### Install CodelistGenerator Development Version

Source: https://github.com/darwin-eu/codelistgenerator/blob/main/README.md

Install the latest development version of CodelistGenerator from GitHub using the remotes package.

```r
install.packages("remotes")
remotes::install_github("darwin-eu/CodelistGenerator")
```

--------------------------------

### Install CodelistGenerator from CRAN

Source: https://github.com/darwin-eu/codelistgenerator/blob/main/README.md

Use this command to install the stable version of the CodelistGenerator package from CRAN.

```r
install.packages("CodelistGenerator")
```

--------------------------------

### Get Vocabulary Version

Source: https://github.com/darwin-eu/codelistgenerator/blob/main/README.md

Retrieve the version of the OMOP CDM vocabulary used in the connected CDM database.

```r
vocabularyVersion(cdm = cdm)
```

--------------------------------

### Get Candidate Codes for Asthma (Excluding Childhood)

Source: https://github.com/darwin-eu/codelistgenerator/blob/main/README.md

Refine the search for 'asthma' by excluding concepts containing 'childhood'. This helps in focusing the search on relevant conditions.

```r
asthma_codes2 <- getCandidateCodes(
  cdm = cdm,
  keywords = "asthma",
  exclude = "childhood",
  domains = "Condition"
) 
asthma_codes2 |> 
  glimpse()
```

--------------------------------

### Get Drug Ingredient Codes

Source: https://github.com/darwin-eu/codelistgenerator/blob/main/README.md

Extract concept IDs for specified drug ingredients (e.g., aspirin, diclofenac) from the OMOP CDM vocabulary. The output is a list where each element contains the concept IDs for a given ingredient.

```r
ing <- getDrugIngredientCodes(cdm = cdm, 
                       name = c("aspirin", "diclofenac"),
                       nameStyle = "{concept_name}")
ing$aspirin
ing$diclofenac
```

--------------------------------

### Get Candidate Codes for Asthma (Initial Search)

Source: https://github.com/darwin-eu/codelistgenerator/blob/main/README.md

Perform an initial systematic search for concepts related to 'asthma' within the 'Condition' domain. The results include concept ID, name, domain, vocabulary, and standard concept status.

```r
asthma_codes1 <- getCandidateCodes(
  cdm = cdm,
  keywords = "asthma",
  domains = "Condition"
) 
asthma_codes1 |> 
  glimpse()
```

--------------------------------

### Connect to Eunomia CDM Database

Source: https://github.com/darwin-eu/codelistgenerator/blob/main/README.md

Connect to the Eunomia dataset using duckdb and create a CDMConnector object. Ensure Eunomia is required first.

```r
requireEunomia()
db <- DBI::dbConnect(duckdb::duckdb(), dbdir = eunomiaDir())
cdm <- cdmFromCon(db, 
                  cdmSchema = "main", 
                  writeSchema = "main", 
                  writePrefix = "cg_")
```

--------------------------------

### Load Required Libraries

Source: https://github.com/darwin-eu/codelistgenerator/blob/main/README.md

Load dplyr, CDMConnector, and CodelistGenerator libraries for data manipulation and OMOP CDM operations.

```r
library(dplyr)
library(CDMConnector)
library(CodelistGenerator)
```

--------------------------------

### Summarise Code Use with Flextable

Source: https://github.com/darwin-eu/codelistgenerator/blob/main/README.md

Summarize the usage of a codelist (e.g., asthma codes) within the CDM and display the results using a styled flextable. This requires the flextable package.

```r
library(flextable)
asthma_code_use <- summariseCodeUse(list("asthma" = asthma_codes1$concept_id) |> 
                                           newCodelist(),
  cdm = cdm
)
tableCodeUse(asthma_code_use, type = "flextable", style = "darwin")
```

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