---
title: "MSF Outbreak Dictionaries"
output: 
  rmarkdown::html_vignette:
    toc: true
vignette: >
  %\VignetteIndexEntry{MSF outbreak dictionaries}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  echo = FALSE
)
```

There are four MSF outbreak dictionaries available:

 - Cholera/Acute watery diarrhea ("Cholera")
 - Meningitis ("Meningitis)
 - Measles/Rubella ("Measles")
 - Acute Jaundice Syndrome (often suspected to be Hepatitis E) ("AJS")

> You can read more about the outbreak dictionaries at <https://r4epis.netlify.com/outbreaks>

# Acute Jaundice Syndrome (AJS)

## Variables in the dictionary

The AJS dictionary contains definitions for `r nrow(epidict::msf_dict("AJS"))` variables:

```{r ajs, results="asis"}
library(epidict)
ajs <- msf_dict("AJS")
names_desc <- ajs[c("data_element_formname", "data_element_shortname", "data_element_description", "data_element_valuetype")]
DT::datatable(names_desc)
```

## Option codes

The dictionaries are exported using option codes that can be translated to
human-readable format. This table shows how they are translated.

```{r ajs_values, results = "asis"}
ajs_codes <- tidyr::unnest(ajs, cols = options)[c("data_element_shortname", "data_element_valuetype", "option_code", "option_name", "option_order_in_set")]
DT::datatable(ajs_codes)
```

# Cholera

## Variables in the dictionary

The Cholera dictionary contains definitions for `r nrow(epidict::msf_dict("Cholera"))` variables:

```{r cholera, results="asis"}
library(epidict)
cholera <- msf_dict("Cholera")
names_desc <- cholera[c("data_element_formname", "data_element_shortname", "data_element_description", "data_element_valuetype")]
DT::datatable(names_desc)
```

## Option codes

The dictionaries are exported using option codes that can be translated to
human-readable format. This table shows how they are translated.

```{r cholera_values, results = "asis"}
cholera_codes <- tidyr::unnest(cholera, cols = options)[c("data_element_shortname", "data_element_valuetype", "option_code", "option_name", "option_order_in_set")]
DT::datatable(cholera_codes)
```


# Measles

## Variables in the dictionary

The Measles dictionary contains definitions for `r nrow(epidict::msf_dict("Measles"))` variables:

```{r measles, results="asis"}
library(epidict)
measles <- msf_dict("Measles")
names_desc <- measles[c("data_element_formname", "data_element_shortname", "data_element_description", "data_element_valuetype")]
DT::datatable(names_desc)
```

## Option codes

The dictionaries are exported using option codes that can be translated to
human-readable format. This table shows how they are translated.

```{r measles_values, results = "asis"}
measles_codes <- tidyr::unnest(measles, cols = options)[c("data_element_shortname", "data_element_valuetype", "option_code", "option_name", "option_order_in_set")]
DT::datatable(measles_codes)
```

# Meningitis

## Variables in the dictionary

The Meningitis dictionary contains definitions for `r nrow(epidict::msf_dict("Meningitis"))` variables:

```{r meningitis, results="asis"}
library(epidict)
meningitis <- msf_dict("Meningitis")
names_desc <- meningitis[c("data_element_formname", "data_element_shortname", "data_element_description", "data_element_valuetype")]
DT::datatable(names_desc)
```

## Option codes

The dictionaries are exported using option codes that can be translated to
human-readable format. This table shows how they are translated.

```{r meningitis_values, results = "asis"}
meningitis_codes <- tidyr::unnest(meningitis, cols = options)[c("data_element_shortname", "data_element_valuetype", "option_code", "option_name", "option_order_in_set")]
DT::datatable(meningitis_codes)
```


# Exploring the dictionaries

You can explore the excel-formatted dictionaries with `browseURL(system.file("extdata", "MSF-outbreak-dict.xlsx", package = "epidict"))`, but treat it as read-only.