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Format the result of summariseOrphanCodes into a table.

tableOrphanCodes.Rd

Format the result of summariseOrphanCodes into a table.

Usage

tableOrphanCodes(
  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 "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.

.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

# \donttest{
cdm <- mockVocabRef("database")
#> Warning: There are observation period end dates after the current date: 2025-02-19
#> ℹ The latest max observation period end date found is 2025-12-31
#> Warning: There are observation period end dates after the current date: 2025-02-19
#> ℹ The latest max observation period end date found is 2025-12-31
codes <- getCandidateCodes(cdm = cdm,
keywords = "Musculoskeletal disorder",
domains = "Condition",
includeDescendants = FALSE)
#> Limiting to domains of interest
#> Getting concepts to include
#> Search completed. Finishing up.
#> ✔ 1 candidate concept identified
#> Time taken: 0 minutes and 0 seconds

orphan_codes <- summariseOrphanCodes(x = list("msk" = codes$concept_id),
cdm = cdm)
#> PHOEBE results not available
#> ℹ The concept_recommended table is not present in the cdm.
#> Getting orphan codes for msk
#> 

tableOrphanCodes(orphan_codes)



  

      
        
Database name

      		
    

      
        
mock

      		
    
Codelist name
      Domain ID
      Standard concept name
      Standard concept ID
      Standard concept
      Vocabulary ID
      
        
Estimate name

      		
    
Record count
    
msk
condition
Osteoarthritis of knee
4
standard
SNOMED
400


Osteoarthritis of hip
5
standard
SNOMED
200

CDMConnector::cdmDisconnect(cdm)
# }