CodelistGenerator (version 3.5.0)

tableUnmappedCodes: Format the result of summariseUnmappedCodeUse into a table

Description

Format the result of summariseUnmappedCodeUse into a table

Usage

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

Value

A table with a formatted version of the summariseUnmappedCodes result.

Arguments

result

A <summarised_result> with results of the type "umapped_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.

.options

Named list with additional formatting options. visOmopResults::tableOptions() shows allowed arguments and their default values.

Examples

# \donttest{
cdm <- mockVocabRef("database")
codes <- list("Musculoskeletal disorder" = 1)
cdm <- omopgenerics::insertTable(cdm, "condition_occurrence",
dplyr::tibble(person_id = 1,
              condition_occurrence_id = 1,
              condition_concept_id = 0,
              condition_start_date  = as.Date("2000-01-01"),
              condition_type_concept_id  = NA,
              condition_source_concept_id = 7))
unmapped_codes <- summariseUnmappedCodes(x = list("osteoarthritis" = 2),
cdm = cdm, table = "condition_occurrence")
tableUnmappedCodes(unmapped_codes)

cdm <- omopgenerics::insertTable(
 cdm,
 "measurement",
 dplyr::tibble(
   person_id = 1,
   measurement_id = 1,
   measurement_concept_id = 0,
   measurement_date  = as.Date("2000-01-01"),
   measurement_type_concept_id  = NA,
   measurement_source_concept_id = 7
 )
)
table <- summariseUnmappedCodes(x = list("cs" = 2),
                               cdm = cdm,
                               table = c("measurement"))
tableUnmappedCodes(unmapped_codes)

CDMConnector::cdmDisconnect(cdm)
# }