-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")))
- ),
- 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$style(type = "text/css",
- "summary h4 { display: inline; }")
+ui <- function() {
+ shiny::fluidPage(
+ # Title.
+ shiny::titlePanel(shiny::HTML(
+ paste0("Rnaught: An Estimation Suite for R", shiny::tags$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_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"),
),
- # 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"))
+ # 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 & Pagano (WP) method.
+WP_collapse <- function() {
+ shiny::tags$details(
+ shiny::tags$summary(shiny::h4("White & Pagano (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)))
+}
git.nmode.ca / Rnaught / blobdiff
