inst/doc/a04_GenerateVocabularyBasedCodelist.R

In CodelistGenerator: Identify Relevant Clinical Codes and Evaluate Their Use

## ----include = FALSE----------------------------------------------------------
NOT_CRAN <- identical(tolower(Sys.getenv("NOT_CRAN")), "true")

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  eval = NOT_CRAN
)

CDMConnector::requireEunomia("synpuf-1k", "5.3")

## ----message=FALSE, warning=FALSE---------------------------------------------
#  library(DBI)
#  library(duckdb)
#  library(dplyr)
#  library(CDMConnector)
#  library(CodelistGenerator)
#  
#  # Connect to the database and create the cdm object
#  con <- dbConnect(duckdb(),
#                   eunomiaDir("synpuf-1k", "5.3"))
#  cdm <- cdmFromCon(con = con,
#                    cdmName = "Eunomia Synpuf",
#                    cdmSchema = "main",
#                    writeSchema = "main",
#                    achillesSchema = "main")

## -----------------------------------------------------------------------------
#  availableIngredients(cdm) |> glimpse()

## -----------------------------------------------------------------------------
#  acetaminophen_codes <- getDrugIngredientCodes(
#    cdm = cdm,
#    name = c("acetaminophen")
#  )
#  
#  acetaminophen_codes

## -----------------------------------------------------------------------------
#  acetaminophen_codes <- getDrugIngredientCodes(
#    cdm = cdm,
#    name = 1125315
#  )
#  
#  acetaminophen_codes

## -----------------------------------------------------------------------------
#  acetaminophen_two_or_more_ingredients <- getDrugIngredientCodes(
#    cdm = cdm,
#    name = "acetaminophen",
#    ingredientRange = c(2, Inf),
#    type = "codelist_with_details"
#  )
#  
#  acetaminophen_two_or_more_ingredients
#  
#  acetaminophen_two_or_more_ingredients[[1]] |>
#    pull("concept_name") |>
#    head(n = 5) # Only the first five will be shown

## -----------------------------------------------------------------------------
#  acetaminophen_one_ingredient <- getDrugIngredientCodes(
#    cdm = cdm,
#    name = "acetaminophen",
#    ingredientRange = c(1, 1),
#    type = "codelist_with_details"
#  )
#  
#  acetaminophen_one_ingredient
#  
#  acetaminophen_one_ingredient[[1]] |>
#    pull("concept_name") |>
#    head(n = 5) # Only the first five will be shown

## -----------------------------------------------------------------------------
#  getDoseForm(cdm) |> glimpse()

## -----------------------------------------------------------------------------
#  acetaminophen_injections <- getDrugIngredientCodes(
#    cdm = cdm,
#    name = "acetaminophen",
#    doseForm = "injection",
#    type = "codelist_with_details"
#  )
#  
#  acetaminophen_injections[[1]] |>
#    pull("concept_name") |>
#    head(n = 5)

## -----------------------------------------------------------------------------
#  getDoseUnit(cdm) |> glimpse()

## -----------------------------------------------------------------------------
#  acetaminophen_miligram <- getDrugIngredientCodes(
#    cdm = cdm,
#    name = "acetaminophen",
#    doseUnit = "milligram",
#    type = "codelist_with_details"
#  )
#  
#  acetaminophen_miligram[[1]] |>
#    pull("concept_name") |>
#    head(n = 5)

## -----------------------------------------------------------------------------
#  getRouteCategories(cdm) |> glimpse()

## -----------------------------------------------------------------------------
#  acetaminophen_inhalable <- getDrugIngredientCodes(
#    cdm = cdm,
#    name = "acetaminophen",
#    routeCategory = "inhalable",
#    type = "codelist_with_details"
#  )
#  
#  acetaminophen_inhalable[[1]] |>
#    pull("concept_name") |>
#    head(n = 5)

## -----------------------------------------------------------------------------
#  acetaminophen_heparin_codes <- getDrugIngredientCodes(
#    cdm = cdm,
#    name = c("acetaminophen", "heparin")
#    )
#  
#  acetaminophen_heparin_codes

## -----------------------------------------------------------------------------
#  availableATC(cdm, level = c("ATC 1st")) |> glimpse()
#  availableATC(cdm, level = c("ATC 2nd")) |> glimpse()
#  availableATC(cdm, level = c("ATC 3rd")) |> glimpse()
#  availableATC(cdm, level = c("ATC 4th")) |> glimpse()
#  availableATC(cdm, level = c("ATC 5th")) |> glimpse()

## -----------------------------------------------------------------------------
#  atc_codelist <- getATCCodes(
#    cdm = cdm,
#    level = "ATC 1st",
#    name = "alimentary tract and metabolism"
#  )
#  
#  atc_codelist