Split ui.R into components

[Rnaught] / R / ui.R

diff --git a/R/ui.R b/R/ui.R
index 63e21eb5304fc82f618d9843172cf8ad80b1e743..355b08ecb0b124599ce45c20c27668df3e518c78 100644 (file)
--- a/R/ui.R
+++ b/R/ui.R
@@ -1,130 +1,192 @@
 ui <- function() {
 ui <- function() {

-    shiny::fluidPage(
-        # Title.
-        shiny::titlePanel(shiny::HTML(paste0("Rnaught: an estimation suite for R", shiny::tags$sub("0")))),
-  
-        # Sidebar layout.
-        shiny::sidebarLayout(
-            # Sidebar. Hidden if the 'About' tab is selected.
-            shiny::conditionalPanel(condition="input.tabset != 'About'",
-                shiny::sidebarPanel(id="sidebar",
-                    # Data tab sidebar.
-                    shiny::conditionalPanel(condition="input.tabset == 'Data'",
-                        shiny::h4("Enter data"),
-                        # Data input method selection.
-                        shiny::radioButtons(inputId="dataInputMethod", label="", choices=list("Manually"=1, "Upload a .csv file"=2, "Paste a .csv file"=3)),
-                        # Option 1: Manual entry.
-                        shiny::conditionalPanel(condition="input.dataInputMethod == '1'",
-                            shiny::textInput(inputId="dataName", label="Dataset name"),
-                            shiny::span(shiny::textOutput(outputId="dataNameWarn"), style="color: red"),
-                            shiny::fluidRow(
-                                shiny::column(8, shiny::textInput(inputId="dataCounts", label=shiny::HTML(paste0("Case counts", shiny::tags$sup(id="dataCountsHelp", "[?]"))))),
-                                shiny::column(4, shiny::selectInput(inputId="dataUnits", label="Reporting frequency", choices=list("Daily", "Weekly")))
-                            ),
-                            shinyBS::bsTooltip(id="dataCountsHelp", "Enter as a comma-separated list of positive integers, with at least two entries. Ex: 1,1,2,3,5,8", placement="right", trigger="hover"),
-                            shiny::span(shiny::textOutput(outputId="dataCountsWarn"), style="color: red")
-                        ),
-                        # Option 2: Upload .csv file.
-                        shiny::conditionalPanel(condition="input.dataInputMethod == '2'",
-                            shiny::fileInput(inputId="dataUpload", label="", accept=c("text/csv", "text/comma-separated-values,text/plain", ".csv")),
-                        ),
-                        # Option 3: Paste .csv file.
-                        shiny::conditionalPanel(condition="input.dataInputMethod == '3'",
-                            shiny::textAreaInput(inputId="dataPaste", label="", rows=8, resize="none"),
-                        ),
-                        # Warning text for .csv upload / paste.
-                        shiny::conditionalPanel(condition="['2', '3'].includes(input.dataInputMethod)",
-                            shiny::span(shiny::textOutput(outputId="dataCSVWarn"), style="color: red"),
-                        ),
-                        # Button to add data.
-                        shiny::actionButton(inputId="addData", label="Add"),
-                    ),
-                    # Estimators tab sidebar
-                    shiny::conditionalPanel(condition="input.tabset == 'Estimators'",
-                        shiny::h4("Estimators"),
-                        # Collapsible menu for estimation methods.
-                        shinyBS::bsCollapse(id="estCollapse",
-                            # WHITE & PANAGO (WP).
-                            shinyBS::bsCollapsePanel(title="White & Panago (WP)",
-                                "This is a description of the method.",
-                                shiny::br(), shiny::br(),
-                                shiny::radioButtons(inputId="serialWPKnown", label="Is the mean serial interval known?", inline=TRUE, choices=list("Yes"=1, "No"=2)),
-                                # Known serial interval.
-                                shiny::conditionalPanel(condition="input.serialWPKnown == '1'",
-                                    shiny::fluidRow(
-                                        shiny::column(8, shiny::textInput(inputId="serialWPInput", label="Mean Serial Interval")),
-                                        shiny::column(4, shiny::selectInput(inputId="serialWPUnits", label="Time units", choices=list("Days", "Weeks")))
-                                    ),
-                                    shiny::span(shiny::textOutput(outputId="serialWPWarn"), style="color: red")
-                                ),
-                                # Unknown serial interval.
-                                shiny::conditionalPanel(condition="input.serialWPKnown == '2'",
-                                    shiny::h5("Grid Search Parameters"),
-                                    shiny::fluidRow(
-                                        shiny::column(4, shiny::textInput(inputId="gridLengthInput", label="Grid length", value="100")),
-                                        shiny::column(4, shiny::textInput(inputId="gridShapeInput", label="Max. shape", value="10")),
-                                        shiny::column(4, shiny::textInput(inputId="gridScaleInput", label="Max. scale", value="10"))
-                                    ),
-                                    shiny::fluidRow(
-                                        shiny::column(4, shiny::span(shiny::textOutput(outputId="gridLengthWarn"), style="color: red")),
-                                        shiny::column(4, shiny::span(shiny::textOutput(outputId="gridShapeWarn"), style="color: red")),
-                                        shiny::column(4, shiny::span(shiny::textOutput(outputId="gridScaleWarn"), style="color: red"))
-                                    )
-                                ),
-                                shiny::actionButton(inputId="addWP", label="Add")
-                            ),
-                            # SEQUENTIAL BAYES (seqB).
-                            shinyBS::bsCollapsePanel(title="Sequential Bayes (seqB)",
-                                "This is a description of the method.",
-                                shiny::br(), shiny::br(),
-                                shiny::fluidRow(
-                                    shiny::column(8, shiny::textInput(inputId="serialseqBInput", label="Mean Serial Interval")),
-                                    shiny::column(4, shiny::selectInput(inputId="serialseqBUnits", label="Time units", choices=list("Days", "Weeks")))
-                                ),
-                                shiny::span(shiny::textOutput(outputId="serialseqBWarn"), style="color: red"),
-                                shiny::textInput(inputId="kappaInput", label=shiny::HTML(paste0("Maximum value of the uniform prior", shiny::tags$sup(id="kappaTool", "[?]"))), value="20"),
-                                shinyBS::bsTooltip(id="kappaTool", "Some information. By default, this is set to 20.", placement="right", trigger="hover"),
-                                shiny::span(shiny::textOutput(outputId="kappaWarn"), style="color: red"),
-                                shiny::actionButton(inputId="addseqB", label="Add")
-                            ),
-                            # INCIDENCE DECAY (ID).
-                            shinyBS::bsCollapsePanel(title="Incidence Decay (ID)",
-                                "This is a description of the method.",
-                                shiny::br(), shiny::br(),
-                                shiny::fluidRow(
-                                    shiny::column(8, shiny::textInput(inputId="serialIDInput", label="Mean Serial Interval")),
-                                    shiny::column(4, shiny::selectInput(inputId="serialIDUnits", label="Time units", choices=list("Days", "Weeks")))
-                                ),
-                                shiny::span(shiny::textOutput(outputId="serialIDWarn"), style="color: red"),
-                                shiny::actionButton(inputId="addID", label="Add")
-                            ),
-                            # INCIDENCE DECAY & EXPONENTIAL ADJUSTEMENT (IDEA).
-                            shinyBS::bsCollapsePanel(title="Incidence Decay and Exponential Adjustement (IDEA)",
-                                "This is a description of the method.",
-                                shiny::br(), shiny::br(),
-                                shiny::fluidRow(
-                                    shiny::column(8, shiny::textInput(inputId="serialIDEAInput", label="Mean Serial Interval")),
-                                    shiny::column(4, shiny::selectInput(inputId="serialIDEAUnits", label="Time units", choices=list("Days", "Weeks")))
-                                ),
-                                shiny::span(shiny::textOutput(outputId="serialIDEAWarn"), style="color: red"),
-                                shiny::actionButton(inputId="addIDEA", label="Add")
-                            )
-                        )
-                    )
-                )
-            ),
-            # Main panel.
-            shiny::mainPanel(id="main",
-                shiny::tabsetPanel(id="tabset", type="tabs",
-                    shiny::tabPanel("About", shiny::br(), "Hello"),
-                    shiny::tabPanel("Data", shiny::br(), shiny::dataTableOutput(outputId="dataTable"), shiny::tags$style(type="text/css", '#dataTable tfoot {display:none;}')),
-                    shiny::tabPanel("Estimators", shiny::br(),
-                        shiny::dataTableOutput(outputId="estTable"),
-                        shiny::tags$style(type="text/css", "#estTable tfoot {display:none;}"),
-                        shiny::downloadButton(outputId="downloadEst", label="Download table as .csv")
-                    ),
-                )
-            )
+  shiny::fluidPage(
+    # Title.
+    shiny::titlePanel(shiny::HTML(
+      paste0("Rnaught: An Estimation Suite for R", shiny::tags$sub("0")))),
+    # Sidebar layout.
+    shiny::sidebarLayout(
+      # Sidebar. Hidden if the 'About' tab is selected.
+      shiny::conditionalPanel(condition = "input.tabset != 'About'",
+        shiny::sidebarPanel(id = "sidebar", data_sidebar(), est_sidebar())),
+      # Main panel.
+      shiny::mainPanel(id = "main",
+        shiny::tabsetPanel(id = "tabset", type = "tabs",
+          shiny::tabPanel("About", shiny::br(), "Hello"),
+          shiny::tabPanel("Data", shiny::br(),
+            shiny::dataTableOutput(outputId = "dataTable"),
+            shiny::tags$style(type = "text/css",
+                              "#dataTable tfoot { display:none; }")),
+          shiny::tabPanel("Estimators", shiny::br(),
+            shiny::dataTableOutput(outputId = "estTable"),
+            shiny::tags$style(type = "text/css",
+                              "#estTable tfoot { display:none; }"),
+            shiny::downloadButton(outputId = "downloadEst",
+                                  label = "Download table as .csv"))

         )
         )

+      )

     )
     )

+  )
+}
+
+# Data tab sidebar.
+data_sidebar <- function() {
+  shiny::conditionalPanel(condition = "input.tabset == 'Data'",
+    shiny::h3("Enter data"),
+    # Data input method selection.
+    shiny::radioButtons(inputId = "dataInputMethod", label = "",
+      choices=list("Manually" = 1, "Upload a .csv file" = 2,
+                   "Paste a .csv file" = 3)),
+    # Option 1: Manual entry.
+    shiny::conditionalPanel(condition = "input.dataInputMethod == '1'",
+      shiny::textInput(inputId = "dataName", label = "Dataset name"),
+      shiny::span(shiny::textOutput(outputId = "dataNameWarn"),
+                  style = "color: red;"),
+      shiny::fluidRow(
+        shiny::column(8,
+          shiny::textInput(inputId = "dataCounts",
+            label = help_tool("Case counts", paste0("Enter as a ",
+              "comma-separated list of positive integers, with at least two ",
+              "entries. (Example: 1,1,2,3,5,8)")))),
+        shiny::column(4, shiny::selectInput(inputId = "dataUnits",
+          label = "Reporting frequency", choices = list("Daily", "Weekly")))
+      ),
+      shiny::span(shiny::textOutput(outputId = "dataCountsWarn"),
+                  style = "color: red;")
+    ),
+    # Option 2: Upload .csv file.
+    shiny::conditionalPanel(condition = "input.dataInputMethod == '2'",
+      shiny::fileInput(inputId = "dataUpload", label = "",
+        accept = c("text/csv", "text/comma-separated-values,text/plain",
+                   ".csv")),
+    ),
+    # Option 3: Paste .csv file.
+    shiny::conditionalPanel(condition = "input.dataInputMethod == '3'",
+      shiny::textAreaInput(inputId = "dataPaste", label = "",
+                           rows = 8, resize = "none"),
+    ),
+    # Warning text for .csv upload / paste.
+    shiny::conditionalPanel(
+      condition = "['2', '3'].includes(input.dataInputMethod)",
+      shiny::span(shiny::textOutput(outputId = "dataCSVWarn"),
+                  style = "color: red;"),
+    ),
+    # Button to add data.
+    shiny::actionButton(inputId = "addData", label = "Add")
+  )
+}
+
+# Estimators tab sidebar.
+est_sidebar <- function() {
+  shiny::conditionalPanel(condition = "input.tabset == 'Estimators'",
+    shiny::h3("Estimators"),
+    WP_collapse(),
+    seqB_collapse(),
+    ID_collapse(),
+    IDEA_collapse(),
+
+    shiny::tags$style(type = "text/css",
+                      "summary { display: list-item; cursor: pointer; }"),
+    shiny::tags$style(type = "text/css", "summary h4 { display: inline; }")
+  )
+}
+
+# Collapsable entry for White & Panago (WP) method.
+WP_collapse <- function() {
+  shiny::tags$details(
+    shiny::tags$summary(shiny::h4("White & Panago (WP)")),
+    shiny::p("Method due to White and Pagano (2008), assumes a branching process
+             based model. Serial distribution can be assumed known or can be
+             estimated using maximum likelihood;  When serial interval is
+             unknown the method takes longer to compute, though is still
+             real-time."),
+    shiny::br(),
+    shiny::radioButtons(inputId = "serialWPKnown",
+                        label = "Is the mean serial interval known?",
+                        inline = TRUE, choices = list("Yes" = 1, "No" = 2)),
+    # Known serial interval.
+    shiny::conditionalPanel(condition = "input.serialWPKnown == '1'",
+      serial_fields("WP")),
+    # Unknown serial interval.
+    shiny::conditionalPanel(condition = "input.serialWPKnown == '2'",
+      shiny::h5("Grid Search Parameters"),
+      shiny::fluidRow(
+        shiny::column(4, shiny::textInput(inputId = "gridLengthInput",
+          label = "Grid length", value = "100")),
+        shiny::column(4, shiny::textInput(inputId = "gridShapeInput",
+          label = "Max. shape", value = "10")),
+        shiny::column(4, shiny::textInput(inputId = "gridScaleInput",
+          label = "Max. scale", value = "10"))
+      ),
+      shiny::fluidRow(
+        shiny::column(4, shiny::span(shiny::textOutput(
+          outputId = "gridLengthWarn"), style = "color: red;")),
+        shiny::column(4, shiny::span(shiny::textOutput(
+          outputId = "gridShapeWarn"), style = "color: red;")),
+        shiny::column(4, shiny::span(shiny::textOutput(
+          outputId = "gridScaleWarn"), style = "color: red;"))
+      )
+    ),
+    shiny::actionButton(inputId = "addWP", label = "Add")
+  )
+}
+
+# Collapsable entry for Sequential Bayes (seqB) method.
+seqB_collapse <- function() {
+  shiny::tags$details(
+    shiny::tags$summary(shiny::h4("Sequential Bayes (seqB)")),
+    shiny::p("This is a description of the method."),
+    shiny::br(),
+    serial_fields("seqB"),
+    shiny::textInput(inputId = "kappaInput",
+      label = help_tool("Maximum value", paste0("This describes the prior ",
+        "belief of R0, and should be set to a higher value if R0 is believed ",
+        "be larger. (Default: 20)")), value = "20"),
+    shiny::span(shiny::textOutput(outputId = "kappaWarn"),
+                style = "color: red;"),
+    shiny::actionButton(inputId = "addseqB", label = "Add")
+  )
+}
+
+# Collapsable entry for Incidence Decay (ID) method.
+ID_collapse <- function() {
+  shiny::tags$details(
+    shiny::tags$summary(shiny::h4("Incidence Decay (ID)")),
+    shiny::p("This is a description of the method."),
+    shiny::br(),
+    serial_fields("ID"),
+    shiny::actionButton(inputId = "addID", label = "Add")
+  )
+}
+
+# Collapsable entry for Incidence Decay & Exponential Adjustment (IDEA) method.
+IDEA_collapse <- function() {
+  shiny::tags$details(
+    shiny::tags$summary(
+      shiny::h4("Incidence Decay and Exponential Adjustment (IDEA)")),
+    shiny::p("This is a description of the method."),
+    shiny::br(),
+    serial_fields("IDEA"),
+    shiny::actionButton(inputId = "addIDEA", label = "Add")
+  )
+}
+
+# Input fields and warning text for the mean serial interval.
+serial_fields <- function(method) {
+  shiny::HTML(paste0(
+    shiny::fluidRow(
+      shiny::column(8, shiny::textInput(
+        inputId = paste0("serial", method, "Input"),
+        label = "Mean Serial Interval")),
+      shiny::column(4, shiny::selectInput(
+        inputId = paste0("serial", method, "Units"),
+        label = "Time units", choices = list("Days", "Weeks")))
+    ),
+    shiny::span(shiny::textOutput(outputId = paste0("serial", method, "Warn")),
+                style = "color: red;")
+  ))
+}
+
+# Display help information on hover.
+help_tool <- function(label, help_text) {
+  shiny::HTML(paste0(label, shiny::tags$sup("[?]", title = help_text)))

 }
 }