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Format the result of summariseAchillesCodeUse into a table

tableAchillesCodeUse.Rd

Format the result of summariseAchillesCodeUse into a table

Usage

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

Arguments

result

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

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 summariseCohortCodeUse result.

Examples

# \donttest{
library(CodelistGenerator)
library(omopgenerics)

cdm <- mockVocabRef("database")
oa <- getCandidateCodes(cdm = cdm, keywords = "osteoarthritis")
#> Limiting to domains of interest
#> Getting concepts to include
#> Adding descendants
#> Search completed. Finishing up.
#> ✔ 2 candidate concepts identified
#> Time taken: 0 minutes and 0 seconds
result_achilles <- summariseAchillesCodeUse(newCodelist(list(oa = oa$concept_id)),
                                            cdm = cdm)
#> 
tableAchillesCodeUse(result_achilles)



  

      
        
Database name

      		
    

      
        
mock

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

      		
    
Record count
      Person count
    
oa
condition
Osteoarthritis of knee
4
SNOMED
NA
400
400


Osteoarthritis of hip
5
SNOMED
NA
200
200
CDMConnector::cdmDisconnect(cdm)
# }