ui.R
In mi-erasmusmc/COPE: Test Shiny server code using GitHub Actions
shiny::shinyUI(
shinydashboardPlus::dashboardPage(
skin = "black",
title = "COPE",
shinydashboard::dashboardHeader(
title = "COPE",
tags$li(
tags$div(
p("Covid Outcome Prediction"),
p("in the Emergency Department"),
style = "padding-top:12px;font-style:italic;line-height:6px;
padding-right:10px;font-size: min(3vw, 14px)"
),
class = "dropdown"
),
tags$li(
div(
tags$a(
img(
src = "ce_logo.png",
title = "CE",
height = "40px",
width = "50px"
)
)
# style = "padding-top:10px;padding-bottom:0px;padding-right:2px"
),
class = "dropdown"
),
tags$li(
div(
tags$a(
img(
src = "EMC.jpg",
title = "Erasmus MC",
height = "50px",
width = "50px"
),
href = "https://www.publichealthrotterdam.com/"
)
# style = "padding-top:10px;padding-bottom:0px;padding-right:2px"
),
class = "dropdown"
)
),
shinydashboard::dashboardSidebar(
shinydashboard::sidebarMenu(
id = "menu1",
shinydashboard::menuItem(
tabName = "calculation",
text = "Calculate risk",
icon = shiny::icon("calculator")
),
shinydashboard::menuItem(
tabName = "about",
text = "About",
icon = shiny::icon("info-circle")
),
shinydashboard::menuItem(
tabName = "population",
text = "Population",
icon = shiny::icon("users")
),
shinydashboard::menuItem(
tabName = "model",
text = "Model",
icon = shiny::icon("clipboard")
),
shinydashboard::menuItem(
tabName = "performance",
text = "Performance",
icon = shiny::icon("tasks")
),
shinydashboard::menuItem(
tabName = "supplier",
text = "Supplier",
icon = shiny::icon("tools")
)
)
),
shinydashboard::dashboardBody(
shinyWidgets::setShadow(class = "box"),
shinyalert::useShinyalert(),
shinydashboard::tabItems(
shinydashboard::tabItem(
tabName = "supplier",
shiny::includeHTML(
"html/supplier.html"
)
),
shinydashboard::tabItem(
tabName = "about",
shiny::includeHTML(
"html/description_abstract.html"
),
shiny::downloadButton(
"manual",
label = "User manual"
)
),
shinydashboard::tabItem(
tabName = "calculation",
shinydashboard::box(
status = "primary",
width = 4,
column(
width = 6,
shinyBS::popify(
shiny::numericInput(
inputId = "age",
label = shiny::div(
shiny::HTML(
"Age <em>(years)</em>"
)
),
value = 70,
min = 0,
max = 100
),
title = "<b>Age</b>",
content = shiny::includeHTML(
path = "html/calculation_age.html"
),
placement = "bottom",
options = list(
container = "body"
)
),
shinyBS::popify(
shiny::numericInput(
inputId = "respiratoryRate",
label = shiny::div(
shiny::HTML(
"<b>Respiratory rate</b> <em>(per min)</em>"
)
),
value = 19,
min = 10,
max = 60
),
title = "<b>Respiratory rate</b>",
content = shiny::includeHTML(
path = "html/calculation_respiratoryRate.html"
),
placement = "bottom",
options = list(
container = "body"
)
),
shinyBS::popify(
shiny::numericInput(
inputId = "ldh",
label = shiny::div(
shiny::HTML(
"LDH <em>(U per L)</em>"
)
),
value = 244,
min = 100,
max = 1000
),
title = "<b>LDH</b>",
content = shiny::includeHTML(
path = "html/calculation_ldh.html"
),
placement = "bottom",
options = list(
container = "body"
)
)
),
column(
width = 6,
shinyBS::popify(
shiny::numericInput(
inputId = "crp",
label = shiny::div(
shiny::HTML(
"CRP <em>(mg per L)</em>"
)
),
value = 48,
min = 1,
max = 400
),
title = "<b>CRP</b>",
content = shiny::includeHTML(
path = "html/calculation_crp.html"
),
placement = "bottom",
options = list(
container = "body"
)
),
shinyBS::popify(
shiny::numericInput(
inputId = "albumin",
label = shiny::div(
shiny::HTML(
"Serum albumin <em>(g per L)</em>"
)
),
value = 39,
min = 10,
max = 60
),
title = "<b>Serum albumin</b>",
content = shiny::includeHTML(
path = "html/calculation_albumin.html"
),
placement = "bottom",
options = list(
container = "body"
)
),
shinyBS::popify(
shiny::numericInput(
inputId = "urea",
label = shiny::div(
shiny::HTML(
"Serum urea <em>(mmol per L)</em>"
)
),
value = 6.5,
min = 1,
max = 80
),
title = "<b>Serum urea</b>",
content = shiny::includeHTML(
path = "html/calculation_urea.html"
),
placement = "bottom",
options = list(
container = "body"
)
),
shiny::actionButton(
inputId = "calculatePredictionButton",
label = "Calculate",
icon = shiny::icon("calculator"),
class = "btn-lg"
)
)
),
shiny::conditionalPanel(
condition = "input.calculatePredictionButton",
shinydashboard::box(
status = "primary",
title = shiny::uiOutput(
outputId = "titleMortalityRiskBox"
),
width = 4,
height = "320px",
shinycssloaders::withSpinner(
type = 4,
plotly::plotlyOutput(
outputId = "calculationPlotMortality",
height = "250px"
)
)
),
shinydashboard::box(
status = "primary",
title = shiny::uiOutput(
outputId = "titleIcuRiskBox"
),
width = 4,
height = "320px",
shinycssloaders::withSpinner(
type = 4,
plotly::plotlyOutput(
outputId = "calculationPlotIcu",
height = "250px"
)
)
),
shinydashboard::box(
status = "primary",
title = "Result Explanation",
width = 12,
# height = "300px",
shiny::htmlOutput(
outputId = "resultExplanationBox"
),
tags$head(
tags$style("#resultExplanationBox{
font-size: 15px;
}"
)
)
)
)
),
shinydashboard::tabItem(
tabName = "population",
shiny::tabsetPanel(
id = "tab1",
shiny::tabPanel(
title = "Development",
DT::dataTableOutput(
outputId = "developmentTable1"
)
),
shiny::tabPanel(
title = "Validation",
DT::dataTableOutput(
outputId = "validationTable1"
)
)
)
),
shinydashboard::tabItem(
tabName = "model",
shinydashboard::box(
title = "Mortality",
status = "primary",
width = 12,
# height = "300px",
shiny::withMathJax(
shiny::helpText(
shiny::p(
"The probability of mortality within 28 days
was estimated using a logistic regression
model. The linear predictor of the model
is given by:
$$
\\begin{align}
\\ LP_{mort} = &-13.6 \\\\
\\ & + 0.046\\times Age + 1.654\\times log(RR) \\\\
\\ & + 0.169\\times log(CRP) + 1.197\\times log(LDH) \\\\
\\ & - 1.585\\times log(Albumin) + 0.595\\times log(Urea)
\\end{align}
$$
Then the probability of death in 28 days is given
from:
$$
Pr(Death) = \\frac{1}{1+exp(-LP_{mort})}
$$
"
)
)
),
tags$head(
tags$style(".help-block p {font-size: 15px;}")
)
),
shinydashboard::box(
title = "ICU admission",
status = "primary",
width = 12,
# height = "300px",
shiny::withMathJax(
shiny::helpText(
shiny::p(
"The probability of admission to the ICU
within 28 days was estimated using a
re-calibrated version of the model for
28-day mortality. More specifically, the linear
predictor of the model for
ICU admission is given from:
$$
LP_{ICU} = -0.089 + 0.597\\times LP_{mort}
$$
Then, the probability for 28-day ICU
admission can be estimated from:
$$
Pr(ICU) = \\frac{1}{1+exp(-LP_{ICU})}
$$
"
),
shiny::hr(),
shiny::em(
"Note: here",
shiny::strong("log"),
"is the natural logarithm and",
shiny::strong("exp"),
"is the natural exponential"
)
)
)
)
),
shinydashboard::tabItem(
tabName = "performance",
shiny::tabsetPanel(
shiny::tabPanel(
title = "Overall",
shinydashboard::box(
title = "Calibration plot for mortality",
status = "primary",
width = 6,
height = "450px",
shinycssloaders::withSpinner(
type = 4,
plotly::plotlyOutput(
outputId = "calibrationMortalityOverall",
height = "380px"
)
)
),
shinydashboard::box(
title = "Calibration plot for ICU admission",
status = "primary",
width = 6,
height = "450px",
shinycssloaders::withSpinner(
type = 4,
plotly::plotlyOutput(
outputId = "calibrationIcuOverall",
height = "380px"
)
)
),
shinydashboard::box(
title = "Evaluation metrics",
status = "primary",
width = 12,
# height = "280px",
shiny::includeHTML(
"html/performance_text.html"
)
)
),
shiny::tabPanel(
title = "By hospital",
shiny::tabsetPanel(
id = "byHospital",
type = "pills",
shiny::tabPanel(
title = "Mortality",
shinydashboard::box(
title = "Calibration plot for: Hospital 1",
status = "primary",
width = 3,
height = "350px",
shinycssloaders::withSpinner(
type = 4,
plotly::plotlyOutput(
outputId = "calibrationMortalityCenter1",
height = "280px"
)
)
),
shinydashboard::box(
title = "Hospital 2",
status = "primary",
width = 3,
height = "350px",
shinycssloaders::withSpinner(
type = 4,
plotly::plotlyOutput(
outputId = "calibrationMortalityCenter2",
height = "280px"
)
)
),
shinydashboard::box(
title = "Hospital 3",
status = "primary",
width = 3,
height = "350px",
shinycssloaders::withSpinner(
type = 4,
plotly::plotlyOutput(
outputId = "calibrationMortalityCenter3",
height = "280px"
)
)
),
shinydashboard::box(
title = "Hospital 4",
status = "primary",
width = 3,
height = "350px",
shinycssloaders::withSpinner(
type = 4,
plotly::plotlyOutput(
outputId = "calibrationMortalityCenter4",
height = "280px"
)
)
)
),
shiny::tabPanel(
title = "ICU",
shinydashboard::box(
title = "Calibration plot for: Hospital 1",
status = "primary",
width = 3,
height = "350px",
shinycssloaders::withSpinner(
type = 4,
plotly::plotlyOutput(
outputId = "calibrationIcuHospital1",
height = "280px"
)
)
),
shinydashboard::box(
title = "Hospital 2",
status = "primary",
width = 3,
height = "350px"
),
shinydashboard::box(
title = "Hospital 3",
status = "primary",
width = 3,
height = "350px",
shinycssloaders::withSpinner(
type = 4,
plotly::plotlyOutput(
outputId = "calibrationIcuHospital3",
height = "280px"
)
)
),
shinydashboard::box(
title = "Hospital 4",
status = "primary",
width = 3,
height = "350px"
),
)
),
shinydashboard::box(
title = "Evaluation metrics",
status = "primary",
width = 12,
# height = "280px",
shiny::includeHTML(
"html/performance_text.html"
)
)
)
)
)
)
)
)
)
mi-erasmusmc/COPE documentation built on June 15, 2021, 11:19 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
shiny::shinyUI(
shinydashboardPlus::dashboardPage(
skin = "black",
title = "COPE",
shinydashboard::dashboardHeader(
title = "COPE",
tags$li(
tags$div(
p("Covid Outcome Prediction"),
p("in the Emergency Department"),
style = "padding-top:12px;font-style:italic;line-height:6px;
padding-right:10px;font-size: min(3vw, 14px)"
),
class = "dropdown"
),
tags$li(
div(
tags$a(
img(
src = "ce_logo.png",
title = "CE",
height = "40px",
width = "50px"
)
)
# style = "padding-top:10px;padding-bottom:0px;padding-right:2px"
),
class = "dropdown"
),
tags$li(
div(
tags$a(
img(
src = "EMC.jpg",
title = "Erasmus MC",
height = "50px",
width = "50px"
),
href = "https://www.publichealthrotterdam.com/"
)
# style = "padding-top:10px;padding-bottom:0px;padding-right:2px"
),
class = "dropdown"
)
),
shinydashboard::dashboardSidebar(
shinydashboard::sidebarMenu(
id = "menu1",
shinydashboard::menuItem(
tabName = "calculation",
text = "Calculate risk",
icon = shiny::icon("calculator")
),
shinydashboard::menuItem(
tabName = "about",
text = "About",
icon = shiny::icon("info-circle")
),
shinydashboard::menuItem(
tabName = "population",
text = "Population",
icon = shiny::icon("users")
),
shinydashboard::menuItem(
tabName = "model",
text = "Model",
icon = shiny::icon("clipboard")
),
shinydashboard::menuItem(
tabName = "performance",
text = "Performance",
icon = shiny::icon("tasks")
),
shinydashboard::menuItem(
tabName = "supplier",
text = "Supplier",
icon = shiny::icon("tools")
)
)
),
shinydashboard::dashboardBody(
shinyWidgets::setShadow(class = "box"),
shinyalert::useShinyalert(),
shinydashboard::tabItems(
shinydashboard::tabItem(
tabName = "supplier",
shiny::includeHTML(
"html/supplier.html"
)
),
shinydashboard::tabItem(
tabName = "about",
shiny::includeHTML(
"html/description_abstract.html"
),
shiny::downloadButton(
"manual",
label = "User manual"
)
),
shinydashboard::tabItem(
tabName = "calculation",
shinydashboard::box(
status = "primary",
width = 4,
column(
width = 6,
shinyBS::popify(
shiny::numericInput(
inputId = "age",
label = shiny::div(
shiny::HTML(
"Age <em>(years)</em>"
)
),
value = 70,
min = 0,
max = 100
),
title = "<b>Age</b>",
content = shiny::includeHTML(
path = "html/calculation_age.html"
),
placement = "bottom",
options = list(
container = "body"
)
),
shinyBS::popify(
shiny::numericInput(
inputId = "respiratoryRate",
label = shiny::div(
shiny::HTML(
"<b>Respiratory rate</b> <em>(per min)</em>"
)
),
value = 19,
min = 10,
max = 60
),
title = "<b>Respiratory rate</b>",
content = shiny::includeHTML(
path = "html/calculation_respiratoryRate.html"
),
placement = "bottom",
options = list(
container = "body"
)
),
shinyBS::popify(
shiny::numericInput(
inputId = "ldh",
label = shiny::div(
shiny::HTML(
"LDH <em>(U per L)</em>"
)
),
value = 244,
min = 100,
max = 1000
),
title = "<b>LDH</b>",
content = shiny::includeHTML(
path = "html/calculation_ldh.html"
),
placement = "bottom",
options = list(
container = "body"
)
)
),
column(
width = 6,
shinyBS::popify(
shiny::numericInput(
inputId = "crp",
label = shiny::div(
shiny::HTML(
"CRP <em>(mg per L)</em>"
)
),
value = 48,
min = 1,
max = 400
),
title = "<b>CRP</b>",
content = shiny::includeHTML(
path = "html/calculation_crp.html"
),
placement = "bottom",
options = list(
container = "body"
)
),
shinyBS::popify(
shiny::numericInput(
inputId = "albumin",
label = shiny::div(
shiny::HTML(
"Serum albumin <em>(g per L)</em>"
)
),
value = 39,
min = 10,
max = 60
),
title = "<b>Serum albumin</b>",
content = shiny::includeHTML(
path = "html/calculation_albumin.html"
),
placement = "bottom",
options = list(
container = "body"
)
),
shinyBS::popify(
shiny::numericInput(
inputId = "urea",
label = shiny::div(
shiny::HTML(
"Serum urea <em>(mmol per L)</em>"
)
),
value = 6.5,
min = 1,
max = 80
),
title = "<b>Serum urea</b>",
content = shiny::includeHTML(
path = "html/calculation_urea.html"
),
placement = "bottom",
options = list(
container = "body"
)
),
shiny::actionButton(
inputId = "calculatePredictionButton",
label = "Calculate",
icon = shiny::icon("calculator"),
class = "btn-lg"
)
)
),
shiny::conditionalPanel(
condition = "input.calculatePredictionButton",
shinydashboard::box(
status = "primary",
title = shiny::uiOutput(
outputId = "titleMortalityRiskBox"
),
width = 4,
height = "320px",
shinycssloaders::withSpinner(
type = 4,
plotly::plotlyOutput(
outputId = "calculationPlotMortality",
height = "250px"
)
)
),
shinydashboard::box(
status = "primary",
title = shiny::uiOutput(
outputId = "titleIcuRiskBox"
),
width = 4,
height = "320px",
shinycssloaders::withSpinner(
type = 4,
plotly::plotlyOutput(
outputId = "calculationPlotIcu",
height = "250px"
)
)
),
shinydashboard::box(
status = "primary",
title = "Result Explanation",
width = 12,
# height = "300px",
shiny::htmlOutput(
outputId = "resultExplanationBox"
),
tags$head(
tags$style("#resultExplanationBox{
font-size: 15px;
}"
)
)
)
)
),
shinydashboard::tabItem(
tabName = "population",
shiny::tabsetPanel(
id = "tab1",
shiny::tabPanel(
title = "Development",
DT::dataTableOutput(
outputId = "developmentTable1"
)
),
shiny::tabPanel(
title = "Validation",
DT::dataTableOutput(
outputId = "validationTable1"
)
)
)
),
shinydashboard::tabItem(
tabName = "model",
shinydashboard::box(
title = "Mortality",
status = "primary",
width = 12,
# height = "300px",
shiny::withMathJax(
shiny::helpText(
shiny::p(
"The probability of mortality within 28 days
was estimated using a logistic regression
model. The linear predictor of the model
is given by:
$$
\\begin{align}
\\ LP_{mort} = &-13.6 \\\\
\\ & + 0.046\\times Age + 1.654\\times log(RR) \\\\
\\ & + 0.169\\times log(CRP) + 1.197\\times log(LDH) \\\\
\\ & - 1.585\\times log(Albumin) + 0.595\\times log(Urea)
\\end{align}
$$
Then the probability of death in 28 days is given
from:
$$
Pr(Death) = \\frac{1}{1+exp(-LP_{mort})}
$$
"
)
)
),
tags$head(
tags$style(".help-block p {font-size: 15px;}")
)
),
shinydashboard::box(
title = "ICU admission",
status = "primary",
width = 12,
# height = "300px",
shiny::withMathJax(
shiny::helpText(
shiny::p(
"The probability of admission to the ICU
within 28 days was estimated using a
re-calibrated version of the model for
28-day mortality. More specifically, the linear
predictor of the model for
ICU admission is given from:
$$
LP_{ICU} = -0.089 + 0.597\\times LP_{mort}
$$
Then, the probability for 28-day ICU
admission can be estimated from:
$$
Pr(ICU) = \\frac{1}{1+exp(-LP_{ICU})}
$$
"
),
shiny::hr(),
shiny::em(
"Note: here",
shiny::strong("log"),
"is the natural logarithm and",
shiny::strong("exp"),
"is the natural exponential"
)
)
)
)
),
shinydashboard::tabItem(
tabName = "performance",
shiny::tabsetPanel(
shiny::tabPanel(
title = "Overall",
shinydashboard::box(
title = "Calibration plot for mortality",
status = "primary",
width = 6,
height = "450px",
shinycssloaders::withSpinner(
type = 4,
plotly::plotlyOutput(
outputId = "calibrationMortalityOverall",
height = "380px"
)
)
),
shinydashboard::box(
title = "Calibration plot for ICU admission",
status = "primary",
width = 6,
height = "450px",
shinycssloaders::withSpinner(
type = 4,
plotly::plotlyOutput(
outputId = "calibrationIcuOverall",
height = "380px"
)
)
),
shinydashboard::box(
title = "Evaluation metrics",
status = "primary",
width = 12,
# height = "280px",
shiny::includeHTML(
"html/performance_text.html"
)
)
),
shiny::tabPanel(
title = "By hospital",
shiny::tabsetPanel(
id = "byHospital",
type = "pills",
shiny::tabPanel(
title = "Mortality",
shinydashboard::box(
title = "Calibration plot for: Hospital 1",
status = "primary",
width = 3,
height = "350px",
shinycssloaders::withSpinner(
type = 4,
plotly::plotlyOutput(
outputId = "calibrationMortalityCenter1",
height = "280px"
)
)
),
shinydashboard::box(
title = "Hospital 2",
status = "primary",
width = 3,
height = "350px",
shinycssloaders::withSpinner(
type = 4,
plotly::plotlyOutput(
outputId = "calibrationMortalityCenter2",
height = "280px"
)
)
),
shinydashboard::box(
title = "Hospital 3",
status = "primary",
width = 3,
height = "350px",
shinycssloaders::withSpinner(
type = 4,
plotly::plotlyOutput(
outputId = "calibrationMortalityCenter3",
height = "280px"
)
)
),
shinydashboard::box(
title = "Hospital 4",
status = "primary",
width = 3,
height = "350px",
shinycssloaders::withSpinner(
type = 4,
plotly::plotlyOutput(
outputId = "calibrationMortalityCenter4",
height = "280px"
)
)
)
),
shiny::tabPanel(
title = "ICU",
shinydashboard::box(
title = "Calibration plot for: Hospital 1",
status = "primary",
width = 3,
height = "350px",
shinycssloaders::withSpinner(
type = 4,
plotly::plotlyOutput(
outputId = "calibrationIcuHospital1",
height = "280px"
)
)
),
shinydashboard::box(
title = "Hospital 2",
status = "primary",
width = 3,
height = "350px"
),
shinydashboard::box(
title = "Hospital 3",
status = "primary",
width = 3,
height = "350px",
shinycssloaders::withSpinner(
type = 4,
plotly::plotlyOutput(
outputId = "calibrationIcuHospital3",
height = "280px"
)
)
),
shinydashboard::box(
title = "Hospital 4",
status = "primary",
width = 3,
height = "350px"
),
)
),
shinydashboard::box(
title = "Evaluation metrics",
status = "primary",
width = 12,
# height = "280px",
shiny::includeHTML(
"html/performance_text.html"
)
)
)
)
)
)
)
)
)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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