Compare overlap between two sets of codes
compareCodelists.RdCompare overlap between two sets of codes
Examples
# \donttest{
library(CodelistGenerator)
library(omock)
# Create a CDM object
downloadMockDataset(datasetName = "GiBleed",
path = NULL,
overwrite = NULL)
#> ℹ Deleting prior version of GiBleed.
cdm <- mockCdmFromDataset(datasetName = "GiBleed")
#> ℹ Reading GiBleed tables.
#> ℹ Adding drug_strength table.
#> ℹ Creating local <cdm_reference> object.
# Compare two candidate_codes object
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.
#> ✔ 2 candidate concepts identified
#> Time taken: 0 minutes and 0 seconds
codes2 <- getCandidateCodes(
cdm = cdm,
keywords = c("osteo"),
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
compareCodelists(
codelist1 = codes1,
codelist2 = codes2)
#> # A tibble: 4 × 3
#> concept_id concept_name codelist
#> <int> <chr> <chr>
#> 1 80180 Osteoarthritis Both
#> 2 80502 Osteoporosis Only in codelist codelis…
#> 3 80809 Rheumatoid arthritis Only in codelist codelis…
#> 4 40480160 Pathological fracture due to osteoporosis Only in codelist codelis…
# Compare two codelists
acetaminophen <- getDrugIngredientCodes(cdm,
name = "acetaminophen",
nameStyle = "{concept_name}",
type = "codelist")
hydrocodone <- getDrugIngredientCodes(cdm,
name = "hydrocodone",
nameStyle = "{concept_name}",
type = "codelist")
compareCodelists(
codelist1 = acetaminophen,
codelist2 = hydrocodone)
#> # A tibble: 8 × 3
#> concept_id concept_name codelist
#> <int> <chr> <chr>
#> 1 1125315 NA Only in codelist acetaminophen
#> 2 1127078 NA Only in codelist acetaminophen
#> 3 1127433 NA Only in codelist acetaminophen
#> 4 1174888 NA Only in codelist hydrocodone
#> 5 19133768 NA Both
#> 6 40162522 NA Both
#> 7 40229134 NA Only in codelist acetaminophen
#> 8 40231925 NA Only in codelist acetaminophen
# Notice that concept_name = NA as `codelist` class does not store this information
# for each concept.
# Compare two codelists_with_details
acetaminophen <- getDrugIngredientCodes(cdm,
name = "acetaminophen",
nameStyle = "{concept_name}",
type = "codelist_with_details")
hydrocodone <- getDrugIngredientCodes(cdm,
name = "hydrocodone",
nameStyle = "{concept_name}",
type = "codelist_with_details")
compareCodelists(
codelist1 = acetaminophen,
codelist2 = hydrocodone)
#> # A tibble: 8 × 3
#> concept_id concept_name codelist
#> <int> <chr> <chr>
#> 1 1125315 Acetaminophen Only in…
#> 2 1127078 Acetaminophen 160 MG Oral Tablet Only in…
#> 3 1127433 Acetaminophen 325 MG Oral Tablet Only in…
#> 4 1174888 Hydrocodone Only in…
#> 5 19133768 Acetaminophen 750 MG / Hydrocodone Bitartrate 7.5 MG Oral… Both
#> 6 40162522 Acetaminophen 325 MG / Hydrocodone Bitartrate 7.5 MG Oral… Both
#> 7 40229134 Acetaminophen 21.7 MG/ML / Dextromethorphan Hydrobromide … Only in…
#> 8 40231925 Acetaminophen 325 MG / Oxycodone Hydrochloride 5 MG Oral … Only in…
# }