nmode's Git Repositories - Rnaught/blob - R/ui.R

   1 ui <- function() { shiny::fluidPage(
   2   # Title.
   3   shiny::titlePanel(shiny::HTML(
   4     paste0("Rnaught: An Estimation Suite for R", shiny::tags$sub("0")))),
   5   # Sidebar layout.
   6   shiny::sidebarLayout(
   7     # Sidebar. Hidden if the 'About' tab is selected.
   8     shiny::conditionalPanel(condition = "input.tabset != 'About'",
   9       shiny::sidebarPanel(id = "sidebar",
  10         # Data tab sidebar.
  11         shiny::conditionalPanel(condition = "input.tabset == 'Data'",
  12           shiny::h3("Enter data"),
  13           # Data input method selection.
  14           shiny::radioButtons(inputId = "dataInputMethod", label = "",
  15             choices=list("Manually" = 1, "Upload a .csv file" = 2,
  16                          "Paste a .csv file" = 3)),
  17           # Option 1: Manual entry.
  18           shiny::conditionalPanel(condition = "input.dataInputMethod == '1'",
  19             shiny::textInput(inputId = "dataName", label = "Dataset name"),
  20             shiny::span(shiny::textOutput(outputId = "dataNameWarn"),
  21                         style = "color: red;"),
  22             shiny::fluidRow(
  23               shiny::column(8,
  24                 shiny::textInput(inputId = "dataCounts", label = shiny::HTML(
  25                   paste0("Case counts", shiny::tags$sup("[?]",
  26                     title = paste0("Enter as a comma-separated list of ",
  27                                    "positive integers, with at least two ",
  28                                    "entries. Example: 1,1,2,3,5,8")))))),
  29               shiny::column(4,
  30                 shiny::selectInput(inputId = "dataUnits",
  31                                    label = "Reporting frequency",
  32                                    choices = list("Daily", "Weekly")))
  33             ),
  34             shiny::span(shiny::textOutput(outputId = "dataCountsWarn"),
  35                         style = "color: red;")
  36           ),
  37           # Option 2: Upload .csv file.
  38           shiny::conditionalPanel(condition = "input.dataInputMethod == '2'",
  39             shiny::fileInput(inputId = "dataUpload", label = "",
  40               accept = c("text/csv", "text/comma-separated-values,text/plain",
  41                          ".csv")),
  42           ),
  43           # Option 3: Paste .csv file.
  44           shiny::conditionalPanel(condition = "input.dataInputMethod == '3'",
  45             shiny::textAreaInput(inputId = "dataPaste", label = "",
  46                                  rows = 8, resize = "none"),
  47           ),
  48           # Warning text for .csv upload / paste.
  49           shiny::conditionalPanel(
  50             condition = "['2', '3'].includes(input.dataInputMethod)",
  51             shiny::span(shiny::textOutput(outputId = "dataCSVWarn"),
  52                         style = "color: red;"),
  53           ),
  54           # Button to add data.
  55           shiny::actionButton(inputId = "addData", label = "Add"),
  56         ),
  57         # Estimators tab sidebar (collapsable entries).
  58         shiny::conditionalPanel(condition = "input.tabset == 'Estimators'",
  59           shiny::h3("Estimators"),
  60           # WHITE & PANAGO (WP).
  61           shiny::tags$details(
  62             shiny::tags$summary(shiny::h4("White & Panago (WP)")),
  63             shiny::p("Method due to White and Pagano (2008), assumes a branching process based model. Serial
  64 distribution can be assumed known or can be estimated using maximum likelihood;  When serial interval is unknown
  65 the method takes longer to compute, though is still real-time."),
  66             shiny::br(),
  67             shiny::radioButtons(inputId = "serialWPKnown",
  68                                 label = "Is the mean serial interval known?",
  69                                 inline = TRUE,
  70                                 choices = list("Yes" = 1, "No" = 2)),
  71             # Known serial interval.
  72             shiny::conditionalPanel(condition = "input.serialWPKnown == '1'",
  73               shiny::fluidRow(
  74                 shiny::column(8,
  75                   shiny::textInput(inputId = "serialWPInput",
  76                                    label = "Mean Serial Interval")),
  77                 shiny::column(4,
  78                   shiny::selectInput(inputId = "serialWPUnits",
  79                                      label = "Time units",
  80                                      choices = list("Days", "Weeks")))
  81               ),
  82               shiny::span(shiny::textOutput(outputId = "serialWPWarn"),
  83                           style = "color: red;")
  84             ),
  85             # Unknown serial interval.
  86             shiny::conditionalPanel(condition = "input.serialWPKnown == '2'",
  87               shiny::h5("Grid Search Parameters"),
  88               shiny::fluidRow(
  89                 shiny::column(4,
  90                   shiny::textInput(inputId = "gridLengthInput",
  91                                    label = "Grid length", value = "100")),
  92                 shiny::column(4,
  93                   shiny::textInput(inputId = "gridShapeInput",
  94                                    label = "Max. shape", value = "10")),
  95                 shiny::column(4,
  96                   shiny::textInput(inputId = "gridScaleInput",
  97                                    label = "Max. scale", value = "10"))
  98               ),
  99               shiny::fluidRow(
 100                 shiny::column(4,
 101                   shiny::span(shiny::textOutput(outputId = "gridLengthWarn"),
 102                               style = "color: red;")),
 103                 shiny::column(4,
 104                   shiny::span(shiny::textOutput(outputId = "gridShapeWarn"),
 105                               style = "color: red;")),
 106                 shiny::column(4,
 107                   shiny::span(shiny::textOutput(outputId = "gridScaleWarn"),
 108                               style = "color: red;"))
 109               )
 110             ),
 111             shiny::actionButton(inputId = "addWP", label = "Add")
 112           ),
 113           # SEQUENTIAL BAYES (seqB).
 114           shiny::tags$details(
 115             shiny::tags$summary(shiny::h4("Sequential Bayes (seqB)")),
 116             shiny::p("This is a description of the method."),
 117             shiny::br(),
 118             shiny::fluidRow(
 119               shiny::column(8,
 120                 shiny::textInput(inputId = "serialseqBInput",
 121                                  label = "Mean Serial Interval")),
 122               shiny::column(4,
 123                 shiny::selectInput(inputId = "serialseqBUnits",
 124                                    label = "Time units",
 125                                    choices = list("Days", "Weeks")))
 126             ),
 127             shiny::span(shiny::textOutput(outputId = "serialseqBWarn"),
 128                         style = "color: red;"),
 129             shiny::textInput(inputId = "kappaInput",
 130               label = shiny::HTML(paste0("Maximum value", shiny::tags$sup("[?]",
 131                 title = paste0("This describes the prior belief of R0, and ",
 132                                "should be set to a higher value if R0 is ",
 133                                "believed to be larger. (Default: 20)")))),
 134               value = "20"),
 135             shiny::span(shiny::textOutput(outputId = "kappaWarn"),
 136                         style = "color: red;"),
 137             shiny::actionButton(inputId = "addseqB", label = "Add")
 138           ),
 139           # INCIDENCE DECAY (ID).
 140           shiny::tags$details(
 141             shiny::tags$summary(shiny::h4("Incidence Decay (ID)")),
 142             shiny::p("This is a description of the method."),
 143             shiny::br(),
 144             shiny::fluidRow(
 145               shiny::column(8,
 146                 shiny::textInput(inputId = "serialIDInput",
 147                                  label = "Mean Serial Interval")),
 148               shiny::column(4,
 149                 shiny::selectInput(inputId = "serialIDUnits",
 150                                    label = "Time units",
 151                                    choices = list("Days", "Weeks")))
 152             ),
 153             shiny::span(shiny::textOutput(outputId = "serialIDWarn"),
 154                         style = "color: red;"),
 155             shiny::actionButton(inputId = "addID", label = "Add")
 156           ),
 157           # INCIDENCE DECAY & EXPONENTIAL ADJUSTEMENT (IDEA).
 158           shiny::tags$details(
 159             shiny::tags$summary(
 160               shiny::h4("Incidence Decay and Exponential Adjustement (IDEA)")),
 161             shiny::p("This is a description of the method."),
 162             shiny::br(),
 163             shiny::fluidRow(
 164               shiny::column(8,
 165                 shiny::textInput(inputId = "serialIDEAInput",
 166                                  label = "Mean Serial Interval")),
 167               shiny::column(4,
 168                 shiny::selectInput(inputId = "serialIDEAUnits",
 169                                    label = "Time units",
 170                                    choices = list("Days", "Weeks")))
 171             ),
 172             shiny::span(shiny::textOutput(outputId = "serialIDEAWarn"),
 173                         style = "color: red;"),
 174             shiny::actionButton(inputId = "addIDEA", label = "Add")
 175           ),
 176           shiny::tags$style(type = "text/css",
 177                             "summary { display: list-item; cursor: pointer; }"),
 178           shiny::tags$style(type = "text/css",
 179                             "summary h4 { display: inline; }")
 180         )
 181       )
 182     ),
 183     # Main panel.
 184     shiny::mainPanel(id = "main",
 185       shiny::tabsetPanel(id = "tabset", type = "tabs",
 186         shiny::tabPanel("About", shiny::br(), "Hello"),
 187         shiny::tabPanel("Data", shiny::br(),
 188                         shiny::dataTableOutput(outputId = "dataTable"),
 189                         shiny::tags$style(type = "text/css",
 190                           "#dataTable tfoot { display:none; }")),
 191         shiny::tabPanel("Estimators", shiny::br(),
 192                         shiny::dataTableOutput(outputId = "estTable"),
 193                         shiny::tags$style(type = "text/css",
 194                           "#estTable tfoot { display:none; }"),
 195                         shiny::downloadButton(outputId = "downloadEst",
 196                                               label = "Download table as .csv"))
 197       )
 198     )
 199   )
 200 )}