---
title: "DrugDuration"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{DrugDuration}
  %\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 duration check
```{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 = "exposureDuration"
)
```

## Drug exposure duration Overall
This shows the drug exposure duration of the drug records summarised on ingredient level. The drug exposure duration is estimated through (drug_exposure_end_date - drug_exposure_start_date + 1) for every individual drug exposure record. 

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

| Column  | Description |
:------------- | :------------- |
ingredient_concept_id | Concept ID of ingredient. |
ingredient  | Name of drug ingredient. |
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. |
n_non_negative_days  | Number of drug records with a duration of one day or more. |
n_negative_days  | Number of drug records with a negative duration (i.e. drug exposure start date after drug exposure end date). |
proportion_negative_days  | Proportion of drug records with a negative duration |
minimum_drug_exposure_days  | Minimum drug exposure duration |
q05_drug_exposure_days  | 5th quantile of drug exposure duration |
q10_drug_exposure_days  | 10th quantile of drug exposure duration |
q25_drug_exposure_days   | 25th quantile of drug exposure duration |   
median_drug_exposure_days  | Median drug exposure duration |
q75_drug_exposure_days  | 75th quantile of drug exposure duration |
q90_drug_exposure_days  | 90th quantile of drug exposure duration |
q95_drug_exposure_days  | 95th quantile of drug exposure duration |
maximum_drug_exposure_days  | Maximum drug exposure duration |
result_obscured | TRUE if count has been suppressed due to being below the minimum cell count, otherwise FALSE. |



## Drug exposure duration by drug concept
This shows the drug exposure duration on the drug concept level. The drug exposure duration is estimated through (drug_exposure_end_date - drug_exposure_start_date + 1) for every individual drug exposure record. 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$drugExposureDurationByConcept,
  rownames = FALSE
)
```