README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%",
  eval = TRUE,
  warning = FALSE,
  message = FALSE
)
```

# epishiny

<!-- badges: start -->
[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
<!-- badges: end -->

__Please note this package is in alpha stage of development and not yet suitable for use in production as the API is likely to change.__

## Motivation

Interactive web-based data visualisations and dashboards are an increasingly common method 
of monitoring infectious disease outbreaks. Whilst R is now a commonly used tool for analysis 
and data visualisation in epidemiology, epidemiologists will often lack the knowledge required 
to be able to produce interactive dashboards directly from within their R workflows, 
resulting in external propriatory software being used instead.

`epishiny` aims to bridge this gap by providing simple functions that produce engaging, 
feature-rich interactive visualisations and dashboards from epidemiological data 
using R's [`shiny`](https://shiny.posit.co/) web-framework.

## Installation

You can install the development version of epishiny from GitHub with either the [pak](https://pak.r-lib.org/) or [remotes](https://remotes.r-lib.org/) package:

``` r
# install.packages("pak")
pak::pkg_install("epicentre-msf/epishiny", dependencies = TRUE)

# install.packages("remotes")
remotes::install_github("epicentre-msf/epishiny", dependencies = TRUE)
```

```{r include=FALSE}
# set to TRUE to take new app screenshots
update_imgs <- FALSE
```

## Demo Dashboard

Launch a demo dashboard with examples of every epishiny module with the `launch_demo_dashboard()` function.
The code for this dashboard can be found in [inst/examples/demo](https://github.com/epicentre-msf/epishiny/tree/main/inst/examples/demo)
of the package repository.

```{r include=FALSE}
if (update_imgs) {
  require("shinytest2")
  pkgload::load_all()

  app_path <- here::here("inst/examples/demo")

  app <- AppDriver$new(app_path, width = 1600, height = 900)

  img_path <- tempfile(fileext = ".png")
  app$get_screenshot(file = img_path, delay = 1)
  fs::file_copy(img_path, "man/figures/dashboard.png", overwrite = TRUE)

  app$stop()
}
```

```{r echo=FALSE}
knitr::include_graphics("man/figures/dashboard.png")
```

## Tutorials

See the articles below on the package website to get started using `epishiny` with your data.

* [Getting started](https://epicentre-msf.github.io/epishiny/articles/epishiny.html) 
* Use cases
  - [Linelist data](https://epicentre-msf.github.io/epishiny/articles/linelist_data.html) 
  - [Aggregated data](https://epicentre-msf.github.io/epishiny/articles/aggregated_data.html) 

## Contributions

Contributions are welcome. See the [contributing article](https://epicentre-msf.github.io/epishiny/articles/contributing.html) 
on the package website for details on how to contribute to `epishiny`.

```{r include=FALSE}
if (update_imgs) {
  require("shinytest2")
  # time module screenshot
  app_path <- here::here("inst/examples/docs/time")
  app <- AppDriver$new(app_path, width = 1000, height = 600)
  img_path <- tempfile(fileext = ".png")
  app$get_screenshot(file = img_path, delay = 1)
  fs::file_copy(img_path, "man/figures/time.png", overwrite = TRUE)
  app$stop()
  # place module screenshot
  app_path <- here::here("inst/examples/docs/place")
  app <- AppDriver$new(app_path, width = 1000, height = 600)
  img_path <- tempfile(fileext = ".png")
  app$get_screenshot(file = img_path, delay = 1)
  fs::file_copy(img_path, "man/figures/place.png", overwrite = TRUE)
  app$stop()
  # person module screenshot
  app_path <- here::here("inst/examples/docs/person")
  app <- AppDriver$new(app_path, width = 1000, height = 600)
  img_path <- tempfile(fileext = ".png")
  app$get_screenshot(file = img_path, delay = 1)
  fs::file_copy(img_path, "man/figures/person.png", overwrite = TRUE)
  app$stop()
}
```