tableOrphanCodes: Format the result of summariseOrphanCodes into a table

In CodelistGenerator: Identify Relevant Clinical Codes and Evaluate Their Use

Format the result of summariseOrphanCodes into a table

Description

Format the result of summariseOrphanCodes into a table

Usage

tableOrphanCodes(
  result,
  type = "gt",
  header = c("cdm_name", "estimate_name"),
  groupColumn = character(),
  hide = character(),
  style = NULL,
  .options = list()
)

Arguments

result	A ⁠<summarised_result>⁠ with results of the type "orphan_codes".
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", "domain_id", "standard_concept_name", "standard_concept_id", "estimate_name", "standard_concept", "vocabulary_id". Alternatively, it can include other names to use as overall header labels.
groupColumn	Variables to use as group labels. Allowed columns are: "cdm_name", "codelist_name", "domain_id", "standard_concept_name", "standard_concept_id", "estimate_name", "standard_concept", "vocabulary_id". These cannot be used in header.
hide	Table columns to exclude, options are: "cdm_name", "codelist_name", "domain_id", "standard_concept_name", "standard_concept_id", "estimate_name", "standard_concept", "vocabulary_id". These cannot be used in header or groupColumn.
style	A character string or custom R code to define the visual formatting of the table. This argument can be provided in two ways: (1) Pre-defined Styles (Character String): Use a name for a built-in style (e.g., "darwin"). See visOmopResults::tableStyle() for available options. (2) Custome Code (Advanced): Supply a block of custom R code. This code must be specific to the table type. See visOmopResults::tableStyleCode() for structural examples.
.options	Named list with additional formatting options. visOmopResults::tableOptions() shows allowed arguments and their default values.

Value

A table with a formatted version of the summariseOrphanCodes result.

Examples

library(CodelistGenerator)
library(omopgenerics)
cdm <- mockVocabRef("database")
codes <- getCandidateCodes(cdm = cdm,
keywords = "Musculoskeletal disorder",
domains = "Condition",
includeDescendants = FALSE)

orphan_codes <- summariseOrphanCodes(x = newCodelist(list("msk" = codes$concept_id)),
cdm = cdm)

tableOrphanCodes(orphan_codes)

CDMConnector::cdmDisconnect(cdm)

CodelistGenerator documentation built on Dec. 17, 2025, 5:06 p.m.