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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(),
  .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.

.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{
cdm <- mockVocabRef("database")
#> Warning: ! 8 column in cdm_source do not match expected column type:
#> • `cdm_source_abbreviation` is logical but expected character
#> • `cdm_holder` is logical but expected character
#> • `source_description` is logical but expected character
#> • `source_documentation_reference` is logical but expected character
#> • `cdm_etl_reference` is logical but expected character
#> • `source_release_date` is logical but expected date
#> • `cdm_release_date` is logical but expected date
#> • `vocabulary_version` is logical but expected character
#> Warning: ! 3 column in concept do not match expected column type:
#> • `valid_start_date` is logical but expected date
#> • `valid_end_date` is logical but expected date
#> • `invalid_reason` is logical but expected character
#> Warning: ! 3 column in concept_relationship do not match expected column type:
#> • `valid_start_date` is logical but expected date
#> • `valid_end_date` is logical but expected date
#> • `invalid_reason` is logical but expected character
#> Warning: ! 1 column in concept_synonym do not match expected column type:
#> • `language_concept_id` is logical but expected integer
#> Warning: ! 4 column in drug_strength do not match expected column type:
#> • `amount_value` is logical but expected numeric
#> • `box_size` is logical but expected integer
#> • `valid_start_date` is logical but expected date
#> • `valid_end_date` is logical but expected date
#> Warning: ! 7 column in achilles_analysis do not match expected column type:
#> • `analysis_name` is numeric but expected character
#> • `stratum_1_name` is logical but expected character
#> • `stratum_2_name` is logical but expected character
#> • `stratum_3_name` is logical but expected character
#> • `stratum_4_name` is logical but expected character
#> • `stratum_5_name` is logical but expected character
#> • `category` is logical but expected character
#> Warning: ! 5 column in achilles_results do not match expected column type:
#> • `stratum_1` is numeric but expected character
#> • `stratum_2` is logical but expected character
#> • `stratum_3` is logical but expected character
#> • `stratum_4` is logical but expected character
#> • `stratum_5` is logical but expected character
#> Warning: ! 14 column in achilles_results_dist do not match expected column type:
#> • `stratum_1` is logical but expected character
#> • `stratum_2` is logical but expected character
#> • `stratum_3` is logical but expected character
#> • `stratum_4` is logical but expected character
#> • `stratum_5` is logical but expected character
#> • `min_value` is logical but expected integer
#> • `max_value` is logical but expected integer
#> • `avg_value` is logical but expected numeric
#> • `stdev_value` is logical but expected numeric
#> • `median_value` is logical but expected numeric
#> • `p10_value` is logical but expected numeric
#> • `p25_value` is logical but expected numeric
#> • `p75_value` is logical but expected numeric
#> • `p90_value` is logical but expected numeric
#> Warning: There are observation period end dates after the current date: 2024-11-26
#> ℹ The latest max observation period end date found is 2025-12-31
#> Warning: There are observation period end dates after the current date: 2024-11-26
#> ℹ The latest max observation period end date found is 2025-12-31
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(list(oa = oa$concept_id), cdm = cdm)
#> 
tableAchillesCodeUse(result_achilles)



  

      
        
Database name

      		
    

      
        
mock

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

      		
    
Record count
    
oa
condition
Osteoarthritis of knee
4
standard
SNOMED
400


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