Introduction To DrugExposureDiagnostics

library(DrugExposureDiagnostics)
library(CDMConnector)
library(dplyr)
library(DT)

First, connect to the database.

cdm <- getEunomiaCdm()

Check for single ingredient.

In the DrugExposureDiagnostics package, all the diagnostics are conducted on ingredient level. We will use “acetaminophen” as an example. Here is a brief look at this ingredient.

Property Value
Concept Name acetaminophen
Domain ID Drug
Concept Class ID Ingredient
Vocabulary ID RxNorm
Concept ID 1125315
Concept code 161
Validity Valid
Concept Standard
Valid start 01-Jan-1970
Valid end 31-Dec-2099

We can run all available checks at the same time using the ´executeChecks()´ function. This will return a list which contains the results of each check.

executeChecks(cdm,
              ingredients = c(1125315), 
              checks = c("missing", "exposureDuration", "type", "route","sourceConcept", "daysSupply", "verbatimEndDate","dailyDose", "sig", "quantity", "histogram"), 
              minCellCount = 5,
              sample = 1000000,
              verbose = FALSE
)

Thecdm is the database reference of the OMOP CDM using the CDMConnector package.
The ingredient is the concept_id of ingredients of interests, by default it is 1125315 for acetaminophen.
checks allows to select the checks to be executed, by default, all the checks will be run.
sample is the number of samples, by default, 1 million drug record samples will be used.
The minCellCount is minimum number of events to report, numbers lower than this will be obscured.

all_checks<-executeChecks(cdm, ingredients = 1125315)
#> population after earliestStartDate smaller than sample, ignoring date for sampling

We can then check what results available from ´executeChecks()´ by

names(all_checks)
#>  [1] "conceptSummary"                "missingValuesOverall"         
#>  [3] "missingValuesByConcept"        "drugExposureDurationOverall"  
#>  [5] "drugExposureDurationByConcept" "drugTypesOverall"             
#>  [7] "drugTypesByConcept"            "drugRoutesOverall"            
#>  [9] "drugRoutesByConcept"           "drugSourceConceptsOverall"    
#> [11] "drugSourceConceptsByConcept"   "drugDaysSupply"               
#> [13] "drugDaysSupplyByConcept"       "drugVerbatimEndDate"          
#> [15] "drugVerbatimEndDateByConcept"  "drugDose"                     
#> [17] "drugDoseByConcept"             "drugSig"                      
#> [19] "drugSigByConcept"              "drugQuantity"                 
#> [21] "drugQuantityByConcept"         "drugIngredientOverview"       
#> [23] "drugIngredientPresence"        "drugDaysSupplyHistogram"      
#> [25] "drugQuantityHistogram"         "drugDurationHistogram"        
#> [27] "diagnostics_summary"

Let’s take a look at the results. ingredientConcepts contains information on the concept ids that are used in the database for a given ingredient. So in the case of acetaminophen, the following drugs contain the acetaminophen as an ingredient.

datatable(all_checks$ingredientConcepts,
  rownames = FALSE
)

After running the checks, we can write the CSV files into a zip file to disk using the writeResultToDisk() function.

writeResultToDisk(all_checks,
                  databaseId = "your_database_id", 
                  outputFolder = "output_folder")