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ui.R
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ui.R
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#------------------------- #
# UI Components
#------------------------- #
developer <- function(lastName, firstName, degree = "", affiliationIndex = 1, href = "") {
tag("address",
list(a(style = "font-weight: bold;",
href = href,
target = "_blank",
lastName,
",",
firstName,
degree,
tag("sup", affiliationIndex))))
}
ui <- fluidPage( # UI ----
tags$head(
tags$style(HTML("
.label-text {
font-size: 16px; /* Adjust label font size as needed */
}
.option-text {
font-size: 12px; /* Adjust option font size as needed */
}
"))
),
theme = bs_theme(version = 4,
primary = "#18536F"),
tags$head(
tags$link(rel = "stylesheet",
type="text/css",
href="spatialEpisimBanner.css"),
tags$link(rel = "stylesheet",
type="text/css",
href="https://cdn.jsdelivr.net/npm/leaflet-timedimension@1.1.1/dist/leaflet.timedimension.control.min.css"),
tags$script(src = "https://cdn.jsdelivr.net/npm/iso8601-js-period@0.2.1/iso8601.min.js"),
tags$script(src = "https://cdn.jsdelivr.net/npm/leaflet-timedimension@1.1.1/dist/leaflet.timedimension.min.js"),
tags$script(src = "addTimeDimension.js")
),
div(
style = "background-color: #18536F; padding: 10px; width: 100%; box-sizing: border-box; display: flex; align-items: center;
height: 100px;",
div(
h1(
strong("The Krishnamurthy Lab Spatio-Temporal Epidemic Modelling app"),
style = "margin: 0px 0px; color: white; font-size: 35px"
)
)),
add_busy_spinner(spin = "cube-grid",
color = "#18536F",
margins = c("50%","50%")),
navbarPage(title = "",
tabPanel(title = "Model",
sidebarLayout(
sidebarPanel( ## sidebar panel ----
shinyjs::useShinyjs(),
shinyjs::inlineCSS(appCSS),
div(
id = "dashboard",
uiOutput("countryDropdown"),
uiOutput("cropStateCheckbox"),
conditionalPanel("input.selectedCountry != ''",
helper(checkboxInput(inputId = "cropLev1",
label = strong("Limit simulation to state(s)/province(s) (crop to selection)"),
value = TRUE),
content = "cropSelectedCountry"),
conditionalPanel(condition = "input.cropLev1", uiOutput("Level1Ui")),
radioButtons(inputId = "appMode",
label = strong("Application mode"),
choices = list("Visualizer",
"Simulator"),
selected = "Simulator",
inline = TRUE)),
# -------------------------------------------- #
# Visualizer Inputs #
# -------------------------------------------- #
conditionalPanel(
condition = "input.appMode == 'Visualizer'",
conditionalPanel(condition = "input.selectedCountry == 'Democratic Republic of Congo'",
fileInput(inputId = "latLonData",
label = strong("Upload Lat-Lon Data:"),
placeholder = "Upload Lat-Lon data (.csv or .xls or .xlsx)",
accept = c(
"text/csv",
"text/comma-separated-values,text/plain",
".csv",
".xls",
".xlsx")),
fileInput(inputId = "incidenceData",
label = strong("Upload Incidence/Death Data:"),
placeholder = "Upload Incidence/Death data (.csv or .xls or .xlsx)",
accept = c(
"text/csv",
"text/comma-separated-values,text/plain",
".csv",
".xls",
".xlsx"))),
uiOutput("resetButton")
),
# -------------------------------------------- #
# Simulation Inputs #
# -------------------------------------------- #
conditionalPanel(
condition = "input.appMode == 'Simulator'",
helper(uiOutput("aggInput"),
content = "rasterAggregationFactor"),
uiOutput("modelRadio"),
uiOutput("stochasticRadio"),
conditionalPanel(
condition = "input.selectedCountry != ''",
withMathJax(),
wellPanel(h5("Model Parameters", style="font-weight: bold; font-size:11.5pt"),
conditionalPanel(id = "SVEIRD",
withMathJax(),
condition = "input.modelSelect == 'SVEIRD'",
uiOutput("alphaInput")),
uiOutput("betaInput"),
uiOutput("gammaInput"),
uiOutput("sigmaInput"),
uiOutput("deltaInput"),
helper(uiOutput("lambdaInput"), content = "lambda")),
wellPanel(helper(uiOutput("seedUpload"),
size = "l",
type = "inline",
title = "Seed data template (for the Democratic Republic of Congo)",
content = HTML(r"--{<div class = "datatables html-widget html-widget-output shiny-report-size html-fill-item" id = "seedDataDT" style = "width:auto;height:auto;"></div>}--")),
uiOutput("seedDataButton"),
uiOutput("seedRadiusInput")),
uiOutput("startDateInput"),
uiOutput("timestepInput")),
# actionButton("go","Run Simulation",
# style="color: #fff; background-color: #337ab7; border-color: #2e6da4"),
# actionButton("resetAll","Reset Values",
# style="color: #fff; background-color: #337ab7; border-color: #2e6da4"),
br(),
br(),
uiOutput("dataAssimCheckbox"),
# --------------------------------------------- #
# Bayesian Assimilation Inputs #
# --------------------------------------------- #
conditionalPanel(
condition = "input.dataAssim == '1'",
helper(checkboxGroupButtons(
inputId = "selectedCompartments",
label = "Select observable compartment(s)",
choices = c("V", "E", "I", "R", "D"),
selected = c("I"),
checkIcon = list(
yes = tags$i(class = "fa fa-check-square",
style = "color: steelblue"),
no = tags$i(class = "fa fa-square-o",
style = "color: steelblue")),
disabled = TRUE
),
content = "selectedCompartmentsUnimplemented"),
br(),
uiOutput("dataAssimZones"),
uiOutput("dataAssimFileI"),
uiOutput("dataAssimFileD"),
h5("Model error covariance matrix (Q) formulation", style="font-weight: bold; font-size:11.5pt"),
uiOutput("varCovarFunc"),
uiOutput("selectRho"),
uiOutput("selectSigma"),
uiOutput("selectNbhd"),
h5(HTML("Model error covariance matrix (Ψ) formulation"), style="font-weight: bold; font-size:11.5pt"),
uiOutput("selectPsiDiag"),
# actionButton("goDA","Run Simulation with DA",
# style ="color: #fff; background-color: #337ab7; border-color: #2e6da4")
),
# br(),
# actionButton("resetAllDA","Reset Values",
# style="color: #fff; background-color: #337ab7; border-color: #2e6da4"),
actionButton(inputId = "go",
label = "Run Simulation",
class = "act-btn"),
actionButton(inputId = "resetAll",
label = "Reset Values",
class = "act-btn"),
)), # div "dashboard"
), # sidebarPanel
mainPanel( ## main panel ----
conditionalPanel(
condition = "input.appMode == 'Visualizer'",
div(id = "maptabPanels",
tabsetPanel(id = 'vizTabSet',
tabPanel(id = "main",
title ="Leaflet Plot",
br(),
leafletOutput("leafletMap",
width = 1024,
height = 768),
br(),
br()
#downloadButton('downloadPlot', 'Save Image')
),
tabPanel(title = "Leaflet Cropped Plot",
value = "Leaflet Cropped Plot",
br(),
leafletOutput("croppedLeafletMap",
width = 1024,
height = 768),
br(),
br()
),
tabPanel(title = "terra Plot",
br(),
imageOutput("terraOutputImage"),
br(),
br()
),
tabPanel(title = "Transmission Path",
br(),
div(style = "width: 100%; height: 80vh; position: relative;",
leafletOutput("transmission", width = "100%", height = "100%")
),
br(),
br()
),
tabPanel(title = "Lollipop Chart",
br(),
plotlyOutput("lollipop",
height = 1000),
br(),
br()
),
tabPanel(title = "Time-Series Graph",
br(),
uiOutput("timeSeriesOptions"),
br(),
plotlyOutput("timeSeries",
height = 800),
br(),
br())
# tabPanel(title ="Population Count by State/Province",
# DT::dataTableOutput("aggTable")
# )
) # tabSet
), # maptabPanels
),
conditionalPanel(
condition = "input.appMode == 'Simulator'",
div(id = "tabsetContainer",
tabsetPanel(id = "tabSet", selected = "Input Summary",
tabPanel(title = "Input Summary",
verbatimTextOutput("summary"),
br(),
DTOutput("summaryTable"),
br(),
br(),
imageOutput("outputImage",
height = "768px",
width = "768px"),
#imageOutput("croppedOutputImage"),
#imageOutput("seededOutputImage"),
#downloadButton(outputId = "downloadSummary", label = "Save Input Summary as a PDF File")
),
tabPanel(title = "Model", id = "modelTab",
h3("Schematic Diagram"),
br(),
imageOutput("flowchartImg",
height = "400px"),
br(),
br(),
h3("Mathematical Model"),
br(),
imageOutput("modelImg",
height = "400px")
),
# tabPanel(title = "Schematic Diagram", id = "flowchartTab",
#
# ),
tabPanel(title = "Initial Seed Data",
DTOutput("tableSeed"),
br(),
leafletOutput("seedPlot",
width = 1024,
height = 768)
),
tabPanel(title = "MP4 Animation",
br(),
br(),
uiOutput("outputVideo")#,
#downloadButton(outputId = "downloadMP4", label = "Save MP4 Animation")
),
tabPanel(title = "Output Summary",
DTOutput("outputSummary") ,
downloadButton(outputId = "downloadOutputSummary", label = "Download as Excel")
),
tabPanel(title = "Plot", id = "plotTab",
plotlyOutput("infectedExposedPlot", width = 800, height = 600),
plotlyOutput("cumulativeDeaths", width = 800, height = 600),
plotlyOutput("dailyIncidence", width = 800, height = 600),
plotlyOutput("cumulativeIncidence", width = 800, height = 600),
plotlyOutput("fullPlot", width = 800, height = 600),
# imageOutput("fracSusPlot"),
#downloadButton(outputId = "downloadPlot", label = "Save Image")
)
) # tabsetPanel
)
)
), # mainPanel
) # sidebarLayout
), # Model tabPanel
ModelAuthorshipTab <- nav_panel(
title = "Authors",
h2("Principal investigator", style = "font-weight:bold"),
## TODO: Reformat Ashok's information so the digital links aren't ugly.
tag("address",
list(
p(a("Ashok Krishnamurthy, Ph.D.", href = "https://bit.ly/2YKrXjX", target = "_blank", style = "font-weight: bold;"), br(),
"Mount Royal University", br(),
"Department of Mathematics & Computing,", br(),
"Calgary, AB, Canada", br(),
a("akrishnamurthy@mtroyal.ca", href = "mailto:akrishnamurthy@mtroyal.ca"), br(),
a("SpatialEpisim GitHub", href = "https://github.com/ashokkrish/spatialEpisim", target = "_blank")),
style = r"(a[href^='mailto']::before {content: '📧 ';} a[href^='tel']::before {content: '📞 ';})")),
#TODO: Need the link for research assistants who have not had
h2("Research Assistants", style = "font-weight:bold"),
developer("Carson", "Bryce", "B.Sc", href = "https://github.com/bryce-carson/"),
developer("Le", "Khanh", href = "https://github.com/kle6951/"),
developer("Wondwossen", "Tobias", href = "https://github.com/Toby-exe"),
h2("Affiliations", style = "font-weight:bold"),
p(tag("sup", 1), "Mount Royal University", br(),
"4825 Mount Royal Gate SW", br(),
"Calgary, Alberta, Canada", br(),
"T3E 6K6"),
h2("Acknowledgment", style = "font-weight:bold"),
list(p("Dr. Loren Cobb, Dr. Bedrich Sousedik, Michael Myer, Tom Bayliss White, Crystal Wai, Gursimran Dhaliwal, Timothy Pulfer, Ryan Darby, Jason Szeto, and Jake Doody.", br(),
)),
h2("Disclaimer", style ="font-weight:bold"),
p("This tool uses a mathematical model to simulate a variety of CoViD-19, Ebola, and
Measles outbreaks based on user-defined parameters. The output of the model
depends on model assumptions, parameter choices, and human mobility patterns. It
is not a medical predictor, and should be used for informational and research
purposes only. Please carefully consider the parameters you choose. Interpret
and use the simulated results responsibly. Authors are not liable for any direct
or indirect consequences of this usage."),
h2("Credits", style ="font-weight:bold"),
p("We would like to express our gratitude to the authors of the following R packages used in our project:"),
worldPopPanel <- bsCollapsePanel(
title = "WorldPop",
content = tags$div(style = "padding: 10px;",
HTML(
paste0(
"WorldPop (www.worldpop.org - School of Geography and Environmental Science, University of Southampton; ",
"Department of Geography and Geosciences, University of Louisville; Departement de Geographie, Universite de Namur) ",
"and Center for International Earth Science Information Network (CIESIN), Columbia University (2018). ",
"Global High Resolution Population Denominators Project - Funded by The Bill and Melinda Gates Foundation (OPP1134076). ",
"<a href='https://dx.doi.org/10.5258/SOTON/WP00671' target='_blank'>Link to the website</a>"
)
)
),
style = "primary"
),
uiOutput("packageList"),
), #Author Tab Panel
) # navbarPage
)