---
title: "Routes"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Routes}
  %\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 the route check 
All possible routes can be seen in athena. https://athena.ohdsi.org/search-terms/terms?vocabulary=SNOMED&invalidReason=Valid&domain=Route&page=1&pageSize=15&query=

```{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 = "route"
)
```

## Route Overall
This shows the routes of the drug records summarised on ingredient level.

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

| Column  | Description |
:------------- | :------------- |
ingredient_concept_id | Concept ID of ingredient. |
ingredient  | Name of drug ingredient. |
route_concept_id  | Concept ID of route |  
route_type  | Concept name for route |     
n_records | Number of records for ingredient 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. |


## Route by drug concept
This shows the route of the drug records on the drug concept level. The tables are identical to the overall just including two more columns at the beginning. \


| Column  | Description |
:------------- | :------------- |
drug_concept_id  | ID of the drug concept. |
drug  | Name of the drug concept. |

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