Format the result of summariseUnmappedCodeUse into a table

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()
)

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.

Value

A table with a formatted version of the summariseUnmappedCodes result.

Examples

# \donttest{
cdm <- mockVocabRef("database")
#> Warning: There are observation period end dates after the current date: 2025-04-11
#> ℹ The latest max observation period end date found is 2025-12-31
#> Warning: There are observation period end dates after the current date: 2025-04-11
#> ℹ The latest max observation period end date found is 2025-12-31
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")
#> Warning: ! `codelist` casted to integers.
#> Searching for unmapped codes related to osteoarthritis
tableUnmappedCodes(unmapped_codes)


  

      

        
Database name
      
    

      

        
mock
      
    
Codelist name
      
Unmapped concept name
      
Unmapped concept ID
      

        
Estimate name
      
    
Record count
    
osteoarthritis
Degenerative arthropathy
7
1

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"))
#> Warning: ! `codelist` casted to integers.
#> Searching for unmapped codes related to cs
tableUnmappedCodes(unmapped_codes)


  

      

        
Database name
      
    

      

        
mock
      
    
Codelist name
      
Unmapped concept name
      
Unmapped concept ID
      

        
Estimate name
      
    
Record count
    
osteoarthritis
Degenerative arthropathy
7
1

CDMConnector::cdmDisconnect(cdm)
# }