# CodelistGenerator search options: codes for osteoarthritis

## Creating a codelist for osteoarthritis

For this example we are going to generate a candidate codelist for osteoarthritis, looking at the impact of alternative search strategies.

    library(DBI)
    library(RPostgres)

    # postgres database connection details
    serverDbi <- Sys.getenv("server")
    user <- Sys.getenv("user")
    password <- Sys.getenv("password")
    port <- Sys.getenv("port")
    host <- Sys.getenv("host")

    db <- dbConnect(RPostgres::Postgres(),
      dbname = serverDbi,
      port = port,
      host = host,
      user = user,
      password = password
    )

    # name of vocabulary schema
    vocabularyDatabaseSchema <- "vocabulary"

    # create cdm reference
    cdm <- CDMConnector::cdm_from_con(
      con = db,
      cdm_schema = vocabularyDatabaseSchema
    )

## Search strategies

### Condition domain, without searching synonyms, with exclusions, without including descendants or ancestor

To start we will search for “osteoarthritis”, while excluding “post-infection” and “post-traumatic”, but without searching synonyms, without searching via non-standard codes, and without including descendants or the direct ancestor of the included concepts.

    oaCodes1 <- getCandidateCodes(
      cdm = cdm,
      keywords = "osteoarthritis",
      domains = "Condition",
      searchInSynonyms = FALSE,
      searchNonStandard = FALSE,
      exclude = c(
        "post-infection",
        "post-traumatic"
      ),
      includeDescendants = FALSE,
      includeAncestor = FALSE
    )

What is the candidate codelist?

    oaCodes1 %>%
      glimpse()
    #> Rows: 151
    #> Columns: 6
    #> $ concept_id       <int> 72993, 73840, 75036, 77631, 78505, 79904, 80180, 8018…
    #> $ found_from       <chr> "From initial search", "From initial search", "From i…
    #> $ concept_name     <chr> "Localized, primary osteoarthritis", "Localized, prim…
    #> $ domain_id        <chr> "Condition", "Condition", "Condition", "Condition", "…
    #> $ vocabulary_id    <chr> "SNOMED", "SNOMED", "SNOMED", "SNOMED", "SNOMED", "SN…
    #> $ standard_concept <chr> "standard", "standard", "standard", "standard", "stan…

### Including descendants

Now we will also include the descendants of included concepts.

    oaCodes2 <- getCandidateCodes(
      cdm = cdm,
      keywords = "osteoarthritis",
      domains = "Condition",
      searchInSynonyms = FALSE,
      searchNonStandard = FALSE,
      exclude = c(
        "post-infection",
        "post-traumatic"
      ),
      includeDescendants = TRUE,
      includeAncestor = FALSE
    )

What new codes do we pick up?

    newCodes1To2 <- compareCodelists(oaCodes1, oaCodes2) %>%
      filter(codelist == "Only codelist 2") %>%
      select(-"codelist")

    newCodes1To2 %>%
      glimpse()
    #> Rows: 262
    #> Columns: 2
    #> $ concept_id   <int> 72401, 72405, 72709, 72990, 73287, 73550, 73554, 74132, 7…
    #> $ concept_name <chr> "Kashin-Bek disease", "Degenerative joint disease of shou…

### Including observation domain

Now we will search the observation domain as well as the condition domain.

    oaCodes3 <- getCandidateCodes(
      cdm = cdm,
      keywords = "osteoarthritis",
      domains = c("Condition", "Observation"),
      searchInSynonyms = FALSE,
      searchNonStandard = FALSE,
      exclude = c(
        "post-infection",
        "post-traumatic"
      ),
      includeDescendants = FALSE,
      includeAncestor = FALSE
    )

What new codes do we pick up?

    newCodes1To3 <- compareCodelists(oaCodes1, oaCodes3) %>%
      filter(codelist == "Only codelist 2") %>%
      select(-"codelist")

    newCodes1To3 %>%
      glimpse()
    #> Rows: 18
    #> Columns: 2
    #> $ concept_id   <int> 1988221, 1988793, 2101879, 2102817, 2108437, 2617599, 261…
    #> $ concept_name <chr> "Knee injury and osteoarthritis outcome score - physical …

### Search synonyms

Now we will search the concept synonym table to identify concepts to include.

    oaCodes4 <- getCandidateCodes(
      cdm = cdm,
      keywords = "osteoarthritis",
      domains = "Condition",
      searchInSynonyms = TRUE,
      searchNonStandard = FALSE,
      exclude = c(
        "post-infection",
        "post-traumatic"
      ),
      includeDescendants = FALSE,
      includeAncestor = FALSE
    )

What new codes do we pick up?

    newCodes1To4 <- compareCodelists(oaCodes1, oaCodes4) %>%
      filter(codelist == "Only codelist 2") %>%
      select(-"codelist")

    newCodes1To4 %>%
      glimpse()
    #> Rows: 20
    #> Columns: 2
    #> $ concept_id   <int> 72405, 75617, 78227, 80494, 80809, 4143463, 4153359, 4183…
    #> $ concept_name <chr> "Degenerative joint disease of shoulder region", "Degener…

### Search via non-standard

Now we will search the concept synonym table to identify concepts to include.

    oaCodes5 <- getCandidateCodes(
      cdm = cdm,
      keywords = "osteoarthritis",
      domains = "Condition",
      searchInSynonyms = FALSE,
      searchNonStandard = TRUE,
      exclude = c(
        "post-infection",
        "post-traumatic"
      ),
      includeDescendants = FALSE,
      includeAncestor = FALSE
    )

What new codes do we pick up?

    newCodes1To5 <- compareCodelists(oaCodes1, oaCodes5) %>%
      filter(codelist == "Only codelist 2") %>%
      select(-"codelist")

    newCodes1To5 %>%
      glimpse()
    #> Rows: 0
    #> Columns: 2
    #> $ concept_id   <int>
    #> $ concept_name <chr>

### Include ancestor

Now we include the direct ancestor of included terms.

    oaCodes8 <- getCandidateCodes(
      cdm = cdm,
      keywords = "osteoarthritis",
      domains = "Condition",
      searchInSynonyms = FALSE,
      searchNonStandard = FALSE,
      exclude = c(
        "post-infection",
        "post-traumatic"
      ),
      includeDescendants = FALSE,
      includeAncestor = TRUE
    )

What new codes do we pick up?

    newCodes1To8 <- compareCodelists(oaCodes1, oaCodes8) %>%
      filter(codelist == "Only codelist 2") %>%
      select(-"codelist")

    newCodes1To8 %>%
      glimpse()
    #> Rows: 99
    #> Columns: 2
    #> $ concept_id   <int> 72405, 73553, 75620, 75897, 76777, 78227, 80494, 81937, 4…
    #> $ concept_name <chr> "Degenerative joint disease of shoulder region", "Arthrop…