Update app.R

app.R

@@ -1,58 +1,569 @@
+#app.R
 library(shiny)
-library(bslib)
+library(BioAge)
 library(dplyr)
-library(ggplot2)
-
-df <- readr::read_csv("penguins.csv")
-# Find subset of columns that are suitable for scatter plot
-df_num <- df |> select(where(is.numeric), -Year)
-
-ui <- page_sidebar(
-  theme = bs_theme(bootswatch = "minty"),
-  title = "Penguins explorer",
-  sidebar = sidebar(
-    varSelectInput("xvar", "X variable", df_num, selected = "Bill Length (mm)"),
-    varSelectInput("yvar", "Y variable", df_num, selected = "Bill Depth (mm)"),
-    checkboxGroupInput("species", "Filter by species",
-      choices = unique(df$Species), selected = unique(df$Species)
-    ),
-    hr(), # Add a horizontal rule
-    checkboxInput("by_species", "Show species", TRUE),
-    checkboxInput("show_margins", "Show marginal plots", TRUE),
-    checkboxInput("smooth", "Add smoother"),
+#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$style(HTML("
+      .control-label {
+        color: black !important;
+      }
+      
+      .strongy{
+        background-color: #c8e6c9; 
+        padding: 10px
+      }
+      
+      .form-control{
+      border-color: grey !important
+      }
+      
+      #loading {
+        display: none;
+        text-align: center;
+      }
+      .loader {
+        border: 6px solid #f3f3f3; /* Light grey */
+        border-top: 6px solid #3498db; /* Blue */
+        border-radius: 50%;
+        width: 50px;
+        height: 50px;
+        animation: spin 2s linear infinite;
+        margin: 20px auto;
+      }
+      @keyframes spin {
+        0% { transform: rotate(0deg); }
+        100% { transform: rotate(360deg); }
+      }
+    "))
   ),
-  plotOutput("scatter")
+  useShinyjs(),
+  titlePanel("Biological Age Calculator"),
+  
+  sidebarLayout(
+    sidebarPanel(
+      fluidRow(
+        column(6, textInput("Name", "Enter name", query_params$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) {
-  subsetted <- reactive({
-    req(input$species)
-    df |> filter(Species %in% input$species)
-  })
+  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
+  #})
 
-  output$scatter <- renderPlot(
-    {
-      p <- ggplot(subsetted(), aes(!!input$xvar, !!input$yvar)) +
-        theme_light() +
-        list(
-          theme(legend.position = "bottom"),
-          if (input$by_species) aes(color = Species),
-          geom_point(),
-          if (input$smooth) geom_smooth()
+  
+  observeEvent(input$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;"
         )
+      )
+    )
+  }
 
-      if (input$show_margins) {
-        margin_type <- if (input$by_species) "density" else "histogram"
-        p <- p |> ggExtra::ggMarginal(
-          type = margin_type, margins = "both",
-          size = 8, groupColour = input$by_species, groupFill = input$by_species
-        )
-      }
+  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>")
+  })
+  
 
-      p
-    },
-    res = 100
+  
+  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, server)
+shinyApp(ui = ui, server = server)