Shiny app with Reactive Leaflet assigning colors & R crashing

[gabbypaola]

I am having an issue creating a shiny app with a reactive choropleth map in R using leaflet (this is my first time using Shiny).

I have a dataset with death rates, death causes, year ,and states. I am trying to create a reactive filter for the causes so that the user can select a cause of death and see the different rates across all states via the change in color (year is to stay constant at 2010). I've created the filter, now I am not entirely sure if I am defining the domain in palette pal correctly (ie do I define it using the death rate or the death cause) as well as the fillColor value.

Additionally, when I run my chunk containing the Shiny code, R generates the Shiny.app window but then after 20 seconds or so the page and RStudio turns completely white and have to End Task in the Task Manager.

I have reviewed this post already: Leaflet chorolpleth with reactive layer - #2 by williaml, but wasn't sure how to implement it on my code (ie is AREA analogous to icd.chapter or crude.rate?)

Libraries and data:

library(dplyr)
library(leaflet)
library(tigris)
library(plotly)
library(shiny)
library(shinythemes)
library(rsconnect)
library(sf)

###this is a manually created sample of the actual data, there are more causes and more states###
df  <- data.frame(Year = c(2000,2001,2003),
                 State = c("AL","AL","AL"),
                 Rate = c(26.7,27.1,27.1),
                 Cause = c("Certain infectious and parasitic diseases","Certain infectious and parasitic diseases","Certain infectious and parasitic diseases")
                 )

names(df) <- lapply(names(df), tolower)

states <- tigris::states(cb=T)

#change column name on shapefile for left join with death data
states <- states %>% rename("state" = "STUSPS")

#st_crs(states)$epsg
states <- st_transform(states, 4326)

#need to use geo_join in order to get sf type datafram for leaflet
states_merged <- geo_join(data_frame=df, spatial_data= states, by_df= "state", by_sp= "state", by = NULL, how = "inner")

# #remove NA
states_merged <- subset(states_merged, !is.na(crude.rate))

Shiny app map code:

#shiny app UI
ui <- fluidPage(
    titlePanel('Causes of Death Across United States in 2010'),
    sidebarLayout(
        sidebarPanel(
            selectInput(
                inputId = 'cause', 
                label = 'Cause of Death:', 
                choices = unique(states_merged$icd.chapter))
                ),
        
        mainPanel(
           leafletOutput(outputId = 'map', height = 800)
            )
    )
)

#shiny app server
server <- shinyServer(function(input, output, session){
    map_data <- reactive({
      filter(states_merged, year == 2010 & icd.chapter == input$cause)
      })
    #create color palette based on range of Crude.Rate
      pal <- colorNumeric("Reds", domain=states_merged$crude.rate)
    #Setting up the pop up text
      popup_sb <- with(states_merged, 
                 paste(NAME, '<br>',
                       "Crude Rate: ", crude.rate ,'<br>',
                       "Deaths: ", deaths, '<br>',
                       "Population", population))
   
    output$map <- renderLeaflet({
        map_data() %>% 
        leaflet() %>%
        addProviderTiles("CartoDB.Positron") %>%
        setView(-98.483330, 38.712046, zoom = 4) %>% 
        addPolygons( 
              fillColor = ~pal(states_merged$crude.rate), #reference map_data() or states_merged? also do i use the rate value or the cause of death (icd.chapter)
              fillOpacity = 0.7, 
              weight = 0.2, 
              smoothFactor = 0.2, 
              popup = ~popup_sb) %>%
        addLegend(pal = pal, 
            values = states_merged$crude.rate, #reference map_data() or states_merged?
            position = "bottomright", 
            title = "Death Rates")
        
    }
    )
})

shinyApp(ui = ui, server = server)
deployApp()

Static map code:

states_merged_filtered <- filter(states_merged, year == 2010 & icd.chapter == 'Mental and behavioural disorders')

# #create color palette based on range of Crude.Rate
pal <- colorNumeric("Reds", domain=states_merged_filtered$crude.rate)

# Setting up the pop up text
popup_sb <- with(states_merged_filtered,
                 paste(NAME, '<br>',
                       "Crude Rate: ", crude.rate ,'<br>',
                       "Deaths: ", deaths, '<br>',"Population", population))

# Mapping it with the new tiles CartoDB.Positron
leaflet() %>%
  addProviderTiles("CartoDB.Positron") %>%
  setView(-98.483330, 38.712046, zoom = 4) %>%
  addPolygons(data = states_merged_filtered,
              fillColor = ~pal(states_merged_filtered$crude.rate),
              fillOpacity = 0.7,
              weight = 0.2,
              smoothFactor = 0.2,
              popup = ~popup_sb) %>%
  addLegend(pal = pal,
            values = states_merged_filtered$crude.rate,
            position = "bottomright",
            title = "Death Rates")

(this is the map output for the above)

US Death Rates for 2010
Cause: Mental and behavioural disorders

[williaml]

Hi, can you create a reproducible example with a dataset like spData::us_states . It will make it easier for others to troubleshoot.

[gabbypaola]

Thank you for responding and sure, I’ve updated the post to include the libraries and data I am using.

[gabbypaola]

I was able to find a solution using this: Shiny Tutorial Error in R - Stack Overflow.

There were 3 things I did wrong. I was referencing the wrong dataset within my renderLeaflet call for my map. I needed to be referencing the reactive dataset map_data(), also the palette pal and popup text popup_sb both needed to use the map_data() set AND be moved inside the renderLeaflet call.

(Side note: I made year a reactive variable as well so the user can toggle the map by both year and cause of death)

Below is my code for anyone coming across this post with the same issue for future reference.

#shiny app UI
ui <- fluidPage(
    titlePanel(
               "Examining Causes of Death Across the US from 1999-2010"
               ),
    sidebarLayout(
        sidebarPanel(
           selectInput(
                inputId = 'year', 
                label = 'Year:', 
                choices = unique(states_merged$year),
                selected = 2010),
            selectInput(
                inputId = 'cause', 
                label = 'Cause of Death:', 
                choices = unique(states_merged$icd.chapter),
                selected = "Certain infectious and parasitic diseases"),
                ),
        mainPanel(
           leafletOutput(outputId = 'map', height = 800)
            )
    )
)

#shiny app server
server <- shinyServer(function(input, output, session){
    map_data <- reactive({
      filter(states_merged, year == input$year & icd.chapter == input$cause)
      })

    output$map <- renderLeaflet({
     #create color palette based on range of Crude.Rate
      pal <- colorNumeric("Reds", domain=map_data()$crude.rate)
     #Setting up the pop up text
      popup_sb <- with(map_data(), 
                 paste(NAME, '<br>',
                       "Year: ", year, '<br>',
                       "Crude Rate: ", crude.rate ,'<br>',
                       "Deaths: ", deaths, '<br>',
                       "Population: ", population))
      #create map  
        map_data() %>% 
        leaflet() %>%
        addProviderTiles("CartoDB.Positron")%>%
        addControl(title, position = "topleft", className="map-title") %>%
        setView(-98.483330, 38.712046, zoom = 4) %>% 
        addPolygons( 
              fillColor = ~pal(map_data()$crude.rate), #reference map_data() 
              fillOpacity = 0.7, 
              weight = 0.2, 
              smoothFactor = 0.2, 
              popup = ~popup_sb) %>%
        addLegend(pal = pal, 
            values = map_data()$crude.rate, #reference map_data() 
            position = "bottomright", 
            title = "Deaths per 100,000 persons")
        
    }
    )
})

shinyApp(ui = ui, server = server)
deployApp()