app.R

#app.R
library(shiny)
library(BioAge)
library(dplyr)
#library(RSQLite)
library(googlesheets4)
library(googledrive)
library(shinyvalidate)
library(shinyjs)
library(plotly)
library(lubridate)
library(pander)
library(tidyr)
library(shiny.router)



#options(gargle_oauth_cache = ".secrets")

createReactiveDataset <- function() {
  return(reactiveVal(data.frame(date = as.Date(character()), quantity = integer(), item = character())))
}

# Define dataset and its reactive variable
dataset <- createReactiveDataset()

# Dummy dataset for development
localDataset <- reactiveVal(data.frame(
  date = as.Date(c('2024-12-01', '2024-12-02')),
  quantity = c(10, 20),
  item = c('Apples', 'Oranges')
))

# For local development, bypass authentication
isLocal <- TRUE

home_route <- route("/", function() {
  fluidPage(
    h1("Home Page"),
    DT::dataTableOutput("dataTable")
  )
})


checkRange <- function(value, min, max){
  if(!is.na(value) & (value < min || value > max)){
    paste0("Please specify a number that is between ", min, " and ", max, ",  thank you!")
  } else {
    ""
  }
}

search_string = ""
query_params <- parseQueryString(search_string)

#if !is.null()
emiglio = query_params$useremail
nomignolo = paste0(query_params$firstname, " ", query_params$lastname)

phone_prefix_regex <- "^\\+?\\d{1,3}$"
phone_number_regex <- "^[0-9]{10,10}$"

validatePhone <- function(value, n_char_min){
  if(value != ""){
    
    if(grepl("^[0-9]{1,100}$", value)){
      if (nchar(value) == n_char_min) {
        ""
      } else{
        paste0("Please specify a number that contains ", n_char_min, " digits")
      }
    }else{
      "Please enter only digits"
    }
  } else{
    ""
  }
  
}


ui <- fluidPage(
  tags$head(
    tags$link(rel = "stylesheet", href = "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.0.0-beta3/css/all.min.css"),
    tags$style(HTML("
      .control-label {
        color: black !important;
      }
      
      .strongy{
        background-color: #c8e6c9; 
        padding: 10px
      }
      
      .form-control{
      border-color: grey !important
      }
      
      #loading {
        display: none;
        text-align: center;
      }
      .loader {
        border: 6px solid #f3f3f3; /* Light grey */
        border-top: 6px solid #3498db; /* Blue */
        border-radius: 50%;
        width: 50px;
        height: 50px;
        animation: spin 2s linear infinite;
        margin: 20px auto;
      }
      @keyframes spin {
        0% { transform: rotate(0deg); }
        100% { transform: rotate(360deg); }
      }
    "))
  ),
  useShinyjs(),
  titlePanel("Biological Age Calculator"),
  
  sidebarLayout(
    sidebarPanel(
      fluidRow(
        column(6, textInput("Name", "Enter name", query_params$firstname)),
        column(6, textInput("Surname", "Enter your last name", query_params$lastname))
      ),
      fluidRow(
        column(6, textInput("phone_prefix", "Enter Country Code", "+91")),
        column(6, textInput("phone_number", "Enter your phone number", ""))
      ),
      dateInput("dob", "Date of Birth*", value="1990-01-01"),
      dateInput("bloodTestDate", "Date of TEST", value = Sys.Date()),
      numericInput("albumin", "Albumin (g/dL)", value = NA, min = 0),
      verbatimTextOutput("values"),
      numericInput("lymph", "Lymphocytes (%)", value = NA, min = 0),
      numericInput("mcv", "Mean Cell Volume (MCV)", value = NA, min = 0),
      numericInput("glucose", "Glucose (mg/L)", value = NA, min = 0),
      numericInput("rdw", "Red Cell Dist Width (RDW)", value = NA, min = 0),
      numericInput("creat", "Creatinine (mg/dL)", value = NA, min = 0),
      numericInput("crp", "CRP (mg/L)", value = NA, min = 0),
      numericInput("alp", "Alkaline Phosphatase (U/L)", value = NA, min = 0),
      numericInput("wbc", "White Blood Cells (cells/mL)", value = NA, min = 0),
      actionButton("submit", "Submit", title = "Fill in the phone number field to enable")
    ),
    mainPanel(
      tabsetPanel(
        tabPanel("Calculator",
                 div(id = "loading", class = "loader", style = "display: none"),  # Loading spinner
                 uiOutput("results"),
                 uiOutput("message")),
        tabPanel("My historical data - Plot", 
                 uiOutput("notlogged"),
                 actionLink("openLinkButton", "Create an account here / log in here", href = "", style = "background-color:#c8e6c9; padding: 10px; font-size: 2em"),
                 plotOutput("biologicalAgePlot"))
        ,
        tabPanel("My historical data - Table", 
                 tableOutput("table"),
                 actionLink("openLinkButton", "Create an account here / log in here", href = "", style = "background-color:#c8e6c9; padding: 10px; font-size: 2em"),
                 uiOutput("notlogged1"))
      )
    )
  )
)



server <- function(input, output, session) {
  sheet_id <- "https://docs.google.com/spreadsheets/d/1xQpghper_5FCWkYFByIpdVKFmBofgM7uVrG_bsaGW58/edit?gid=0#gid=0"
  values <- reactiveVal(data.frame()) 
  
  router_server(
    list(home_route)
  )
  
  # Dummy dataset
  #dataset <- data.frame(date = as.Date(c('2024-12-01', '2024-12-02')), 
                        #quantity = c(10, 20), 
                        #item = c('Apples', 'Oranges'))
  
  # Render the dataset in a table
  #output$dataTable <- DT::renderDataTable({
    #dataset
  #})

  
  observeEvent(input$submit, {
    shinyjs::show(id = "loading")  # Show loading spinner
    
    # Collecting inputs
    name <- paste0(input$Name, " ", input$Surname)
    ageAtTestDate <- round(as.numeric(difftime(Sys.Date(), input$dob, units = "days")) / 365.25, 1)
    biological_age <- runif(1, min = ageAtTestDate - 5, max = ageAtTestDate + 5)  # Simulated calculation
    
    bioage_color <- if (biological_age < ageAtTestDate) "green" else if (biological_age > ageAtTestDate) "red" else "yellow"
    
    # Show the BioAge Modal
    show_bioage_modal(name, ageAtTestDate, biological_age, bioage_color)
    
    output$results <- renderUI({
      paste("Thank you for submitting your details. Your biological age will be calculated based on the provided data.")
    })
    
  })
    
  # Define show_bioage_modal function outside observeEvent
  show_bioage_modal <- function(name, ageAtTestDate, biological_age, bioage_color) {
    diff <- round(abs(biological_age - ageAtTestDate), 2)
    message <- if (biological_age < ageAtTestDate) {
      tags$p(
        paste0(
          name,", your healthy choices show! your BioAge is ", diff, " years younger than your calendar Age."
        ),
        style = "padding-bottom: 24px; font-size: 16px; font-weight: bold; font-family: sans-serif; font-variant: contextual;"
      )
    } else if (biological_age > ageAtTestDate) {
      tags$p(
        paste0(
          name,", your BioAge is ", diff, " years higher than your Calendar Age. Don’t worry—small, consistent steps in the right direction can help you close the gap!"
        ),
        style = "padding-bottom: 24px; font-size: 16px; font-weight: bold; font-family: sans-serif; font-variant: contextual;"
      )
    } else {
      tags$p(
        paste0(
          name,", your BioAge matches your Calendar Age, indicating balanced health markers."
        ),
        style = "padding-bottom: 24px; font-size: 16px; font-weight: bold; font-family: sans-serif; font-variant: contextual;"
      )
    }
    
    showModal(
      modalDialog(
        title = NULL,
        div(
          style = "background-color: #0E406B; color: white; padding: 24px; text-align: center; 
               border-top-left-radius: 5px; border-top-right-radius: 5px; margin: -15px -15px 0 -15px; font-family: 'Archia', sans-serif;",
          h3(
            paste0(name,"'s BioAge Results"),
            style = "margin: 0; padding: 0; font-size: 26px; text-align: center; font-family: 'Archia', sans-serif; font-variant: common-ligatures; color: white; line-height: 1;"
          )
        ),
        div(
          style = "background-color: white; text-align: center; font-family: 'Archia', sans-serif; padding-top: 20px;",
          fluidRow(
            column(5, div(
              tags$p("Calendar Age", style = "font-weight: bold; font-size: 20px; color: black;"),
              tags$p(paste(ageAtTestDate, "years"), style = "font-size: 24px; font-weight: bold; color: black;")
            )),
            column(2, div(
              tags$p("→", style = "font-size: 59px; font-weight: bold; color: darkblue; margin-top: 8px;")
            )),
            column(5, div(
              tags$p("BioAge", style = "font-weight: bold; font-size: 20px; color: black;"),
              tags$p(
                paste(round(biological_age, 2), "years"),
                style = sprintf("font-size: 24px; font-weight: bold; color: %s;", bioage_color)
              )
            ))
          )
        ),
        div(
          style = "text-align: center; margin-top: 20px; color: #333333; margin-bottom: 0px;",
          message
        ),
        div(
          style = "text-align: center;",
          tags$p("Complete report sent to your WhatsApp",
                 tags$i(class = "fa-brands fa-whatsapp fa-beat", 
                        style = "color: #25D366; margin-left: 5px; font-size: 16px;"),
                 style = "font-size: 14px; color: black; margin-bottom: 0px;"),
          tags$p("xxxxxxxx4321", style = "font-size: 14px; color: black; margin-bottom: -16px;")
        ),
        easyClose = FALSE,
        footer = tags$button(
          "Close",
          onclick = "Shiny.setInputValue('close_modal', true);",
          style = "background-color: #86D1F1; color: black; border: none; padding: 10px 20px; border-radius: 5px; font-size: 16px; cursor: pointer;"
        )
      )
    )
  }

  output$message <- renderUI({
    HTML("<div class='biological-age-text'>
    <h2>What is Biological Age?</h2>
    <p>Biological age refers to how old a person seems based on the functioning and condition of their
    body systems, rather than the time since birth (chronological age). It is influenced by genetics,
    lifestyle, and environmental factors, and can provide a more accurate representation of an
    individual's health and longevity prospects.</p>
    <h3 class = 'strongy'>Our tool can estimate your biological age using even one blood test parameter. However, for the most accurate results, we recommend including as many parameters as possible.</h3>
    <h2>Here is what each of the parameters mean for your health:</h2>
    <ol>
    <li><strong>Albumin:</strong> A protein in the blood that helps maintain fluid balance and transport hormones,
    vitamins, and drugs; low levels can indicate liver or kidney disease.</li>
    <li><strong>Creatinine:</strong> A waste product from muscle metabolism; its blood level is a marker of kidney
    function, with high levels indicating potential kidney impairment.</li>
    <li><strong>Glucose:</strong> The main sugar found in the blood and the body's primary energy source; levels
    are used to diagnose and monitor diabetes.</li>
    <li><strong>C-reactive Protein (CRP):</strong> A substance produced by the liver in response to inflammation;
    high CRP levels can indicate infection or chronic inflammatory diseases.</li>
    <li><strong>Lymphocyte (Lymphs):</strong> A type of white blood cell involved in the immune response;
    changes in lymphocyte levels can indicate infections, autoimmune diseases, or blood disorders.</li>
    <li><strong>Mean Cell Volume (MCV):</strong> The average size of red blood cells; it helps diagnose and classify
    anemias, with high MCV indicating macrocytic anemia and low MCV indicating microcytic
    anemia.</li>
    <li><strong>Red Cell Distribution Width (RDW):</strong> A measure of the variation in red blood cell size;
    increased RDW can indicate anemia and has been associated with cardiovascular diseases.</li>
    <li><strong>Alkaline Phosphatase:</strong> An enzyme found in the liver, bones, and other tissues; high levels
    can indicate liver disease, bone disorders, or bile duct obstruction.</li>
    <li><strong>White Blood Cells (WBCs):</strong> Cells in the immune system that help defend against infections;
    abnormal levels can indicate infection, inflammation, or immune system disorders.</li>
    </ol>

    <h2>Based on scientific data:</h2>
    <p>We have based this calculation of your biological age on scientific data from the National Health
    and Nutrition Examination Survey (NHANES). The package uses published biomarker
    algorithms to calculate three biological aging measures: Klemera-Doubal Method (KDM)
    biological age, phenotypic age, and homeostatic dysregulation.</p>

    <h2>Citation:</h2>
    <p>Kwon, D., Belsky, D.W. A toolkit for quantification of biological age from blood chemistry and organ function
    test data: BioAge. GeroScience 43, 2795–2808 (2021).</p>

    <h2>Disclaimer:</h2>
    <p>These results are solely for informational use and shouldn't replace professional medical advice,
    diagnosis, or treatment. Always seek the guidance of a healthcare provider for any medical
    conditions or before making changes to your health regimen, including starting new diets,
    exercises, or supplements, or altering medication. Never discontinue medication or follow any
    health advice without consulting your healthcare provider.</p></div>")
  })
  

  
  observeEvent(input$submit, {
    # Handle form submission
    output$results <- renderUI({
      paste("Thank you for submitting your details. Your biological age will be calculated based on the provided data.")
    })
  })
  
  output$notlogged <- renderUI({
    if (is.null(emiglio)){
      HTML("<div class='biological-age-text'>
    <h2>Please log in to View your history</h2>")
    } else {
      ""
    }
    
  })
  
  output$notlogged1 <- renderUI({
    if (is.null(emiglio)){
      HTML("<div class='biological-age-text'>
    <h2>Please log in to View your history</h2>")
    } else {
      ""
    }
    
  })
  
  
  output$biologicalAgePlot <- renderPlot(
    if (!is.null(emiglio)){
      if(nrow(values %>% filter(email == emiglio))>0){
        values %>% 
          filter(email == emiglio) %>% 
          select(c(age, age_bio, date)) %>% 
          group_by(date) %>% 
          mutate(age = mean(age, na.rm = T), age_bio = mean(age_bio, na.rm = T)) %>% 
          rename(
            `Actual age` = age,
            `Biological age` = age_bio
          ) %>% 
          mutate(Date = as_date(date)) %>% 
          pivot_longer(cols = c(1:2), names_to = "name", values_to = "value") %>% 
          ggplot(aes(
            x = Date, 
            y = value, 
            color = name
          )
          )+
          geom_line(size = 1.3)+
          theme_bw()+
          scale_color_discrete(name = "")+
          scale_y_continuous(breaks = round(seq(min(c(values$age, values$age_bio)), max(c(values$age, values$age_bio)), by = 2),0))      
      }
    }
  )
  
  output$table <- renderTable(
    if (!is.null(emiglio)){
      
      if(nrow(values %>% filter(email == emiglio))>0){
        values %>% 
          filter(email == emiglio) %>% 
          mutate_at(c(1, 11), round, 1) %>% 
          select(c(15, 2:10, 1, 11)) %>% 
          #arrange(-date) %>% 
          mutate(date = as.character(as.Date(date)))%>% 
          rename(
            Creatinine = creat, 
            `Lymphocyte (Lymphs)` = lymph,
            `CRP (C-reactive Protein)` = crp,
            `White Blood Cells` = wbc,
            `Mean Cell Volume` = mcv,
            `Red cells distribution width` = rdw,
            Glucose = glucose,
            `Alkaline Phosphatase` = alp,
            `Actual Age` = age,
            `Biological Age` = age_bio      
          )
        
      }
    }
  )
  
  observe({
    iv <- InputValidator$new()
    iv$add_rule("albumin", checkRange, 2, 8)
    iv$add_rule("creat", checkRange, .2, 2)
    iv$add_rule("rdw", checkRange, 10, 20)
    iv$add_rule("crp", checkRange, 0, 50)
    iv$add_rule("lymph", checkRange, 0, 100)
    iv$add_rule("glucose", checkRange, 40, 400)
    iv$add_rule("wbc", checkRange, 2, 25)
    iv$add_rule("alp", checkRange, 0, 300)
    iv$add_rule("mcv", checkRange, 70, 120)
    iv$add_rule("phone_number", validatePhone, 10)
    
    iv$enable()
    
    output$values <- renderPrint({
      req(iv$is_valid())
    })
  })
  
  observeEvent(input$submit, {
    shinyjs::show(id = "loading")  # Show loading spinner
    
    nome = paste0(input$Name, " ", input$Surname)
    
    ageAtTestDate <- round(as.numeric(difftime(Sys.Date(), input$dob, units = "days")) / 365.25, 1)
    
    if (!is.null(input$dob)) {
      allInputs <- data.frame(
        age = as.numeric(difftime(Sys.Date(), input$dob, units = "days")) / 365.25,
        albumin = input$albumin,
        lymph = input$lymph,
        mcv = input$mcv,
        glucose = input$glucose,
        rdw = input$rdw,
        creat = input$creat,
        crp = input$crp,
        alp = input$alp,
        wbc = input$wbc
      )
    }
    
    if (!is.null(input$phone_number) && !is.null(phone_number_regex) &&
        grepl(phone_prefix_regex, input$phone_prefix) &&
        grepl(phone_number_regex, input$phone_number)) {
      validated_phone <- paste(input$phone_prefix, input$phone_number)
    } else {
      validated_phone = NA
    }
    
    mrkrs = colnames(allInputs[, colSums(is.na(allInputs)) < nrow(allInputs)])
    
    train = phenoage_calc(NHANES3, biomarkers = mrkrs)
    
    biological_age <- phenoage_calc(allInputs, biomarkers = mrkrs, fit = train$fit)$data$phenoage
    
    allInputs_tosave = allInputs %>%
      mutate(
        age_bio = biological_age,
        email = ifelse(is.null(emiglio), "", emiglio),
        name = nome,
        phone = validated_phone,
        date= input$bloodTestDate
      )
    
    biologicalAge <- if (!is.null(input$dob)) {
      paste("Your biological age is approximately:", round(biological_age, 1), "years")
    } else {
      "Please enter at least your date of birth"
    }
    
    observeEvent(input$close_modal, {
      removeModal()
    })
    
    output$results <- renderUI(
      HTML(
        paste0(
          "<div style='background-color: #c8e6c9; padding: 10px;'>",
          "<h2>Hello ", nome, "</h2>",
          "<p>Your biological age is ", round(biological_age, 1), " years </p>",
          "<p>Your actual age is ", ageAtTestDate, " years</p></div>"
        )
      )
    )
    
    # Append data to Google Sheet
    if (nrow(allInputs_tosave) == 1) {
      if (nrow(values()) == 0) {
        sheet_write(data = allInputs_tosave, ss = sheet_id, sheet = "longevity")
      } else {
        sheet_append(data = allInputs_tosave, ss = sheet_id, sheet = "longevity")
      }
    }
    
    # Update values to reflect the new data
    values(read_sheet(ss = sheet_id, sheet = "longevity"))
    
    shinyjs::hide(id = "loading")  # Hide loading spinner
    
    # Generate biological age plot
    output$biologicalAgePlot <- renderPlot({
      if (!is.null(emiglio)) {
        if (nrow(values() %>% filter(email == emiglio)) > 0) {
          values() %>%
            filter(email == emiglio) %>%
            select(c(age, age_bio, date)) %>%
            group_by(date) %>%
            mutate(age = mean(age, na.rm = TRUE), age_bio = mean(age_bio, na.rm = TRUE)) %>%
            rename(`Actual age` = age, `Biological age` = age_bio) %>%
            mutate(Date = as_date(date)) %>%
            pivot_longer(cols = c(1:2), names_to = "name", values_to = "value") %>%
            ggplot(aes(x = Date, y = value, color = name)) +
            geom_line(size = 1.3) +
            theme_bw() +
            scale_color_discrete(name = "") +
            scale_y_continuous(breaks = round(seq(min(c(values()$age, values()$age_bio)), 
                                                  max(c(values()$age, values()$age_bio)), by = 2), 0))
        }
      }
    })
    
    # Generate biological age table
    output$table <- renderTable({
      if (!is.null(emiglio)) {
        if (nrow(values() %>% filter(email == emiglio)) > 0) {
          values() %>%
            filter(email == emiglio) %>%
            mutate_at(c(1, 11), round, 1) %>%
            select(c(15, 2:10, 1, 11)) %>%
            mutate(date = as.character(as.Date(date))) %>%
            rename(
              Creatinine = creat, 
              `Lymphocyte (Lymphs)` = lymph,
              `CRP (C-reactive Protein)` = crp,
              `White Blood Cells` = wbc,
              `Mean Cell Volume` = mcv,
              `Alkaline Phosphatase` = alp,
              Glucose = glucose,
              `Red cells distribution width` = rdw,
              `Actual Age` = age,
              `Biological Age` = age_bio      
            )
        }
      }
    })
  })
  
  
  
}

shinyApp(ui = ui, server = server)