Remove 'shinyBS' dependency

diff --git a/DESCRIPTION b/DESCRIPTION
index d9fdfad64f3d6c017c83a8181bb0d41aeb551c17..74a472bb7bbc9662fafc6506bc3fdb4ba5fcabe6 100644 (file)
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -17,9 +17,7 @@ Imports:
     methods,
     stats,
     utils
     methods,
     stats,
     utils

-Suggests:
-    shiny,
-    shinyBS
+Suggests: shiny

 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.2.3
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.2.3

diff --git a/R/app.R b/R/app.R
index 64b5d2a3925eb163e9ee7ef0cab8eea83ec9d85d..1bf3e93bd53ac37183355463c0c4ef8f2b7a4e06 100644 (file)
--- a/R/app.R
+++ b/R/app.R
@@ -4,8 +4,6 @@
 app <- function() {
     if (!requireNamespace("shiny", quietly=TRUE))
         stop("The package 'shiny' must be installed to launch the Rnaught web application.")
 app <- function() {
     if (!requireNamespace("shiny", quietly=TRUE))
         stop("The package 'shiny' must be installed to launch the Rnaught web application.")

-    if (!requireNamespace("shinyBS", quietly=TRUE))
-        stop("The package 'shinyBS' must be installed to launch the Rnaught web application.")

 
     shiny::shinyApp(ui(), server)
 }
 
     shiny::shinyApp(ui(), server)
 }

diff --git a/R/ui.R b/R/ui.R
index 63e21eb5304fc82f618d9843172cf8ad80b1e743..d6102f97a442d9716ca14c63b920f315260f4bff 100644 (file)
--- a/R/ui.R
+++ b/R/ui.R
@@ -1,7 +1,7 @@
 ui <- function() {
     shiny::fluidPage(
         # Title.
 ui <- function() {
     shiny::fluidPage(
         # Title.

-        shiny::titlePanel(shiny::HTML(paste0("Rnaught: an estimation suite for R", shiny::tags$sub("0")))),
+        shiny::titlePanel(shiny::HTML(paste0("Rnaught: An Estimation Suite for R", shiny::tags$sub("0")))),

   
         # Sidebar layout.
         shiny::sidebarLayout(
   
         # Sidebar layout.
         shiny::sidebarLayout(


@@ -10,19 +10,20 @@ ui <- function() {
                 shiny::sidebarPanel(id="sidebar",
                     # Data tab sidebar.
                     shiny::conditionalPanel(condition="input.tabset == 'Data'",
                 shiny::sidebarPanel(id="sidebar",
                     # Data tab sidebar.
                     shiny::conditionalPanel(condition="input.tabset == 'Data'",

-                        shiny::h4("Enter 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"),
                         # 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::span(shiny::textOutput(outputId="dataNameWarn"), style="color: red;"),

                             shiny::fluidRow(
                             shiny::fluidRow(

-                                shiny::column(8, shiny::textInput(inputId="dataCounts", label=shiny::HTML(paste0("Case counts", shiny::tags$sup(id="dataCountsHelp", "[?]"))))),
+                                shiny::column(8, shiny::textInput(inputId="dataCounts", label=shiny::HTML(paste0(
+                                    "Case counts", shiny::tags$sup("[?]", title="Enter as a comma-separated list of positive integers, with at least two entries. Ex: 1,1,2,3,5,8"))))
+                                ),

                                 shiny::column(4, shiny::selectInput(inputId="dataUnits", label="Reporting frequency", choices=list("Daily", "Weekly")))
                             ),
                                 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")
+                            shiny::span(shiny::textOutput(outputId="dataCountsWarn"), style="color: red;")

                         ),
                         # Option 2: Upload .csv file.
                         shiny::conditionalPanel(condition="input.dataInputMethod == '2'",
                         ),
                         # Option 2: Upload .csv file.
                         shiny::conditionalPanel(condition="input.dataInputMethod == '2'",


@@ -34,82 +35,87 @@ ui <- function() {
                         ),
                         # Warning text for .csv upload / paste.
                         shiny::conditionalPanel(condition="['2', '3'].includes(input.dataInputMethod)",
                         ),
                         # Warning text for .csv upload / paste.
                         shiny::conditionalPanel(condition="['2', '3'].includes(input.dataInputMethod)",

-                            shiny::span(shiny::textOutput(outputId="dataCSVWarn"), style="color: red"),
+                            shiny::span(shiny::textOutput(outputId="dataCSVWarn"), style="color: red;"),

                         ),
                         # Button to add data.
                         shiny::actionButton(inputId="addData", label="Add"),
                     ),
                         ),
                         # Button to add data.
                         shiny::actionButton(inputId="addData", label="Add"),
                     ),

-                    # Estimators tab sidebar
+                    # Estimators tab sidebar (collapsable entries).

                     shiny::conditionalPanel(condition="input.tabset == 'Estimators'",
                     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::h3("Estimators"),
+                        # WHITE & PANAGO (WP).
+                        shiny::tags$details(
+                            shiny::tags$summary(shiny::h4("White & Panago (WP)")),
+                            shiny::p("This is a description of the method."),
+                            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::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::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="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")
+                                shiny::span(shiny::textOutput(outputId="serialWPWarn"), style="color: red;")

                             ),
                             ),

-                            # INCIDENCE DECAY (ID).
-                            shinyBS::bsCollapsePanel(title="Incidence Decay (ID)",
-                                "This is a description of the method.",
-                                shiny::br(), shiny::br(),
+                            # Unknown serial interval.
+                            shiny::conditionalPanel(condition="input.serialWPKnown == '2'",
+                                shiny::h5("Grid Search Parameters"),

                                 shiny::fluidRow(
                                 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::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::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::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")
-                            )
-                        )
+                                    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).
+                        shiny::tags$details(
+                            shiny::tags$summary(shiny::h4("Sequential Bayes (seqB)")),
+                            shiny::p("This is a description of the method."),
+                            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$sup("[?]", title="This describes the prior belief of R0, and should be set to a higher value if R0 is believed to be larger. (Default: 20)"))),
+                                value="20"
+                            ),
+                            shiny::span(shiny::textOutput(outputId="kappaWarn"), style="color: red;"),
+                            shiny::actionButton(inputId="addseqB", label="Add")
+                        ),
+                        # INCIDENCE DECAY (ID).
+                        shiny::tags$details(
+                            shiny::tags$summary(shiny::h4("Incidence Decay (ID)")),
+                            shiny::p("This is a description of the method."),
+                            shiny::br(),
+                            shiny::fluidRow(
+                                shiny::column(8, shiny::textInput(inputId="serialIDInput", label="Mean Serial Interval")),
+                                shiny::column(4, shiny::selectInput(inputId="serialIDUnits", label="Time units", choices=list("Days", "Weeks")))
+                            ),
+                            shiny::span(shiny::textOutput(outputId="serialIDWarn"), style="color: red;"),
+                            shiny::actionButton(inputId="addID", label="Add")
+                        ),
+                        # INCIDENCE DECAY & EXPONENTIAL ADJUSTEMENT (IDEA).
+                        shiny::tags$details(
+                            shiny::tags$summary(shiny::h4("Incidence Decay and Exponential Adjustement (IDEA)")),
+                            shiny::p("This is a description of the method."),
+                            shiny::br(),
+                            shiny::fluidRow(
+                                shiny::column(8, shiny::textInput(inputId="serialIDEAInput", label="Mean Serial Interval")),
+                                shiny::column(4, shiny::selectInput(inputId="serialIDEAUnits", label="Time units", choices=list("Days", "Weeks")))
+                            ),
+                            shiny::span(shiny::textOutput(outputId="serialIDEAWarn"), style="color: red;"),
+                            shiny::actionButton(inputId="addIDEA", label="Add")
+                        ),
+                        shiny::tags$style(type="text/css", "summary { display: list-item; cursor: pointer; }"),
+                        shiny::tags$style(type="text/css", "summary h4 { display: inline; }")

                     )
                 )
             ),
                     )
                 )
             ),


@@ -117,12 +123,12 @@ ui <- function() {
             shiny::mainPanel(id="main",
                 shiny::tabsetPanel(id="tabset", type="tabs",
                     shiny::tabPanel("About", shiny::br(), "Hello"),
             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$style(type="text/css", '#dataTable tfoot {display:none;}')),
+                    shiny::tabPanel("Data", shiny::br(), shiny::dataTableOutput(outputId="dataTable"), shiny::tags$style(type="text/css", "#dataTable tfoot { display:none; }")),

                     shiny::tabPanel("Estimators", shiny::br(),
                         shiny::dataTableOutput(outputId="estTable"),
                     shiny::tabPanel("Estimators", shiny::br(),
                         shiny::dataTableOutput(outputId="estTable"),

-                        shiny::tags$style(type="text/css", "#estTable tfoot {display:none;}"),
+                        shiny::tags$style(type="text/css", "#estTable tfoot { display:none; }"),

                         shiny::downloadButton(outputId="downloadEst", label="Download table as .csv")
                         shiny::downloadButton(outputId="downloadEst", label="Download table as .csv")

-                    ),
+                    )

                 )
             )
         )
                 )
             )
         )