---
title: "Drug Sig"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{DrugSig}
  %\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 Sig 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 = "sig"
)
```

## Sig 
This shows the sig(netur) of the drug records summarised on ingredient level. The signetur of a prescription contains the information of when, how often, and how much of a drug a patient shall use. 

```{r}
datatable(acetaminophen_checks$drugSig,
  rownames = FALSE
)
```
| Column  | Description |
:------------- | :------------- |
ingredient_concept_id | Concept ID of ingredient. |
ingredient  | Name of drug ingredient. |
sig | The signetur of a prescription. The sig is usually only available for prescription and often contains free text or only semi-standardised information. |  
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. |

## Sig by concept
This shows the sig(netur) on the drug concept level. The signetur of a prescription contains the information of when, how often, and how much of a drug a patient shall use. 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$drugSigByConcept,
  rownames = FALSE
)
```