tableCohortCodeUse: Format the result of summariseCohortCodeUse into a table.

In CodelistGenerator: Identify Relevant Clinical Codes and Evaluate Their Use

Format the result of summariseCohortCodeUse into a table.

Description

Format the result of summariseCohortCodeUse into a table.

Usage

tableCohortCodeUse(
  result,
  type = "gt",
  header = c("cdm_name", "estimate_name"),
  groupColumns = NULL,
  timing = FALSE,
  hide = character(),
  .options = list(),
  excludeColumns = lifecycle::deprecated(),
  splitStrata = lifecycle::deprecated(),
  conceptId = lifecycle::deprecated(),
  sourceConcept = lifecycle::deprecated()
)

Arguments

result	A summarised result with results of the type "cohort_code_use".
type	Type of desired formatted table. To see supported formats use visOmopResults::tableType()
header	A vector specifying the elements to include in the header. The order of elements matters, with the first being the topmost header. The header vector can contain one of the following variables: "cdm_name", "codelist_name", "standard_concept_name", "standard_concept_id", "estimate_name", "source_concept_name", "source_concept_id", "domain_id". If results are stratified, "year", "sex", "age_group" can also be used. Alternatively, it can include other names to use as overall header labels.
groupColumns	Variables to use as group labels. Allowed columns are: "cdm_name", "codelist_name", "standard_concept_name", "standard_concept_id", "estimate_name", "source_concept_name", "source_concept_id", "domain_id". If results are stratified, "year", "sex", "age_group" can also be used. These cannot be used in header.
timing	If TRUE the timing setting will be displayed.
hide	Table columns to exclude, options are: "cdm_name", "codelist_name", "year", "sex", "age_group", "standard_concept_name", "standard_concept_id", "estimate_name", "source_concept_name", "source_concept_id", "domain_id". If results are stratified, "year", "sex", "age_group" can also be used. These cannot be used in header or groupColumn.
.options	Named list with additional formatting options. visOmopResults::tableOptions() shows allowed arguments and their default values.
excludeColumns	Deprecated.
splitStrata	Deprecated.
conceptId	Deprecated.
sourceConcept	Deprecated.

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)

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