Compare two codelists

Compare two codelists

Usage

compareCodelists(codelist1, codelist2)

Arguments

codelist1

Output of getCandidateCodes

codelist2

Output of getCandidateCodes

Value

tibble

Examples

# \donttest{
cdm <- mockVocabRef()
#> 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
codes1 <- getCandidateCodes(
 cdm = cdm,
 keywords = "Arthritis",
 domains = "Condition",
 includeDescendants = TRUE
)
#> Limiting to domains of interest
#> Getting concepts to include
#> Adding descendants
#> Search completed. Finishing up.
#> ✔ 3 candidate concepts identified
#> Time taken: 0 minutes and 0 seconds
codes2 <- getCandidateCodes(
 cdm = cdm,
 keywords = c("knee osteoarthritis", "arthrosis"),
 domains = "Condition",
 includeDescendants = TRUE
)
#> 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
compareCodelists(
 codelist1 = codes1,
 codelist2 = codes2
)
#> # A tibble: 4 × 3
#>   concept_id concept_name           codelist       
#>        <int> <chr>                  <chr>          
#> 1          3 Arthritis              Only codelist 1
#> 2          4 Osteoarthritis of knee Both           
#> 3          5 Osteoarthritis of hip  Only codelist 1
#> 4          2 Osteoarthrosis         Only codelist 2
# }