Skip to contents

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(),
  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

# \donttest{
library(CodelistGenerator)
library(omopgenerics)
cdm <- mockVocabRef("database")
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 = newCodelist(list("msk" = codes$concept_id)),
cdm = cdm)
#> Warning: The domains "Device", "Measurement", "Procedure", and "Visit" are 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
      Vocabulary ID
      Source concept name
      Relationship
      
        
Estimate name

      		
    
Record count
      Person count
    
msk
condition
Osteoarthritis of knee
4
SNOMED
NA
Descendant
400
400


Osteoarthritis of hip
5
SNOMED
NA
Descendant
200
200

CDMConnector::cdmDisconnect(cdm)
# }