-ui <- function() {
- shiny::fluidPage(
- shinyjs::useShinyjs(),
-
- # Title.
- shiny::titlePanel(shiny::HTML(paste0("Rnaught: an estimation suite for R", shiny::tags$sub("0")))),
-
- # Sidebar layout.
- shiny::sidebarLayout(
- # Sidebar.
- shiny::sidebarPanel(id="sidebar",
- # Data tab sidebar.
- shiny::conditionalPanel(condition="input.tabset == 'Data'",
- shiny::h4("Enter data"),
- # Data input method selection.
- shiny::radioButtons(inputId="dataInputMethod", label="", choices=list("Manually"=1, "Upload a .csv file"=2, "Paste a .csv file"=3)),
- # Option 1: Manual entry.
- shiny::conditionalPanel(condition="input.dataInputMethod == '1'",
- shiny::textInput(inputId="dataName", label="Dataset name"),
- shiny::span(shiny::textOutput(outputId="dataNameWarn"), style="color: red"),
- shiny::fluidRow(
- shiny::column(8, shiny::textInput(inputId="dataCounts", label=shiny::HTML(paste0("Case counts", shiny::tags$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$sup(id="kappaTool", "[?]"))), value="20"),
- shinyBS::bsTooltip(id="kappaTool", "Some information. By default, this is set to 20.", placement="right", trigger="hover"),
- shiny::span(shiny::textOutput(outputId="kappaWarn"), style="color: red"),
- shiny::actionButton(inputId="addseqB", label="Add")
- ),
- # INCIDENCE DECAY (ID).
- shinyBS::bsCollapsePanel(title="Incidence Decay (ID)",
- "This is a description of the method.",
- shiny::br(), shiny::br(),
- shiny::fluidRow(
- shiny::column(8, shiny::textInput(inputId="serialIDInput", label="Mean Serial Interval")),
- shiny::column(4, shiny::selectInput(inputId="serialIDUnits", label="Time units", choices=list("Days", "Weeks")))
- ),
- shiny::span(shiny::textOutput(outputId="serialIDWarn"), style="color: red"),
- shiny::actionButton(inputId="addID", label="Add")
- ),
- # INCIDENCE DECAY & EXPONENTIAL ADJUSTEMENT (IDEA).
- shinyBS::bsCollapsePanel(title="Incidence Decay and Exponential Adjustement (IDEA)",
- "This is a description of the method.",
- shiny::br(), shiny::br(),
- shiny::fluidRow(
- shiny::column(8, shiny::textInput(inputId="serialIDEAInput", label="Mean Serial Interval")),
- shiny::column(4, shiny::selectInput(inputId="serialIDEAUnits", label="Time units", choices=list("Days", "Weeks")))
- ),
- shiny::span(shiny::textOutput(outputId="serialIDEAWarn"), style="color: red"),
- shiny::actionButton(inputId="addIDEA", label="Add")
- )
- )
- )
+ui <- function() { shiny::fluidPage(
+ # Title.
+ shiny::titlePanel(shiny::HTML(
+ paste0("Rnaught: An Estimation Suite for R", shiny::tags$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::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 = shiny::HTML(
+ paste0("Case counts", shiny::tags$sup("[?]",
+ title = paste0("Enter as a comma-separated list of ",
+ "positive integers, with at least two ",
+ "entries. Example: 1,1,2,3,5,8")))))),
+ shiny::column(4,
+ shiny::selectInput(inputId = "dataUnits",
+ label = "Reporting frequency",
+ choices = list("Daily", "Weekly")))
),
- # Main panel.
- shiny::mainPanel(id="main",
- shiny::tabsetPanel(id="tabset", type="tabs",
- shiny::tabPanel("About", shiny::br(), "Hello"),
- shiny::tabPanel("Data", shiny::br(), shiny::dataTableOutput(outputId="dataTable"), shiny::tags$style(type="text/css", '#dataTable tfoot {display:none;}')),
- shiny::tabPanel("Estimators", shiny::br(),
- shiny::dataTableOutput(outputId="estTable"),
- shiny::tags$style(type="text/css", "#estTable tfoot {display:none;}"),
- shiny::downloadButton(outputId="downloadEst", label="Download table as .csv")
- ),
- )
- )
+ shiny::span(shiny::textOutput(outputId = "dataCountsWarn"),
+ style = "color: red;")
+ ),
+ # Option 2: Upload .csv file.
+ shiny::conditionalPanel(condition = "input.dataInputMethod == '2'",
+ shiny::fileInput(inputId = "dataUpload", label = "",
+ accept = c("text/csv", "text/comma-separated-values,text/plain",
+ ".csv")),
+ ),
+ # Option 3: Paste .csv file.
+ shiny::conditionalPanel(condition = "input.dataInputMethod == '3'",
+ shiny::textAreaInput(inputId = "dataPaste", label = "",
+ rows = 8, resize = "none"),
+ ),
+ # Warning text for .csv upload / paste.
+ shiny::conditionalPanel(
+ condition = "['2', '3'].includes(input.dataInputMethod)",
+ shiny::span(shiny::textOutput(outputId = "dataCSVWarn"),
+ style = "color: red;"),
+ ),
+ # Button to add data.
+ shiny::actionButton(inputId = "addData", label = "Add"),
+ ),
+ # Estimators tab sidebar (collapsable entries).
+ shiny::conditionalPanel(condition = "input.tabset == 'Estimators'",
+ shiny::h3("Estimators"),
+ # WHITE & PANAGO (WP).
+ shiny::tags$details(
+ shiny::tags$summary(shiny::h4("White & Panago (WP)")),
+ shiny::p("Method due to [White and Pagano(2008)], assumes a branching process based model. Serial
+distribution can be assumed known or can be estimated using maximum likelihood; When serial interval is unknown
+the method takes longer to compute, though is still real-time."),
+ shiny::br(),
+ shiny::radioButtons(inputId = "serialWPKnown",
+ label = "Is the mean serial interval known?",
+ inline = TRUE,
+ choices = list("Yes" = 1, "No" = 2)),
+ # Known serial interval.
+ shiny::conditionalPanel(condition = "input.serialWPKnown == '1'",
+ shiny::fluidRow(
+ shiny::column(8,
+ shiny::textInput(inputId = "serialWPInput",
+ label = "Mean Serial Interval")),
+ shiny::column(4,
+ shiny::selectInput(inputId = "serialWPUnits",
+ label = "Time units",
+ choices = list("Days", "Weeks")))
+ ),
+ shiny::span(shiny::textOutput(outputId = "serialWPWarn"),
+ style = "color: red;")
+ ),
+ # Unknown serial interval.
+ shiny::conditionalPanel(condition = "input.serialWPKnown == '2'",
+ shiny::h5("Grid Search Parameters"),
+ shiny::fluidRow(
+ shiny::column(4,
+ shiny::textInput(inputId = "gridLengthInput",
+ label = "Grid length", value = "100")),
+ shiny::column(4,
+ shiny::textInput(inputId = "gridShapeInput",
+ label = "Max. shape", value = "10")),
+ shiny::column(4,
+ shiny::textInput(inputId = "gridScaleInput",
+ label = "Max. scale", value = "10"))
+ ),
+ shiny::fluidRow(
+ shiny::column(4,
+ shiny::span(shiny::textOutput(outputId = "gridLengthWarn"),
+ style = "color: red;")),
+ shiny::column(4,
+ shiny::span(shiny::textOutput(outputId = "gridShapeWarn"),
+ style = "color: red;")),
+ shiny::column(4,
+ shiny::span(shiny::textOutput(outputId = "gridScaleWarn"),
+ style = "color: red;"))
+ )
+ ),
+ shiny::actionButton(inputId = "addWP", label = "Add")
+ ),
+ # SEQUENTIAL BAYES (seqB).
+ shiny::tags$details(
+ shiny::tags$summary(shiny::h4("Sequential Bayes (seqB)")),
+ shiny::p("This is a description of the method."),
+ shiny::br(),
+ shiny::fluidRow(
+ shiny::column(8,
+ shiny::textInput(inputId = "serialseqBInput",
+ label = "Mean Serial Interval")),
+ shiny::column(4,
+ shiny::selectInput(inputId = "serialseqBUnits",
+ label = "Time units",
+ choices = list("Days", "Weeks")))
+ ),
+ shiny::span(shiny::textOutput(outputId = "serialseqBWarn"),
+ style = "color: red;"),
+ shiny::textInput(inputId = "kappaInput",
+ label = shiny::HTML(paste0("Maximum value", shiny::tags$sup("[?]",
+ title = paste0("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; }")
)
+ )
+ ),
+ # 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"))
+ )
)
-}
+ )
+)}
git.nmode.ca / Rnaught / blobdiff
