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

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