---
title: "Drug Source Concepts"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{DrugSourceConcepts}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
options(rmarkdown.html_vignette.check_title = FALSE)
knitr::opts_chunk$set(
  warning = FALSE,
  message = FALSE,
  collapse = TRUE,
  comment = "#>"
)
```

## Run checks 
```{r setup}
library(DrugExposureDiagnostics)
library(dplyr)
library(DT)

# acetaminophen concept id is 1125315
acetaminophen <- 1125315
cdm <- mockDrugExposure()
acetaminophen_checks <- executeChecks(
  cdm = cdm,
  ingredients = acetaminophen,
  checks = "sourceConcept"
)
```

## Drug Source by Concept
This shows the drug source concepts next to the mapped drug concepts. This check only exists "byConcept" to depict the required detail. Do not get confused by the name of the object being "Overall". 

```{r}
datatable(acetaminophen_checks$drugSourceConceptsOverall,
  rownames = FALSE
)
```

| Column  | Description |
:------------- | :------------- |
ingredient_concept_id | Concept ID of ingredient. |
ingredient  | Name of drug ingredient. |
drug_concept_id  | ID of the drug concept. |
drug  | Name of the drug concept. |
drug_source_concept_id  | Concept ID of source concept |  
drug_source_type | Concept name for source concept |     
drug_source_value | Concept code of source concept in the original vocabulary |   
n_records | Number of records for drug concept. If n_records is the same as n_sample this means that there are more records but the number was cut at the pre-specified sample number for efficiency reasons. |
n_sample | The pre-specified maximum sample. If n_records is smaller than the sample it means that sampling was ignored because the total number of records was already too small. |
n_person | Number of individuals. |
result_obscured | TRUE if count has been suppressed due to being below the minimum cell count, otherwise FALSE. |