tableOrphanCodes: Format the result of summariseOrphanCodes into a visual...

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

Format the result of summariseOrphanCodes into a visual table.

Description

Usage

tableOrphanCodes(
  result,
  type = "gt",
  header = c("cdm_name", "estimate"),
  conceptId = TRUE,
  standard = TRUE,
  vocabulary = TRUE,
  relationship = TRUE,
  groupColumns = NULL,
  settings = character(),
  excludeColumns = c("result_id", "estimate_type"),
  .options = list()
)

Arguments

result	A summarised result with results of the type "orphan_codes".
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.
conceptId	If TRUE concept ids will be displayed.
standard	If TRUE a column indicating if the code is standard will be displayed.
vocabulary	If TRUE vocabulary id will be displayed.
relationship	If TRUE relationship id will be displayed.
groupColumns	Columns to use as group labels. Allowed columns are cdm_name and/or codelist_name.
settings	Vector with the settings columns to display.
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 summariseOrphanCodes result.

Examples

## Not run: 
cdm <- mockVocabRef("database")
codes <- getCandidateCodes(cdm = cdm,
keywords = "Musculoskeletal disorder",
domains = "Condition",
includeDescendants = FALSE)

orphan_codes <- summariseOrphanCodes(x = list("msk" = codes$concept_id),
cdm = cdm,
domains = "Condition",
standardConcept = "Standard",
searchInSynonyms = FALSE,
searchNonStandard = FALSE,
includeDescendants = TRUE,
includeAncestor = FALSE)

tableOrphanCodes(orphan_codes)

CDMConnector::cdmDisconnect(cdm)

## End(Not run)

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