# 43 Dashboards with Shiny

Dashboards are often a great way to share results from analyses with others. Producing a dashboard with shiny requires a relatively advanced knowledge of the R language, but offers incredible customization and possibilities.

It is recommended that someone learning dashboards with shiny has good knowledge of data transformation and visualisation, and is comfortable debugging code, and writing functions. Working with dashboards is not intuitive when you’re starting, and is difficult to understand at times, but is a great skill to learn and gets much easier with practice!

This page will give a short overview of how to make dashboards with shiny and its extensions. For an alternative method of making dashboards that is faster, easier, but perhaps less customizeable, see the page on flextable (Dashboards with R Markdown).

## 43.1 Preparation

In this handbook we emphasize p_load() from pacman, which installs the package if necessary and loads it for use. You can also load installed packages with library() from base R. See the page on R basics for more information on R packages.

We begin by installing the shiny R package:

pacman::p_load("shiny")

### Import data

If you try to re-construct the app using these files, please be aware of the R project folder structure that is created over the course of the demonstration (e.g. folders for “data” and for “funcs”).

## 43.2 The structure of a shiny app

### Basic file structures

To understand shiny, we first need to understand how the file structure of an app works! We should make a brand new directory before we start. This can actually be made easier by choosing New project in Rstudio, and choosing Shiny Web Application. This will create the basic structure of a shiny app for you.

When opening this project, you’ll notice there is a .R file already present called app.R. It is essential that we have one of two basic file structures:

1. One file called app.R, or
2. Two files, one called ui.R and the other server.R

In this page, we will use the first approach of having one file called app.R. Here is an example script:

# an example of app.R

library(shiny)

ui <- fluidPage(

# Application title
titlePanel("My app"),

# Sidebar with a slider input widget
sidebarLayout(
sidebarPanel(
sliderInput("input_1")
),

# Show a plot
mainPanel(
plotOutput("my_plot")
)
)
)

# Define server logic required to draw a histogram
server <- function(input, output) {

plot_1 <- reactive({
plot_func(param = input_1)
})

output$my_plot <- renderPlot({ plot_1() }) } # Run the application shinyApp(ui = ui, server = server) If you open this file, you’ll notice that two objects are defined - one called ui and another called server. These objects must be defined in every shiny app and are central to the structure of the app itself! In fact, the only difference between the two file structures described above is that in structure 1, both ui and server are defined in one file, whereas in structure 2 they are defined in separate files. Note: we can also (and we should if we have a larger app) have other .R files in our structure that we can source() into our app. ### The server and the ui We next need to understand what the server and ui objects actually do. Put simply, these are two objects that are interacting with each other whenever the user interacts with the shiny app. The UI element of a shiny app is, on a basic level, R code that creates an HTML interface. This means everything that is displayed in the UI of an app. This generally includes: • “Widgets” - dropdown menus, check boxes, sliders, etc that can be interacted with by the user • Plots, tables, etc - outputs that are generated with R code • Navigation aspects of an app - tabs, panes, etc. • Generic text, hyperlinks, etc • HTML and CSS elements (addressed later) The most important thing to understand about the UI is that it receives inputs from the user and displays outputs from the server. There is no active code running in the ui at any time - all changes seen in the UI are passed through the server (more or less). So we have to make our plots, downloads, etc in the server The server of the shiny app is where all code is being run once the app starts up. The way this works is a little confusing. The server function will effectively react to the user interfacing with the UI, and run chunks of code in response. If things change in the server, these will be passed back up to the ui, where the changes can be seen. Importantly, the code in the server will be executed non-consecutively (or it’s best to think of it this way). Basically, whenever a ui input affects a chunk of code in the server, it will run automatically, and that output will be produced and displayed. This all probably sounds very abstract for now, so we’ll have to dive into some examples to get a clear idea of how this actually works. ### Before you start to build an app Before you begin to build an app, its immensely helpful to know what you want to build. Since your UI will be written in code, you can’t really visualise what you’re building unless you are aiming for something specific. For this reason, it is immensely helpful to look at lots of examples of shiny apps to get an idea of what you can make - even better if you can look at the source code behind these apps! Some great resources for this are: Once you get an idea for what is possible, it’s also helpful to map out what you want yours to look like - you can do this on paper or in any drawing software (PowerPoint, MS paint, etc.). It’s helpful to start simple for your first app! There’s also no shame in using code you find online of a nice app as a template for your work - its much easier than building something from scratch! ## 43.3 Building a UI When building our app, its easier to work on the UI first so we can see what we’re making, and not risk the app failing because of any server errors. As mentioned previously, its often good to use a template when working on the UI. There are a number of standard layouts that can be used with shiny that are available from the base shiny package, but it’s worth noting that there are also a number of package extensions such as shinydashboard. We’ll use an example from base shiny to start with. A shiny UI is generally defined as a series of nested functions, in the following order 1. A function defining the general layout (the most basic is fluidPage(), but more are available) 2. Panels within the layout such as: • a sidebar (sidebarPanel()) • a “main” panel (mainPanel()) • a tab (tabPanel()) • a generic “column” (column()) 3. Widgets and outputs - these can confer inputs to the server (widgets) or outputs from the server (outputs) • Widgets generally are styled as xxxInput() e.g. selectInput() • Outputs are generally styled as xxxOutput() e.g. plotOutput() It’s worth stating again that these can’t be visualised easily in an abstract way, so it’s best to look at an example! Lets consider making a basic app that visualises our malaria facility count data by district. This data has a lot of differnet parameters, so it would be great if the end user could apply some filters to see the data by age group/district as they see fit! We can use a very simple shiny layout to start - the sidebar layout. This is a layout where widgets are placed in a sidebar on the left, and the plot is placed on the right. Lets plan our app - we can start with a selector that lets us choose the district where we want to visualise data, and another to let us visualise the age group we are interested in. We’ll aim to use these filters to show an epicurve that reflects these parameters. So for this we need: 1. Two dropdown menus that let us choose the district we want, and the age group we’re interested in. 2. An area where we can show our resulting epicurve. This might look something like this: library(shiny) ui <- fluidPage( titlePanel("Malaria facility visualisation app"), sidebarLayout( sidebarPanel( # selector for district selectInput( inputId = "select_district", label = "Select district", choices = c( "All", "Spring", "Bolo", "Dingo", "Barnard" ), selected = "All", multiple = TRUE ), # selector for age group selectInput( inputId = "select_agegroup", label = "Select age group", choices = c( "All ages" = "malaria_tot", "0-4 yrs" = "malaria_rdt_0-4", "5-14 yrs" = "malaria_rdt_5-14", "15+ yrs" = "malaria_rdt_15" ), selected = "All", multiple = FALSE ) ), mainPanel( # epicurve goes here plotOutput("malaria_epicurve") ) ) ) When app.R is run with the above UI code (with no active code in the server portion of app.R) the layout appears looking like this - note that there will be no plot if there is no server to render it, but our inputs are working! This is a good opportunity to discuss how widgets work - note that each widget is accepting an inputId, a label, and a series of other options that are specific to the widget type. This inputId is extremely important - these are the IDs that are used to pass information from the UI to the server. For this reason, they must be unique. You should make an effort to name them something sensible, and specific to what they are interacting with in cases of larger apps. You should read documentation carefully for full details on what each of these widgets do. Widgets will pass specific types of data to the server depending on the widget type, and this needs to be fully understood. For example, selectInput() will pass a character type to the server: • If we select Spring for the first widget here, it will pass the character object "Spring" to the server. • If we select two items from the dropdown menu, they will come through as a character vector (e.g. c("Spring", "Bolo")). Other widgets will pass different types of object to the server! For example: • numericInput() will pass a numeric type object to the server • checkboxInput() will pass a logical type object to the server (TRUE or FALSE) It’s also worth noting the named vector we used for the age data here. For many widgets, using a named vector as the choices will display the names of the vector as the display choices, but pass the selected value from the vector to the server. I.e. here someone can select “15+” from the drop-down menu, and the UI will pass "malaria_rdt_15" to the server - which happens to be the name of the column we’re interested in! There are loads of widgets that you can use to do lots of things with your app. Widgets also allow you to upload files into your app, and download outputs. There are also some excellent shiny extensions that give you access to more widgets than base shiny - the shinyWidgets package is a great example of this. To look at some examples you can look at the following links: ## 43.4 Loading data into our app The next step in our app development is getting the server up and running. To do this however, we need to get some data into our app, and figure out all the calculations we’re going to do. A shiny app is not straightforward to debug, as it’s often not clear where errors are coming from, so it’s ideal to get all our data processing and visualisation code working before we start making the server itself. So given we want to make an app that shows epi curves that change based on user input, we should think about what code we would need to run this in a normal R script. We’ll need to: 1. Load our packages 2. Load our data 3. Transform our data 4. Develop a function to visualise our data based on user inputs This list is pretty straightforward, and shouldn’t be too hard to do. It’s now important to think about which parts of this process need to be done only once and which parts need to run in response to user inputs. This is because shiny apps generally run some code before running, which is only performed once. It will help our app’s performance if as much of our code can be moved to this section. For this example, we only need to load our data/packages and do basic transformations once, so we can put that code outside the server. This means the only thing we’ll need in the server is the code to visualise our data. Lets develop all of these componenets in a script first. However, since we’re visualising our data with a function, we can also put the code for the function outside the server so our function is in the environment when the app runs! First lets load our data. Since we’re working with a new project, and we want to make it clean, we can create a new directory called data, and add our malaria data in there. We can run this code below in a testing script we will eventually delete when we clean up the structure of our app. pacman::p_load("tidyverse", "lubridate") # read data malaria_data <- rio::import(here::here("data", "malaria_facility_count_data.rds")) %>% as_tibble() print(malaria_data) ## # A tibble: 3,038 x 10 ## location_name data_date submitted_date Province District malaria_rdt_0-4 malaria_rdt_5-14 malaria_rdt_15 malaria_tot newid ## <chr> <date> <date> <chr> <chr> <int> <int> <int> <int> <int> ## 1 Facility 1 2020-08-11 2020-08-12 North Spring 11 12 23 46 1 ## 2 Facility 2 2020-08-11 2020-08-12 North Bolo 11 10 5 26 2 ## 3 Facility 3 2020-08-11 2020-08-12 North Dingo 8 5 5 18 3 ## 4 Facility 4 2020-08-11 2020-08-12 North Bolo 16 16 17 49 4 ## 5 Facility 5 2020-08-11 2020-08-12 North Bolo 9 2 6 17 5 ## 6 Facility 6 2020-08-11 2020-08-12 North Dingo 3 1 4 8 6 ## 7 Facility 6 2020-08-10 2020-08-12 North Dingo 4 0 3 7 6 ## 8 Facility 5 2020-08-10 2020-08-12 North Bolo 15 14 13 42 5 ## 9 Facility 5 2020-08-09 2020-08-12 North Bolo 11 11 13 35 5 ## 10 Facility 5 2020-08-08 2020-08-12 North Bolo 19 15 15 49 5 ## # ... with 3,028 more rows It will be easier to work with this data if we use tidy data standards, so we should also transform into a longer data format, where age group is a column, and cases is another column. We can do this easily using what we’ve learned in the Pivoting data page. malaria_data <- malaria_data %>% select(-newid) %>% pivot_longer(cols = starts_with("malaria_"), names_to = "age_group", values_to = "cases_reported") print(malaria_data) ## # A tibble: 12,152 x 7 ## location_name data_date submitted_date Province District age_group cases_reported ## <chr> <date> <date> <chr> <chr> <chr> <int> ## 1 Facility 1 2020-08-11 2020-08-12 North Spring malaria_rdt_0-4 11 ## 2 Facility 1 2020-08-11 2020-08-12 North Spring malaria_rdt_5-14 12 ## 3 Facility 1 2020-08-11 2020-08-12 North Spring malaria_rdt_15 23 ## 4 Facility 1 2020-08-11 2020-08-12 North Spring malaria_tot 46 ## 5 Facility 2 2020-08-11 2020-08-12 North Bolo malaria_rdt_0-4 11 ## 6 Facility 2 2020-08-11 2020-08-12 North Bolo malaria_rdt_5-14 10 ## 7 Facility 2 2020-08-11 2020-08-12 North Bolo malaria_rdt_15 5 ## 8 Facility 2 2020-08-11 2020-08-12 North Bolo malaria_tot 26 ## 9 Facility 3 2020-08-11 2020-08-12 North Dingo malaria_rdt_0-4 8 ## 10 Facility 3 2020-08-11 2020-08-12 North Dingo malaria_rdt_5-14 5 ## # ... with 12,142 more rows And with that we’ve finished preparing our data! This crosses items 1, 2, and 3 off our list of things to develop for our “testing R script”. The last, and most difficult task will be building a function to produce an epicurve based on user defined parameters. As mentioned previously, it’s highly recommended that anyone learning shiny first look at the section on functional programming (Writing functions) to understand how this works! When defining our function, it might be hard to think about what parameters we want to include. For functional programming with shiny, every relevent parameter will generally have a widget associated with it, so thinking about this is usually quite easy! For example in our current app, we want to be able to filter by district, and have a widget for this, so we can add a district parameter to reflect this. We don’t have any app functionality to filter by facility (for now), so we don’t need to add this as a parameter. Lets start by making a function with three parameters: 1. The core dataset 2. The district of choice 3. The age group of choice plot_epicurve <- function(data, district = "All", agegroup = "malaria_tot") { if (!("All" %in% district)) { data <- data %>% filter(District %in% district) plot_title_district <- stringr::str_glue("{paste0(district, collapse = ', ')} districts") } else { plot_title_district <- "all districts" } # if no remaining data, return NULL if (nrow(data) == 0) { return(NULL) } data <- data %>% filter(age_group == agegroup) # if no remaining data, return NULL if (nrow(data) == 0) { return(NULL) } if (agegroup == "malaria_tot") { agegroup_title <- "All ages" } else { agegroup_title <- stringr::str_glue("{str_remove(agegroup, 'malaria_rdt')} years") } ggplot(data, aes(x = data_date, y = cases_reported)) + geom_col(width = 1, fill = "darkred") + theme_minimal() + labs( x = "date", y = "number of cases", title = stringr::str_glue("Malaria cases - {plot_title_district}"), subtitle = agegroup_title ) } We won’t go into great detail about this function, as it’s relatively simple in how it works. One thing to note however, is we handle errors by returning NULL when it would otherwise give an error. This is because when a shiny server produces a NULL object instead of a plot object, nothing will be shown in the ui! This is important, as otherwise errors will often cause your app to stop working. Another thing to note is the use of the %in% operator when evaluating the district input. As mentioned above, this could arrive as a character vector with multiple values, so using %in% is more flexible than say, ==. Let’s test our function! plot_epicurve(malaria_data, district = "Bolo", agegroup = "malaria_rdt_0-4") With our function working, we now have to understand how this all is going to fit into our shiny app. We mentioned the concept of startup code before, but lets look at how we can actually incorporate this into the structure of our app. There are two ways we can do this! 1. Put this code in your app.R file at the start of the script (above the UI), or 2. Create a new file in your app’s directory called global.R, and put the startup code in this file. It’s worth noting at this point that it’s generally easier, especially with bigger apps, to use the second file structure, as it lets you separate your file structure in a simple way. Lets fully develop a this global.R script now. Here is what it could look like: # global.R script pacman::p_load("tidyverse", "lubridate", "shiny") # read data malaria_data <- rio::import(here::here("data", "malaria_facility_count_data.rds")) %>% as_tibble() # clean data and pivot longer malaria_data <- malaria_data %>% select(-newid) %>% pivot_longer(cols = starts_with("malaria_"), names_to = "age_group", values_to = "cases_reported") # define plotting function plot_epicurve <- function(data, district = "All", agegroup = "malaria_tot") { # create plot title if (!("All" %in% district)) { data <- data %>% filter(District %in% district) plot_title_district <- stringr::str_glue("{paste0(district, collapse = ', ')} districts") } else { plot_title_district <- "all districts" } # if no remaining data, return NULL if (nrow(data) == 0) { return(NULL) } # filter to age group data <- data %>% filter(age_group == agegroup) # if no remaining data, return NULL if (nrow(data) == 0) { return(NULL) } if (agegroup == "malaria_tot") { agegroup_title <- "All ages" } else { agegroup_title <- stringr::str_glue("{str_remove(agegroup, 'malaria_rdt')} years") } ggplot(data, aes(x = data_date, y = cases_reported)) + geom_col(width = 1, fill = "darkred") + theme_minimal() + labs( x = "date", y = "number of cases", title = stringr::str_glue("Malaria cases - {plot_title_district}"), subtitle = agegroup_title ) } Easy! One great feature of shiny is that it will understand what files named app.R, server.R, ui.R, and global.R are for, so there is no need to connect them to each other via any code. So just by having this code in global.R in the directory it will run before we start our app!. We should also note that it would improve our app’s organisation if we moved the plotting function to its own file - this will be especially helpful as apps become larger. To do this, we could make another directory called funcs, and put this function in as a file called plot_epicurve.R. We could then read this function in via the following command in global.R source(here("funcs", "plot_epicurve.R"), local = TRUE) Note that you should always specify local = TRUE in shiny apps, since it will affect sourcing when/if the app is published on a server. ## 43.5 Developing an app server Now that we have most of our code, we just have to develop our server. This is the final piece of our app, and is probably the hardest to understand. The server is a large R function, but its helpful to think of it as a series of smaller functions, or tasks that the app can perform. It’s important to understand that these functions are not executed in a linear order. There is an order to them, but it’s not fully necessary to understand when starting out with shiny. At a very basic level, these tasks or functions will activate when there is a change in user inputs that affects them, unless the developer has set them up so they behave differently. Again, this is all quite abstract, but lets first go through the three basic types of shiny objects 1. Reactive sources - this is another term for user inputs. The shiny server has access to the outputs from the UI through the widgets we’ve programmed. Every time the values for these are changed, this is passed down to the server. 2. Reactive conductors - these are objects that exist only inside the shiny server. We don’t actually need these for simple apps, but they produce objects that can only be seen inside the server, and used in other operations. They generally depend on reactive sources. 3. Endpoints - these are outputs that are passed from the server to the UI. In our example, this would be the epi curve we are producing. With this in mind lets construct our server step-by-step. We’ll show our UI code again here just for reference: ui <- fluidPage( titlePanel("Malaria facility visualisation app"), sidebarLayout( sidebarPanel( # selector for district selectInput( inputId = "select_district", label = "Select district", choices = c( "All", "Spring", "Bolo", "Dingo", "Barnard" ), selected = "All", multiple = TRUE ), # selector for age group selectInput( inputId = "select_agegroup", label = "Select age group", choices = c( "All ages" = "malaria_tot", "0-4 yrs" = "malaria_rdt_0-4", "5-14 yrs" = "malaria_rdt_5-14", "15+ yrs" = "malaria_rdt_15" ), selected = "All", multiple = FALSE ) ), mainPanel( # epicurve goes here plotOutput("malaria_epicurve") ) ) ) From this code UI we have: • Two inputs: • District selector (with an inputId of select_district) • Age group selector (with an inputId of select_agegroup) • One output: • The epicurve (with an outputId of malaria_epicurve) As stated previously, these unique names we have assigned to our inputs and outputs are crucial. They must be unique and are used to pass information between the ui and server. In our server, we access our inputs via the syntax input$inputID and outputs and passed to the ui through the syntax output$output_name Lets have a look at an example, because again this is hard to understand otherwise! server <- function(input, output, session) { output$malaria_epicurve <- renderPlot(
plot_epicurve(malaria_data, district = input$select_district, agegroup = input$select_agegroup)
)

}

The server for a simple app like this is actually quite straightforward! You’ll notice that the server is a function with three parameters - input, output, and session - this isn’t that important to understand for now, but its important to stick to this setup! In our server we only have one task - this renders a plot based on our function we made earlier, and the inputs from the server. Notice how the names of the input and output objects correspond exactly to those in the ui.

To understand the basics of how the server reacts to user inputs, you should note that the output will know (through the underlying package) when inputs change, and rerun this function to create a plot every time they change. Note that we also use the renderPlot() function here - this is one of a family of class-specific functions that pass those objects to a ui output. There are a number of functions that behave similarly, but you need to ensure the function used matches the class of object you’re passing to the ui! For example:

• renderText() - send text to the ui
• renderDataTable - send an interactive table to the ui.

Remember that these also need to match the output function used in the ui - so renderPlot() is paired with plotOutput(), and renderText() is matched with textOutput().

So we’ve finally made a functioning app! We can run this by pressing the Run App button on the top right of the script window in Rstudio. You should note that you can choose to run your app in your default browser (rather than Rstudio) which will more accurately reflect what the app will look like for other users.

It is fun to note that in the R console, the app is “listening”! Talk about reactivity!

At this point we’ve finally got a running app, but we have very little functionality. We also haven’t really scratched the surface of what shiny can do, so there’s a lot more to learn about! Lets continue to build our existing app by adding some extra features. Some things that could be nice to add could be:

1. Some explanatory text
2. A download button for our plot - this would provide the user with a high quality version of the image that they’re generating in the app
3. A selector for specific facilities
4. Another dashboard page - this could show a table of our data.

This is a lot to add, but we can use it to learn about a bunch of different shiny featues on the way. There is so much to learn about shiny (it can get very advanced, but its hopefully the case that once users have a better idea of how to use it they can become more comfortable using external learning sources as well).

Lets first discuss adding static text to our shiny app. Adding text to our app is extremely easy, once you have a basic grasp of it. Since static text doesn’t change in the shiny app (If you’d like it to change, you can use text rendering functions in the server!), all of shiny’s static text is generally added in the ui of the app. We wont go through this in great detail, but you can add a number of different elements to your ui (and even custom ones) by interfacing R with HTML and css.

HTML and css are languages that are explicitly involved in user interface design. We don’t need to understand these too well, but HTML creates objects in UI (like a text box, or a table), and css is generally used to change the style and aesthetics of those objects. Shiny has access to a large array of HTML tags - these are present for objects that behave in a specific way, such as headers, paragraphs of text, line breaks, tables, etc. We can use some of these examples like this:

• h1() - this a a header tag, which will make enclosed text automatically larger, and change defaults as they pertain to the font face, colour etc (depending on the overall theme of your app). You can access smaller and smaller sub-heading with h2() down to h6() as well. Usage looks like:

• h1("my header - section 1")
• p() - this is a paragraph tag, which will make enclosed text similar to text in a body of text. This text will automatically wrap, and be of a relatively small size (footers could be smaller for example.) Think of it as the text body of a word document. Usage looks like:

• p("This is a larger body of text where I am explaining the function of my app")
• tags$b() and tags$i() - these are used to create bold tags$b() and italicised tags$i() with whichever text is enclosed!

• tags$ul(), tags$ol() and tags$li() - these are tags used in creating lists. These are all used within the syntax below, and allow the user to create either an ordered list (tags$ol(); i.e. numbered) or unordered list (tags$ul(), i.e. bullet points). tags$li() is used to denote items in the list, regardless of which type of list is used. e.g.:

tags$ol( tags$li("Item 1"),

tags$li("Item 2"), tags$li("Item 3")

)
• br() and hr() - these tags create linebreaks and horizontal lines (with a linebreak) respectively. Use them to separate out the sections of your app and text! There is no need to pass any items to these tags (parentheses can remain empty).

• div() - this is a generic tag that can contain anything, and can be named anything. Once you progress with ui design, you can use these to compartmentalize your ui, give specific sections specific styles, and create interactions between the server and UI elements. We won’t go into these in detail, but they’re worth being aware of!

Note that every one of these objects can be accessed through tags$... or for some, just the function. These are effectively synonymous, but it may help to use the tags$... style if you’d rather be more explicit and not overwrite the functions accidentally. This is also by no means an exhaustive list of tags available. There is a full list of all tags available in shiny here and even more can be used by inserting HTML directly into your ui!

If you’re feeling confident, you can also add any css styling elements to your HTML tags with the style argument in any of them. We won’t go into how this works in detail, but one tip for testing aesthetic changes to a UI is using the HTML inspector mode in chrome (of your shiny app you are running in browser), and editing the style of objects yourself!

Lets add some text to our app

ui <- fluidPage(

titlePanel("Malaria facility visualisation app"),

sidebarLayout(

sidebarPanel(
h4("Options"),
# selector for district
selectInput(
inputId = "select_district",
label = "Select district",
choices = c(
"All",
"Spring",
"Bolo",
"Dingo",
"Barnard"
),
selected = "All",
multiple = TRUE
),
# selector for age group
selectInput(
inputId = "select_agegroup",
label = "Select age group",
choices = c(
"All ages" = "malaria_tot",
"0-4 yrs" = "malaria_rdt_0-4",
"5-14 yrs" = "malaria_rdt_5-14",
"15+ yrs" = "malaria_rdt_15"
),
selected = "All",
multiple = FALSE
),
),

mainPanel(
# epicurve goes here
plotOutput("malaria_epicurve"),
br(),
hr(),
p("Welcome to the malaria facility visualisation app! To use this app, manipulate the widgets on the side to change the epidemic curve according to your preferences! To download a high quality image of the plot you've created, you can also download it with the download button. To see the raw data, use the raw data tab for an interactive form of the table. The data dictionary is as follows:"),
tags$ul( tags$li(tags$b("location_name"), " - the facility that the data were collected at"), tags$li(tags$b("data_date"), " - the date the data were collected at"), tags$li(tags$b("submitted_daate"), " - the date the data were submitted at"), tags$li(tags$b("Province"), " - the province the data were collected at (all 'North' for this dataset)"), tags$li(tags$b("District"), " - the district the data were collected at"), tags$li(tags$b("age_group"), " - the age group the data were collected for (0-5, 5-14, 15+, and all ages)"), tags$li(tags$b("cases_reported"), " - the number of cases reported for the facility/age group on the given date") ) ) ) ) ### Adding a download button Lets move on to the second of the three features. A download button is a fairly common thing to add to an app and is fairly easy to make. We need to add another Widget to our ui, and we need to add another output to our server to attach to it. We can also introduce reactive conductors in this example! Lets update our ui first - this is easy as shiny comes with a widget called downloadButton() - lets give it an inputId and a label. ui <- fluidPage( titlePanel("Malaria facility visualisation app"), sidebarLayout( sidebarPanel( # selector for district selectInput( inputId = "select_district", label = "Select district", choices = c( "All", "Spring", "Bolo", "Dingo", "Barnard" ), selected = "All", multiple = FALSE ), # selector for age group selectInput( inputId = "select_agegroup", label = "Select age group", choices = c( "All ages" = "malaria_tot", "0-4 yrs" = "malaria_rdt_0-4", "5-14 yrs" = "malaria_rdt_5-14", "15+ yrs" = "malaria_rdt_15" ), selected = "All", multiple = FALSE ), # horizontal line hr(), downloadButton( outputId = "download_epicurve", label = "Download plot" ) ), mainPanel( # epicurve goes here plotOutput("malaria_epicurve"), br(), hr(), p("Welcome to the malaria facility visualisation app! To use this app, manipulate the widgets on the side to change the epidemic curve according to your preferences! To download a high quality image of the plot you've created, you can also download it with the download button. To see the raw data, use the raw data tab for an interactive form of the table. The data dictionary is as follows:"), tags$ul(
tags$li(tags$b("location_name"), " - the facility that the data were collected at"),
tags$li(tags$b("data_date"), " - the date the data were collected at"),
tags$li(tags$b("submitted_daate"), " - the date the data were submitted at"),
tags$li(tags$b("Province"), " - the province the data were collected at (all 'North' for this dataset)"),
tags$li(tags$b("District"), " - the district the data were collected at"),
tags$li(tags$b("age_group"), " - the age group the data were collected for (0-5, 5-14, 15+, and all ages)"),
tags$li(tags$b("cases_reported"), " - the number of cases reported for the facility/age group on the given date")
)

)

)
)

Note that we’ve also added in a hr() tag - this adds a horizontal line separating our control widgets from our download widgets. This is another one of the HTML tags that we discussed previously.

Now that we have our ui ready, we need to add the server component. Downloads are done in the server with the downloadHandler() function. Similar to our plot, we need to attach it to an output that has the same inputId as the download button. This function takes two arguments - filename and content - these are both functions. As you might be able to guess, filename is used to specify the name of the downloaded file, and content is used to specify what should be downloaded. content contain a function that you would use to save data locally - so if you were downloading a csv file you could use rio::export(). Since we’re downloading a plot, we’ll use ggplot2::ggsave(). Lets look at how we would program this (we won’t add it to the server yet).

server <- function(input, output, session) {

output$malaria_epicurve <- renderPlot( plot_epicurve(malaria_data, district = input$select_district, agegroup = input$select_agegroup) ) output$download_epicurve <- downloadHandler(
filename = function() {
stringr::str_glue("malaria_epicurve_{input$select_district}.png") }, content = function(file) { ggsave(file, plot_epicurve(malaria_data, district = input$select_district, agegroup = input$select_agegroup), width = 8, height = 5, dpi = 300) } ) } Note that the content function always takes a file argument, which we put where the output file name is specified. You might also notice that we’re repeating code here - we are using our plot_epicurve() function twice in this server, once for the download and once for the image displayed in the app. While this wont massively affect performance, this means that the code to generate this plot will have to be run when the user changes the widgets specifying the district and age group, and again when you want to download the plot. In larger apps, suboptimal decisions like this one will slow things down more and more, so it’s good to learn how to make our app more efficient in this sense. What would make more sense is if we had a way to run the epicurve code when the districts/age groups are changes, and let that be used by the renderPlot() and downloadHandler() functions. This is where reactive conductors come in! Reactive conductors are objects that are created in the shiny server in a reactive way, but are not outputted - they can just be used by other parts of the server. There are a number of different kinds of reactive conductors, but we’ll go through the basic two. 1.reactive() - this is the most basic reactive conductor - it will react whenever any inputs used inside of it change (so our district/age group widgets) 2. eventReactive()- this rective conductor works the same as reactive(), except that the user can specify which inputs cause it to rerun. This is useful if your reactive conductor takes a long time to process, but this will be explained more later. Lets look at the two examples: malaria_plot_r <- reactive({ plot_epicurve(malaria_data, district = input$select_district, agegroup = input$select_agegroup) }) # only runs when the district selector changes! malaria_plot_er <- eventReactive(input$select_district, {

plot_epicurve(malaria_data, district = input$select_district, agegroup = input$select_agegroup)

})

When we use the eventReactive() setup, we can specify which inputs cause this chunk of code to run - this isn’t very useful to us at the moment, so we can leave it for now. Note that you can include multiple inputs with c()

Lets look at how we can integrate this into our server code:

server <- function(input, output, session) {

malaria_plot <- reactive({
plot_epicurve(malaria_data, district = input$select_district, agegroup = input$select_agegroup)
})

output$malaria_epicurve <- renderPlot( malaria_plot() ) output$download_epicurve <- downloadHandler(

filename = function() {
stringr::str_glue("malaria_epicurve_{input$select_district}.png") }, content = function(file) { ggsave(file, malaria_plot(), width = 8, height = 5, dpi = 300) } ) } You can see we’re just calling on the output of our reactive we’ve defined in both our download and plot rendering functions. One thing to note that often trips people up is you have to use the outputs of reactives as if they were functions - so you must add empty brackets at the end of them (i.e. malaria_plot() is correct, and malaria_plot is not). Now that we’ve added this solution our app is a little tidyer, faster, and easier to change since all our code that runs the epicurve function is in one place. ### Adding a facility selector Lets move on to our next feature - a selector for specific facilities. We’ll implement another parameter into our function so we can pass this as an argument from our code. Lets look at doing this first - it just operates off the same principles as the other parameters we’ve set up. Lets update and test our function. plot_epicurve <- function(data, district = "All", agegroup = "malaria_tot", facility = "All") { if (!("All" %in% district)) { data <- data %>% filter(District %in% district) plot_title_district <- stringr::str_glue("{paste0(district, collapse = ', ')} districts") } else { plot_title_district <- "all districts" } # if no remaining data, return NULL if (nrow(data) == 0) { return(NULL) } data <- data %>% filter(age_group == agegroup) # if no remaining data, return NULL if (nrow(data) == 0) { return(NULL) } if (agegroup == "malaria_tot") { agegroup_title <- "All ages" } else { agegroup_title <- stringr::str_glue("{str_remove(agegroup, 'malaria_rdt')} years") } if (!("All" %in% facility)) { data <- data %>% filter(location_name == facility) plot_title_facility <- facility } else { plot_title_facility <- "all facilities" } # if no remaining data, return NULL if (nrow(data) == 0) { return(NULL) } ggplot(data, aes(x = data_date, y = cases_reported)) + geom_col(width = 1, fill = "darkred") + theme_minimal() + labs( x = "date", y = "number of cases", title = stringr::str_glue("Malaria cases - {plot_title_district}; {plot_title_facility}"), subtitle = agegroup_title ) } Let’s test it: plot_epicurve(malaria_data, district = "Spring", agegroup = "malaria_rdt_0-4", facility = "Facility 1") With all the facilites in our data, it isn’t very clear which facilities correspond to which districts - and the end user won’t know either. This might make using the app quite unintuitive. For this reason, we should make the facility options in the UI change dynamically as the user changes the district - so one filters the other! Since we have so many variables that we’re using in the options, we might also want to generate some of our options for the ui in our global.R file from the data. For example, we can add this code chunk to global.R after we’ve read our data in: all_districts <- c("All", unique(malaria_data$District))

# data frame of location names by district
facility_list <- malaria_data %>%
group_by(location_name, District) %>%
summarise() %>%
ungroup()

Let’s look at them:

all_districts
## [1] "All"     "Spring"  "Bolo"    "Dingo"   "Barnard"
facility_list
## # A tibble: 65 x 2
##    location_name District
##    <chr>         <chr>
##  1 Facility 1    Spring
##  2 Facility 10   Bolo
##  3 Facility 11   Spring
##  4 Facility 12   Dingo
##  5 Facility 13   Bolo
##  6 Facility 14   Dingo
##  7 Facility 15   Barnard
##  8 Facility 16   Barnard
##  9 Facility 17   Barnard
## 10 Facility 18   Bolo
## # ... with 55 more rows

We can pass these new variables to the ui without any issue, since they are globally visible by both the server and the ui! Lets update our UI:

ui <- fluidPage(

titlePanel("Malaria facility visualisation app"),

sidebarLayout(

sidebarPanel(
# selector for district
selectInput(
inputId = "select_district",
label = "Select district",
choices = all_districts,
selected = "All",
multiple = FALSE
),
# selector for age group
selectInput(
inputId = "select_agegroup",
label = "Select age group",
choices = c(
"All ages" = "malaria_tot",
"0-4 yrs" = "malaria_rdt_0-4",
"5-14 yrs" = "malaria_rdt_5-14",
"15+ yrs" = "malaria_rdt_15"
),
selected = "All",
multiple = FALSE
),
# selector for facility
selectInput(
inputId = "select_facility",
label = "Select Facility",
choices = c("All", facility_list$location_name), selected = "All" ), # horizontal line hr(), downloadButton( outputId = "download_epicurve", label = "Download plot" ) ), mainPanel( # epicurve goes here plotOutput("malaria_epicurve"), br(), hr(), p("Welcome to the malaria facility visualisation app! To use this app, manipulate the widgets on the side to change the epidemic curve according to your preferences! To download a high quality image of the plot you've created, you can also download it with the download button. To see the raw data, use the raw data tab for an interactive form of the table. The data dictionary is as follows:"), tags$ul(
tags$li(tags$b("location_name"), " - the facility that the data were collected at"),
tags$li(tags$b("data_date"), " - the date the data were collected at"),
tags$li(tags$b("submitted_daate"), " - the date the data were submitted at"),
tags$li(tags$b("Province"), " - the province the data were collected at (all 'North' for this dataset)"),
tags$li(tags$b("District"), " - the district the data were collected at"),
tags$li(tags$b("age_group"), " - the age group the data were collected for (0-5, 5-14, 15+, and all ages)"),
tags$li(tags$b("cases_reported"), " - the number of cases reported for the facility/age group on the given date")
)

)

)
)

Notice how we’re now passing variables for our choices instead of hard coding them in the ui! This might make our code more compact as well! Lastly, we’ll have to update the server. It will be easy to update our function to incorporate our new input (we just have to pass it as an argument to our new parameter), but we should remember we also want the ui to update dynamically when the user changes the selected district. It is important to understand here that we can change the parameters and behaviour of widgets while the app is running, but this needs to be done in the server. We need to understand a new way to output to the server to learn how to do this.

The functions we need to understand how to do this are known as observer functions, and are similar to reactive functions in how they behave. They have one key difference though:

• Reactive functions do not directly affect outputs, and produce objects that can be seen in other locations in the server
• Observer functions can affect server outputs, but do so via side effects of other functions. (They can also do other things, but this is their main function in practice)

Similar to reactive functions, there are two flavours of observer functions, and they are divided by the same logic that divides reactive functions:

1. observe() - this function runs whenever any inputs used inside of it change
2. observeEvent() - this function runs when a user-specified input changes

We also need to understand the shiny-provided functions that update widgets. These are fairly straightforward to run - they first take the session object from the server function (this doesn’t need to be understood for now), and then the inputId of the function to be changed. We then pass new versions of all parameters that are already taken by selectInput() - these will be automatically updated in the widget.

Lets look at an isolated example of how we could use this in our server. When the user changes the district, we want to filter our tibble of facilities by district, and update the choices to only reflect those that are available in that district (and an option for all facilities)

observe({

if (input$select_district == "All") { new_choices <- facility_list$location_name
} else {
new_choices <- facility_list %>%
filter(District == input$select_district) %>% pull(location_name) } new_choices <- c("All", new_choices) updateSelectInput(session, inputId = "select_facility", choices = new_choices) }) And that’s it! we can add it into our server, and that behaviour will now work. Here’s what our new server should look like: server <- function(input, output, session) { malaria_plot <- reactive({ plot_epicurve(malaria_data, district = input$select_district, agegroup = input$select_agegroup, facility = input$select_facility)
})

observe({

if (input$select_district == "All") { new_choices <- facility_list$location_name
} else {
new_choices <- facility_list %>%
filter(District == input$select_district) %>% pull(location_name) } new_choices <- c("All", new_choices) updateSelectInput(session, inputId = "select_facility", choices = new_choices) }) output$malaria_epicurve <- renderPlot(
malaria_plot()
)

output$download_epicurve <- downloadHandler( filename = function() { stringr::str_glue("malaria_epicurve_{input$select_district}.png")
},

content = function(file) {
ggsave(file,
malaria_plot(),
width = 8, height = 5, dpi = 300)
}

)

}

### Adding another tab with a table

Now we’ll move on to the last component we want to add to our app. We’ll want to separate our ui into two tabs, one of which will have an interactive table where the user can see the data they are making the epidemic curve with. To do this, we can use the packaged ui elements that come with shiny relevant to tabs. On a basic level, we can enclose most of our main panel in this general structure:

# ... the rest of ui

mainPanel(

tabsetPanel(
type = "tabs",
tabPanel(
"Epidemic Curves",
...
),
tabPanel(
"Data",
...
)
)
)

Lets apply this to our ui. We also will want to use the DT package here - this is a great package for making interactive tables from pre-existing data. We can see it being used for DT::datatableOutput() in this example.

ui <- fluidPage(

titlePanel("Malaria facility visualisation app"),

sidebarLayout(

sidebarPanel(
# selector for district
selectInput(
inputId = "select_district",
label = "Select district",
choices = all_districts,
selected = "All",
multiple = FALSE
),
# selector for age group
selectInput(
inputId = "select_agegroup",
label = "Select age group",
choices = c(
"All ages" = "malaria_tot",
"0-4 yrs" = "malaria_rdt_0-4",
"5-14 yrs" = "malaria_rdt_5-14",
"15+ yrs" = "malaria_rdt_15"
),
selected = "All",
multiple = FALSE
),
# selector for facility
selectInput(
inputId = "select_facility",
label = "Select Facility",
choices = c("All", facility_list$location_name), selected = "All" ), # horizontal line hr(), downloadButton( outputId = "download_epicurve", label = "Download plot" ) ), mainPanel( tabsetPanel( type = "tabs", tabPanel( "Epidemic Curves", plotOutput("malaria_epicurve") ), tabPanel( "Data", DT::dataTableOutput("raw_data") ) ), br(), hr(), p("Welcome to the malaria facility visualisation app! To use this app, manipulate the widgets on the side to change the epidemic curve according to your preferences! To download a high quality image of the plot you've created, you can also download it with the download button. To see the raw data, use the raw data tab for an interactive form of the table. The data dictionary is as follows:"), tags$ul(
tags$li(tags$b("location_name"), " - the facility that the data were collected at"),
tags$li(tags$b("data_date"), " - the date the data were collected at"),
tags$li(tags$b("submitted_daate"), " - the date the data were submitted at"),
tags$li(tags$b("Province"), " - the province the data were collected at (all 'North' for this dataset)"),
tags$li(tags$b("District"), " - the district the data were collected at"),
tags$li(tags$b("age_group"), " - the age group the data were collected for (0-5, 5-14, 15+, and all ages)"),
tags$li(tags$b("cases_reported"), " - the number of cases reported for the facility/age group on the given date")
)

)
)
)

Now our app is arranged into tabs! Lets make the necessary edits to the server as well. Since we dont need to manipulate our dataset at all before we render it this is actually very simple - we just render the malaria_data dataset via DT::renderDT() to the ui!

server <- function(input, output, session) {

malaria_plot <- reactive({
plot_epicurve(malaria_data, district = input$select_district, agegroup = input$select_agegroup, facility = input$select_facility) }) observe({ if (input$select_district == "All") {
new_choices <- facility_list$location_name } else { new_choices <- facility_list %>% filter(District == input$select_district) %>%
pull(location_name)
}

new_choices <- c("All", new_choices)

choices = new_choices)

})

output$malaria_epicurve <- renderPlot( malaria_plot() ) output$download_epicurve <- downloadHandler(

filename = function() {
stringr::str_glue("malaria_epicurve_{input$select_district}.png") }, content = function(file) { ggsave(file, malaria_plot(), width = 8, height = 5, dpi = 300) } ) # render data table to ui output$raw_data <- DT::renderDT(
malaria_data
)

}

## 43.7 Sharing shiny apps

Now that you’ve developed your app, you probably want to share it with others - this is the main advantage of shiny after all! We can do this by sharing the code directly, or we could publish on a server. If we share the code, others will be able to see what you’ve done and build on it, but this will negate one of the main advantages of shiny - it can eliminate the need for end-users to maintain an R installation. For this reason, if you’re sharing your app with users who are not comfortable with R, it is much easier to share an app that has been published on a server.

If you’d rather share the code, you could make a .zip file of the app, or better yet, publish your app on github and add collaborators. You can refer to the section on github for further information here.

However, if we’re publishing the app online, we need to do a little more work. Ultimately, we want your app to be able to be accessed via a web URL so others can get quick and easy access to it. Unfortunately, to publish you app on a server, you need to have access to a server to publish it on! There are a number of hosting options when it comes to this:

• shinyapps.io: this is the easiest place to publish shiny apps, as it has the smallest amount of configuration work needed, and has some free, but limited licenses.

• RStudio Connect: this is a far more powerful version of an R server, that can perform many operations, including publishing shiny apps. It is however, harder to use, and less recommended for first-time users.

For the purposes of this document, we will use shinyapps.io, since it is easier for first time users. You can make a free account here to start - there are also different price plans for server licesnses if needed. The more users you expect to have, the more expensive your price plan may have to be, so keep this under consideration. If you’re looking to create something for a small set of individuals to use, a free license may be perfectly suitable, but a public facing app may need more licenses.

First we should make sure our app is suitable for publishing on a server. In your app, you should restart your R session, and ensure that it runs without running any extra code. This is important, as an app that requires package loading, or data reading not defined in your app code won’t run on a server. Also note that you can’t have any explicit file paths in your app - these will be invalid in the server setting - using the here package solves this issue very well. Finally, if you’re reading data from a source that requires user-authentication, such as your organisation’s servers, this will not generally work on a server. You will need to liase with your IT department to figure out how to whitelist the shiny server here.

signing up for account

Once you have your account, you can navigate to the tokens page under Accounts. Here you will want to add a new token - this will be used to deploy your app.

From here, you should note that the url of your account will reflect the name of your app - so if your app is called my_app, the url will be appended as xxx.io/my_app/. Choose your app name wisely! Now that you are all ready, click deploy - if successful this will run your app on the web url you chose!

something on making apps in documents?