diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/ui.R | 382 |
1 files changed, 187 insertions, 195 deletions
@@ -1,200 +1,192 @@ -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 & Panago (WP) method. +WP_collapse <- function() { + 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'", + 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))) +} |