.
groupColumns	Columns to use as group labels. Allowed columns are cdm_name, cohort_name and/or codelist_name.
excludeColumns	Columns to drop from the output table.
.options	Named list with additional formatting options. visOmopResults::optionsVisOmopTable() shows allowed arguments and their default values.

Value

A table with a formatted version of the summariseCohortCodeUse result.

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")

tableCohortCodeUse(results_cohort_mult)
CDMConnector::cdmDisconnect(cdm)

## End(Not run)

oxford-pharmacoepi/CodelistGenerator documentation built on May 13, 2024, 2:03 a.m.