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authorNaeem Model <me@nmode.ca>2023-06-27 03:40:33 +0000
committerNaeem Model <me@nmode.ca>2023-06-27 03:40:33 +0000
commit18358add05e58e466ba7098f771e20d8d0599d0e (patch)
tree410fbf865ee68b1412dd7d773b4b7da3d45ed137 /R
parent6caff1be02042720e8f362573533914a975d4e1a (diff)
Remove 'shinyBS' dependency
Diffstat (limited to 'R')
-rw-r--r--R/app.R2
-rw-r--r--R/ui.R154
2 files changed, 80 insertions, 76 deletions
diff --git a/R/app.R b/R/app.R
index 64b5d2a..1bf3e93 100644
--- a/R/app.R
+++ b/R/app.R
@@ -4,8 +4,6 @@
app <- function() {
if (!requireNamespace("shiny", quietly=TRUE))
stop("The package 'shiny' must be installed to launch the Rnaught web application.")
- if (!requireNamespace("shinyBS", quietly=TRUE))
- stop("The package 'shinyBS' must be installed to launch the Rnaught web application.")
shiny::shinyApp(ui(), server)
}
diff --git a/R/ui.R b/R/ui.R
index 63e21eb..d6102f9 100644
--- a/R/ui.R
+++ b/R/ui.R
@@ -1,7 +1,7 @@
ui <- function() {
shiny::fluidPage(
# Title.
- shiny::titlePanel(shiny::HTML(paste0("Rnaught: an estimation suite for R", shiny::tags$sub("0")))),
+ shiny::titlePanel(shiny::HTML(paste0("Rnaught: An Estimation Suite for R", shiny::tags$sub("0")))),
# Sidebar layout.
shiny::sidebarLayout(
@@ -10,19 +10,20 @@ ui <- function() {
shiny::sidebarPanel(id="sidebar",
# Data tab sidebar.
shiny::conditionalPanel(condition="input.tabset == 'Data'",
- shiny::h4("Enter 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::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$sup(id="dataCountsHelp", "[?]"))))),
+ shiny::column(8, shiny::textInput(inputId="dataCounts", label=shiny::HTML(paste0(
+ "Case counts", shiny::tags$sup("[?]", title="Enter as a comma-separated list of positive integers, with at least two entries. Ex: 1,1,2,3,5,8"))))
+ ),
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")
+ shiny::span(shiny::textOutput(outputId="dataCountsWarn"), style="color: red;")
),
# Option 2: Upload .csv file.
shiny::conditionalPanel(condition="input.dataInputMethod == '2'",
@@ -34,82 +35,87 @@ ui <- function() {
),
# Warning text for .csv upload / paste.
shiny::conditionalPanel(condition="['2', '3'].includes(input.dataInputMethod)",
- shiny::span(shiny::textOutput(outputId="dataCSVWarn"), style="color: red"),
+ shiny::span(shiny::textOutput(outputId="dataCSVWarn"), style="color: red;"),
),
# Button to add data.
shiny::actionButton(inputId="addData", label="Add"),
),
- # Estimators tab sidebar
+ # Estimators tab sidebar (collapsable entries).
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::h3("Estimators"),
+ # WHITE & PANAGO (WP).
+ shiny::tags$details(
+ shiny::tags$summary(shiny::h4("White & Panago (WP)")),
+ shiny::p("This is a description of the method."),
+ 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="serialseqBInput", label="Mean Serial Interval")),
- shiny::column(4, shiny::selectInput(inputId="serialseqBUnits", label="Time units", choices=list("Days", "Weeks")))
+ 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="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")
+ shiny::span(shiny::textOutput(outputId="serialWPWarn"), style="color: red;")
),
- # INCIDENCE DECAY (ID).
- shinyBS::bsCollapsePanel(title="Incidence Decay (ID)",
- "This is a description of the method.",
- shiny::br(), shiny::br(),
+ # Unknown serial interval.
+ shiny::conditionalPanel(condition="input.serialWPKnown == '2'",
+ shiny::h5("Grid Search Parameters"),
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::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::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")
- )
- )
+ 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$summary(shiny::h4("Sequential Bayes (seqB)")),
+ shiny::p("This is a description of the method."),
+ shiny::br(),
+ shiny::fluidRow(
+ shiny::column(8, shiny::textInput(inputId="serialseqBInput", label="Mean Serial Interval")),
+ shiny::column(4, shiny::selectInput(inputId="serialseqBUnits", label="Time units", choices=list("Days", "Weeks")))
+ ),
+ shiny::span(shiny::textOutput(outputId="serialseqBWarn"), style="color: red;"),
+ shiny::textInput(inputId="kappaInput", label=shiny::HTML(paste0("Maximum value of the uniform prior",
+ shiny::tags$sup("[?]", title="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; }")
)
)
),
@@ -117,12 +123,12 @@ ui <- function() {
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$style(type="text/css", '#dataTable tfoot {display:none;}')),
+ shiny::tabPanel("Data", shiny::br(), shiny::dataTableOutput(outputId="dataTable"), shiny::tags$style(type="text/css", "#dataTable tfoot { display:none; }")),
shiny::tabPanel("Estimators", shiny::br(),
shiny::dataTableOutput(outputId="estTable"),
- shiny::tags$style(type="text/css", "#estTable tfoot {display:none;}"),
+ shiny::tags$style(type="text/css", "#estTable tfoot { display:none; }"),
shiny::downloadButton(outputId="downloadEst", label="Download table as .csv")
- ),
+ )
)
)
)