ui.R

################################  Sidebar  #####################################

sidebar_menu <- sidebarMenu(id = "my_tabs",
  menuItem2("Calculator", tab_name = "calculator",
    icon = icon2("calculator")
  ),
  menuItem2("Results", tab_name = "results",
    icon = icon2("chart-line")
  ),
  menuItem2("Analysis Details", tab_name = "analysis_details",
    icon = icon2("info")
  ),
  menuItem2("References", tab_name = "references",
    icon = icon2("info")
  )
)
sidebar_menu$attribs$role <- "list"

sidebar_extra <- tagList(
  hr(),
  fluidRow(
    column(width = 12, align = "center",
      sidebarSelectInput("sidebar_select")
    )
  ),
  hr(),
  div(id = "app_info",
    p(em("Authors: "), "S. Wang, J. Ihrie"),
    p(em("App version: "), glob_app_version),
  ),
  div(id = "mail_to",
    "Please",
    a("email John Ihrie",
      href = "mailto:John.Ihrie@fda.hhs.gov", class = "email-link"
    ),
    "with suggestions or bug reports."
  )
)

##############################  Calculator  ####################################

my_calculator <- tabItem(tabName = "calculator",
  tags$section(id = "calculator_section",
    tags$h1("Calculator"),
    fluidRow(
      column(width = 8,
        fluidRow(id = "data_choices_div", align = "center",
          dataChoicesInput("choose_data_entry")
        ),
        #tableOutput("data_model"),  #for testing only
        #verbatimTextOutput("data_object"),  #for testing only
        #verbatimTextOutput("model_results"),  #for testing only
        #htmlOutput("warning_messages_results_UI"),  #for testing only (should be in Results)
        fluidRow(id = "manual_data_panel",
          experimentDescriptionInput("experiment_description",
            title = "Experiment Description",
            glob_default_labs, glob_min_labs, glob_max_labs,
            glob_default_levels, glob_min_levels, glob_max_levels,
            glob_default_size, glob_min_size
          ),
          #tableOutput("manual_test_table"),  #for testing only
          tags$h2("Lab-Level Data", class = "description-title", align = "center"),
          labsInput("lab_data",
            glob_max_labs, glob_default_labs, glob_max_levels, glob_default_levels
          )
        ),
        shinyjs::hidden(
          fluidRow(id = "upload_data_panel", align = "center",
            uploadDataUI("upload_file")
          )
        ),
        shinyjs::hidden(
          fluidRow(id = "example_data_panel", align = "center",
            tags$h2("Example Data"),
            shinydashboard::box(width = 12,
              span(
                "Test portion size:", glob_sample_size_example, glob_sample_unit_example,
                style = "font-size: 20px;"
              ),
              tags$div(id = "example_data_div",
                tableOutput("example_data")
              )
            )
          )
        )
      ),
      column(width = 4, align = "left", style = "min-width: 350px;",
        fluidRow(
          column(width = 10, align = "center", offset = 1,
            runAnalysisInput("calculate")
          )
        ),
        notes,
        data_entry_instructions,
        analysis_instructions
      )
    )
  )
)


#################################  Results  ####################################

my_results <- tabItem(tabName = "results",
  tags$section(id = "results_section",
    tags$h1("Results"),
    fluidRow(
      shinyjs::disabled(
        downloadResultsUI("spreadsheet")
      ),
      helpText2(
        "The Download Results button will be disabled if results are not ready."
      )
    ),
    tabsetPanel(id = "mod", type = "tabs",
      tabPanel(
        title = HTML("<strong>Model Parameters & LOD</strong>"),
        value = "model_params", icon = icon2("table"),
        column(width = 12,
          fluidRow(
            tags$h2("Model Parameter Estimates", class = "results-title"),
            fluidRow(
              valueBoxOutput("log_mean_effect", width = 3),
              valueBoxOutput("se_log_mean_effect", width = 3),
              valueBoxOutput("sigma", width = 3),
              valueBoxOutput("ICC", width = 3)
            )
          )
        ),
        column(width = 9,
          fluidRow(
            tags$h2("Level of Detection", class = "results-title"),
            valueBoxOutput("LOD", width = 4),
            valueBoxOutput("LOD_LCL", width = 4),
            valueBoxOutput("LOD_UCL", width = 4)
          )
        ),
        column(width = 9,
          fluidRow(htmlOutput("warning_messages_results_UI"))#,
          #fluidRow(verbatimTextOutput("test_model"))  #for testing only
        )
      ),
      tabPanel(
        title = HTML("<strong>POD Curves</strong>"), value = "pod_curves",
        icon = icon2("chart-line"),
        tags$div(id = "POD_plots_div",
          plotOutput("POD_plots", width = "75%", height = "650px")
        )
      )
    )
  )
)

#########################  Dashboard layout  ###################################

dashboard_header <- dashboardHeader(title = glob_app_title, titleWidth = 275)
dashboard_header[[3]][[3]][[3]][[2]]$attribs$tabindex <- "0"

dashboard_sidebar <- dashboardSidebar(sidebar_menu, sidebar_extra, width = 275)
dashboard_sidebar$attribs$id <- "my_aside"  #<aside> element

ui <- dashboardPage(
  dashboard_header,
  dashboard_sidebar,
  dashboardBody(
    shinyjs::useShinyjs(),
    tags$html(lang = "en-US"),
    tags$head(
      #https://stackoverflow.com/questions/51294246/how-can-i-include-meta-tags-in-my-r-shiny-app
      tags$meta(charset = "utf-8"),
      tags$meta(name = "description",
        content = paste(
          "The MultiLab POD/LOD/ICC R Shiny app is for interlaboratory",
          "microbiological method validation studies. This app implements the",
          "random intercept complementary log-log model suggested by Jarvis",
          "et al. (2019) to estimate probability of detection (POD) and level",
          "of detection (LOD) from a multi-laboratory validation study for a",
          "qualitative (binary) microbiological assay. This app also",
          "calculates the intra-laboratory correlation coefficient (ICC) to",
          "estimate the proportion of total variance attributable to",
          "between-laboratory variance."
        )
      ),
      tags$meta(name = "viewport", content = "width=device-width, initial-scale=1"),
      tags$script(withMathJax(), defer = "defer"),
      #includeScript("www/jscript.js", defer = "defer"),  #for code development only!!!
      tags$script(src = glob_js_query, type = "text/javascript", defer = "defer"),  #for production
      #includeCSS("www/style.css")  #for code development only!!!
      tags$link(rel = "stylesheet", type = "text/css", href = glob_css_query, defer = "defer")  #for production
    ),
    HTML("<main>"),
      tabItems(
        my_calculator,
        my_results,
        my_analysis_details,
        my_references
      ),
    HTML("</main>")
  ),
  title = glob_page_title
)
################################################################################