E1 second graph addition

.gitignore

@@ -6,21 +6,23 @@
 .Rproj.user/
 *.Rproj
 
+# Folder readme
+FOLDER_INFO.txt
 # Deployment secrets
 
 # Credentials script
+create_credentials.R
 # Constants file
 constants.R
 
-# Data prep script
-data_preparation.R
-
-# 'data' folder #
+# folders to ignrore
+admin/
+archive/
 data/
-
-# infographics folder
+drafts/
 www/infographics
 
+
 # Common text files that may contain data #
 *.[cC][sS][vV]
 *.[tT][xX][tT]

README.md

@@ -1,2 +1,8 @@
 # MHQI-Dashboard
 The Mental Health Team's repo for the Mental Health Quality Indicators Dashboard
+
+## Maintaining
+This dashboard makes use of a file 'stylesheet.css' (which can be found in the www folder - where it must remain in order to work) to define styling of various elements. This styling overrides the default styling set by the Shiny package and enables styling to be changed once in one place and affect every incidence of that element. As a result, editing aesthetics and certain behaviours of this dashboard should be a much simpler process.
+
+To edit an element you need to know what 'class(es)' refers to the element. If you need to find out the class(es) of a particular element you can run the app within RStudio and right click on the element you are interested in. Then click "inspect" and it will bring up the developer window with the relevant bits of code.
+

app.R

@@ -1,50 +1,68 @@
+### Mental Health Quality Indicators Dashboard
+
+# Loading packages
 library(phsstyles)
+library(plotly)
+library(ggplot2) # adding for testing using this before plotly
 library(dplyr)
-library(purrr)
+library(purrr) # for map function to load multiple files
+library(stringr)
 library(shiny)
 library(shinydashboard)
 library(fresh) # for customising shinydashboard look
 library(shinyWidgets)
-
+library(forcats) # added by mahri for fct_reorder() in graph 
+library(gotop) # for return to top button
+library(shinycssloaders) # for graph loading spinners
+library(DT)
+library(shinymanager) # password protection
 
 # Data import section ----------------------------------------------------
 
 # Source constants used throughout app
 source("scot_hub_data.R")
+source("setup.R")
+source("data_preparation.R")
+
+# 6. sourcing functions created for app (see functions folder) -------------------------------
+list.files("functions") %>%
+  map(~ source(paste0("functions/", .)))
 
-# # 6. sourcing functions created for app (see functions folder) -------------------------------
-# list.files("functions") %>% 
-#   map(~ source(paste0("functions/", .)))
+#* Read in credentials for password-protecting the app ----
+# credentials <- readRDS("admin/credentials.rds") # Un-comment if password protection needed
 
-# Source the ui file ----
+### [ UI section ] -------------------------------------------------------------
 
-# ui <- source('ui.R', local = TRUE)$value
 
-ui <- dashboardPage(
+
+ui <- 
+  # secure_app( # Un-comment if password protection is needed.
+  dashboardPage(
 
   dashboardHeader(title = "MH Quality Indicators"),
 
   dashboardSidebar(source("modules/sidebar_ui.R", local = TRUE)$value),
 
   # Define how the various pages of the dashboard look
   dashboardBody(
+
     ## Source styling for shinydashboard elements 
     # - must be before stylesheet so that it doesn't override the css file
     source("www/dashboard_style.R", local = TRUE)$value,
 
     ## load css stylesheet that defines how things look 
     tags$head(includeCSS("www/stylesheet.css")),
 
-
+    ## Tabs ----
     tabItems(
-      # [Introduction Tab] ----------------------------------------------------
+      # [Introduction Tab] ----
       source("modules/introduction_ui.R", local = TRUE)$value,
 
 
-      # [Scotland Hub Tab] ----------------------------------------------------
+      # [Scotland Hub Tab] ----
       source("modules/scot_hub_ui.R", local = TRUE)$value,
 
-      ## Sourcing ui sections for each indicator -------------------------------
+      ## Sourcing ui sections for each indicator ----
       # [Timely] ----
       source("modules/indicators/T1_ui.R", local = TRUE)$value,
       source("modules/indicators/T2_ui.R", local = TRUE)$value,
@@ -81,14 +99,44 @@ ui <- dashboardPage(
 
    ) # End of tabItems
   ) # End of dashboardBody
-) # End of UI
+) # End of dashboardPage
+# ) # End of password-protection wrapper
 
-# Server  ----------------------------------------------------
+
+
+### [ Server ] -----------------------------------------------------------------
 server <- function(input, output, session) {
 
+  ##* Shinymanager authorisation ----
+  # Un-comment this section to password protect the app.
+  # Re-comment out to remove password protection on launch day.
+   # res_auth <- secure_server(
+   # check_credentials = check_credentials(credentials)
+   # )
+   # 
+   # output$auth_output <- renderPrint({
+   # reactiveValuesToList(res_auth)
+   # })
+
   # Navigation buttons ----
   source("modules/nav_buttons_server.R", local = TRUE)
 
+  # Indicator servers
+  source("modules/indicators/E1_server.R", local = TRUE)
+  source("modules/indicators/EQ1_server.R", local = TRUE)
+  source("modules/indicators/EF4_server.R", local = TRUE)
+
+
+  # Keep dashboard active indefinitely to meet accessibility requirements
+  # (Keep at the end of server)
+  auto_invalidate <- reactiveTimer(10000)
+  observe({
+    auto_invalidate()
+    cat(".")
+  })
 }
 
+# Sets language right at the top of source (required this way for screen readers)
+attr(ui, "lang") = "en"
+
 shinyApp(ui, server)

data_preparation.R

@@ -0,0 +1,47 @@
+### Data preparation script
+# N.B. do not use any direct filepaths, ony relational ones
+
+### [Indicators] ----
+## E1 ----
+E1_data <- read.csv("data/E1.csv") %>% 
+  rename(dd_bed_days = delayed_discharge_bed_days,
+         fyear = financial_year)
+
+E1_area_types <- E1_data %>% 
+  distinct(area_type) %>% pull(area_type)
+
+# For E1 plot 2:
+E1_fyear <- E1_data %>% 
+   distinct(fyear) %>% 
+   pull(fyear)
+
+## EQ1 ----
+EQ1_data <- read.csv("data/EQ1.csv") 
+
+unique_area_types <- EQ1_data %>% 
+  distinct(area_type) %>% pull(area_type)
+
+# For EQ1 plot 2:
+EQ1_reformatted_data <- read.csv("data/EQ1_Reformatted.csv")%>% 
+   mutate(Rate = round(Rate))        # because values are e.g. "3158.23942548425913"
+
+unique_area_types_reformatted <- EQ1_reformatted_data %>% 
+  distinct(area_type) %>% pull(area_type)
+
+
+## EF4 ----
+EF4_data <- read.csv("data/EF4.csv") %>% 
+  select(fyear, hb_name, measure, value)
+
+EF4_fyear <- EF4_data %>% 
+  distinct(fyear) %>% pull(fyear)
+
+EF4_hb_names <- EF4_data %>% 
+  distinct(hb_name) %>% pull(hb_name)
+
+EF4_trend_measures <- c('Mental Health Expenditure (%)', 'CAMHS Expenditure (%)')
+
+# EF4_trend_measures <- EF4_data %>% 
+#   distinct(measure) %>% pull(measure) %>% 
+#   filter(measure = )
+

functions/core_functions.R

@@ -0,0 +1,7 @@
+# Load data from shiny_app/data ----
+load_csv_file <- function(csv){
+  # Given a .csv file name in shiny_app/data
+  # this function loads it as a variable with the same name as the
+  # file apart from the extension
+  assign(gsub(".csv", "", csv), read.csv(paste0("data/", csv)), envir = .GlobalEnv)
+}

functions/plot_functions.R

@@ -0,0 +1,70 @@
+### Functions used in plots throughout the app
+
+## PHS colour spinner ----
+
+phs_spinner <- function(plot_name){
+  withSpinner(
+    plotlyOutput(plot_name, width = "100%"),
+    type = 8, size = 0.7,
+    color = "#AF69A9", # color.background = "#E1C7DF",
+    caption = "Loading...",
+    hide.ui = FALSE
+  )
+}
+
+## No Data function ----
+# Function defining what is shown when there is no data to be presented:
+
+noDataPlot <- function(line_colour){
+
+  noDataPlot_text <- list(
+  x = 5, 
+  y = 2, 
+  font = list(color = line_colour, size = 20),
+  text = paste0("No discharges found for these selections."),
+  xref = "x", 
+  yref = "y",  
+  showarrow = FALSE
+)
+
+# Visualise an empty graph with the above message in the middle.
+
+plot_ly() %>% 
+  layout(annotations = noDataPlot_text, 
+         yaxis = list(showline = FALSE, 
+                      showticklabels = FALSE, 
+                      showgrid = FALSE), 
+         xaxis = list(showline = FALSE, 
+                      showticklabels = FALSE, 
+                      showgrid = FALSE)) %>%  
+  config(displayModeBar = FALSE,
+         displaylogo = F, editable = F)
+
+}
+
+### Scatter Line Plot Function ----
+# Aesthetic attributes for line graphs
+
+phs_scatterPlot <- function(plot_data, # Graph reactive ouput
+                            x_var, # variable on x axis
+                            y_var, # variable on y axis
+                            tooltip, # tooltip object name
+                            line_var # line variable name
+                            )
+  {
+
+plotly(
+    data = plot_data(),
+    x = ~x_var, y = ~y_var, 
+    text = tooltip, hoverinfo = "text",
+    color = ~line_var,
+    colors = c("#0078D4", "#3393DD", "#80BCEA", "#B3D7F2"), # line colours
+    type = 'scatter', mode = 'lines+markers',
+    # width = 600, height = 300,
+    line = list(width = 2),
+    linetype = ~line_var,
+    linetypes = c("solid", "dash"),
+    marker = list(size = 8),
+    name = ~str_wrap(line_var, 19))
+
+}

indicator_alt_text.R

@@ -0,0 +1,9 @@
+max_year <- 2024
+
+EF1 <- read_csv('data/EF1.csv')
+
+EF1_rate <- EF1$rate %>%
+   filter(fyear = max_year)
+
+EF1_lag_rate <- EF1$rate %>%
+   filter(fyear = (max_year-1))

modules/appendix_ui.R

@@ -1,4 +1,4 @@
-tabItem(tabName = appendix_tab,
+tabItem(tabName = "appendix_tab",
         fluidPage(
           titlePanel(h1("T1 - % of people who commence psychological therapy 
                            based treatment within 18 weeks of referral"),