server.R

library(shiny)
library(png)
library(shinyBS)
library(shinyjs)
library(shinyDND)
library(ggplot2)
library(dplyr)  ###NEW PACKAGE 
library(shinydashboard)
library(simstudy) ### NEW PACKAGE 
library(lubridate)###NEW PACKGE
library(shinyalert)##NEW PACKAGE
library(shinyWidgets)



####read in dataset###
seaotters <- read.csv("Otter.csv",header=T)

diet <- read.csv("Diet.csv",header=T)
diet$Diet<-as.character(diet$Diet)

bank = read.csv("questionbank.csv")
bank = data.frame(lapply(bank, as.character), stringsAsFactors = FALSE)




shinyServer(function(input, output,session) {

  observeEvent(input$info,{
    sendSweetAlert(
      session = session,
      title = "Instructions:",
      type = NULL,
      closeOnClickOutside = TRUE,
      text = "Pick a data set and variables to view the interaction plot and the associated ANOVA table."
    )
  })
  output$ack2<-renderUI((
    h4('Thanks for the data set and code provided by The University of Sheffield (',url,') and Dr.Dylan Childs(',url2,').')
  ))
  
  url <- a("www.sheffield.ac.uk/mash/data", href="https://www.sheffield.ac.uk/mash/data",target="_blank")
  url2 <- a("github.com/dzchilds", href="https://github.com/dzchilds",target="_blank")
  
  
  
  
  
  output$box1<-renderUI(h4('ANOVA is used for comparing three or more group means. 
                           Different groups are different levels of categorical variables, and group means are calculated from continuous variables.
                           ',br(),br(),'EX. Are the average score of three STAT 200 sections significantly different from each other?'))
  
  output$box2<-renderUI(h4('Regression is used for determining the relationship between two continuous variables. One dependent variable (Y) can also be affected by multiple independent variables (X).  
                           ',br(),br(),'EX. How will crime rate be impacted by population density, unemployment rate, and income.'))
  
  output$box3<-renderUI(h4('ANCOVA is adding continuous variables onto ANOVA analysis, which is called covariate. 
                           Significant different between group means and significant relationship between continuous variables will both be analyzed.
                           ',br(),br(),'EX. Who makes the most money? Will gender or years after graduation influence the income? '))
  
  ####button###
  
  observeEvent(input$go,{
    updateTabItems(session,"tabs","exploring")
  })
  
  observeEvent(input$game,{
    updateTabItems(session,"tabs","game")
  })
  
  observeEvent(input$pre2,{
    updateTabItems(session,"tabs","box")
  })
  
  observeEvent(input$go2,{
    updateTabItems(session,"tabs","instruction")
  })
  
  
  observeEvent(input$start,{
    updateTabItems(session,"tabs","instruction")
  })
  
  
  
  ##########################Download the dataset#################
  
  # Reactive value for selected dataset ----
  datasetInput <- reactive({
    switch(input$menu1,
           'Otter'=seaotters,
           'Diet'=diet)
  })
  
  # Downloadable csv of selected dataset ----
  
  output$downloadData <- downloadHandler(
    filename = function() {
      paste(input$menu1, ".csv", sep = "")
    },
    content = function(con) {
      write.csv(datasetInput(), con)
    }
  )
  
  
  
  ###############################  Exploring  ##############################
  
  
  ###prep the data###
  otters.model <- lm(Otters ~ Location + Year + Location:Year, data = seaotters)
  pred.data <- expand.grid(Year = 1992:2003, Location = c("Lagoon", "Bay"))
  pred.data <- mutate(pred.data, Otters = predict(otters.model, pred.data))
  
  diet.model<-lm(ab_change~gender+Diet+Age+Height+pre.weight+gender:Age+gender:Height+gender:pre.weight+
                   Diet:Age+Diet:Height+Diet:pre.weight,data=diet)
  
  diet.model2<-lm(ab_change~Age+gender+Age:gender,data=diet)
  pred.data2 <- expand.grid(Age = 16:60, gender = c("M", "F"))
  pred.data2 <- mutate(pred.data2, ab_change = predict(diet.model2, pred.data2))
  
  diet.model3<-lm(ab_change~Height+gender+Height:gender,data=diet)
  pred.data3 <- expand.grid(Height = 141:201, gender = c("M", "F"))
  pred.data3 <- mutate(pred.data3, ab_change = predict(diet.model3, pred.data3))
  
  
  diet.model4<-lm(ab_change~pre.weight+gender+pre.weight:gender,data=diet)
  pred.data4 <- expand.grid(pre.weight=58:103, gender = c("M", "F"))
  pred.data4 <- mutate(pred.data4, ab_change = predict(diet.model4, pred.data4))
  
  
  diet.model5<-lm(ab_change~Age+Diet+Age:Diet,data=diet)
  pred.data5 <- expand.grid(Age = 16:60, Diet = c('1','2','3'))
  pred.data5 <- mutate(pred.data5, ab_change = predict(diet.model5, pred.data5))
  
  diet.model6<-lm(ab_change~Height+Diet+Height:Diet,data=diet)
  pred.data6<- expand.grid(Height = 141:201, Diet = c('1','2','3'))
  pred.data6 <- mutate(pred.data6, ab_change = predict(diet.model6, pred.data6))
  
  
  diet.model7<-lm(ab_change~pre.weight+Diet+pre.weight:Diet,data=diet)
  pred.data7 <- expand.grid(pre.weight=58:103, Diet = c('1','2','3'))
  pred.data7 <- mutate(pred.data7, ab_change = predict(diet.model7, pred.data7))
  
  
  ###save random model
  rand<-reactiveValues(rand_mod=NULL)
  
  
  
  ###Graph the plot of interaction###
  
  
  output$plot_gg<-renderPlot(
    if (input$menu1=='Otter') {ggplot(pred.data, aes(x = Year, y = Otters, colour = Location)) + 
        geom_line() + geom_point(data = seaotters) + 
        xlab("Year") + ylab("Otters")+theme(text = element_text(size=20),panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
                                            panel.background = element_blank(), axis.line = element_line(colour = "black"))}
    
    else if (input$menu1=='Diet'){
      
      
      if (input$select_conti=='Age' & input$select_covar=='Gender'){ggplot(pred.data2, aes(x = Age, y = ab_change, colour = gender)) + 
          geom_line() + geom_point(data = diet) + 
          xlab("Age") + ylab("Decrease in Weight")+theme(text = element_text(size=20),panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
                                                         panel.background = element_blank(), axis.line = element_line(colour = "black"))}
      else if (input$select_conti=='Height' & input$select_covar=='Gender'){ggplot(pred.data3, aes(x = Height, y = ab_change, colour = gender)) + 
          geom_line() + geom_point(data = diet) + 
          xlab("Height") + ylab("Decrease in Weight")+theme(text = element_text(size=20),panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
                                                            panel.background = element_blank(), axis.line = element_line(colour = "black"))}
      else if (input$select_conti=='Pre-diet Weight' & input$select_covar=='Gender'){ggplot(pred.data4, aes(x = pre.weight, y = ab_change, colour = gender)) + 
          geom_line() + geom_point(data = diet) + 
          xlab("Pre-diet Weight") + ylab("Decrease in Weight")+theme(text = element_text(size=20),panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
                                                                     panel.background = element_blank(), axis.line = element_line(colour = "black"))}
      else if (input$select_conti=='Age' & input$select_covar=='Diet'){ggplot(pred.data5, aes(x = Age, y = ab_change, colour =Diet)) + 
          geom_line() + geom_point(data = diet) + 
          xlab("Age") + ylab("Decrease in Weight")+theme(text = element_text(size=20),panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
                                                         panel.background = element_blank(), axis.line = element_line(colour = "black"))}
      else if (input$select_conti=='Height' & input$select_covar=='Diet'){ggplot(pred.data6, aes(x = Height, y = ab_change, colour = Diet)) + 
          geom_line() + geom_point(data = diet) + 
          xlab("Height") + ylab("Decrease in Weight")+theme(text = element_text(size=20),panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
                                                            panel.background = element_blank(), axis.line = element_line(colour = "black"))}
      else if (input$select_conti=='Pre-diet Weight' & input$select_covar=='Diet'){ggplot(pred.data7, aes(x = pre.weight, y = ab_change, colour = Diet)) + 
          geom_line() + geom_point(data = diet) + 
          xlab("Pre-diet Weight") + ylab("Decrease in Weight")+theme(text = element_text(size=20),panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
                                                                     panel.background = element_blank(), axis.line = element_line(colour = "black"))}
      
    }
    
    else if (input$menu1=='Random'){
      
      
      ###create data with label A and B with different slope and intersection
      A<-'A'
      B<-'B'
      
      a<-input$inter1
      b<-input$inter2
      
      slope1<-input$slope1
      slope2<-input$slope2
      
      def <- defData(varname = "inter", dist = "nonrandom", formula = a, id = "id")
      
      def<- defData(def,varname = "slope", dist = "nonrandom", formula = slope1, id = "slope")
      def <- defData(def, varname = "X", dist = "uniform", formula = "0;20")
      def <- defData(def, varname = "Y", formula = "inter + X * slope", variance = 11)
      
      def2<- defData(varname = "inter", dist = "nonrandom", formula = b, id = "id")
      
      def2 <- defData(def2,varname = "slope", dist = "nonrandom", formula = slope2, id = "slope")
      def2<- defDataAdd(def2, varname = "X", dist = "uniform", formula = "0;20")
      def2 <- defDataAdd(def2, varname = "Y", formula = "inter + X * slope", variance =11)
      
      
      dt <- genData(input$sample, def)
      dt2<-genData(input$sample,def2)
      
      names(dt2)[1]<-'id'
      
      dt$cov<-'A'
      dt2$cov<-'B'
      
      comb<-rbind(dt,dt2)
      
      
      aov.model<-lm(Y~X+cov+cov:X,data=comb)
      
      
      
      pred.aov <- expand.grid(X =0:20, cov = c("A","B"))
      pred.aov <- mutate(pred.aov, Y = predict(aov.model, pred.aov))
      
      
      ggplot(pred.aov, aes(x = X, y = Y, colour = cov)) + 
        geom_line() + geom_point(data = comb) + 
        xlab("X") + ylab("Y")+theme(text = element_text(size=20),panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
                                    panel.background = element_blank(), axis.line = element_line(colour = "black"))}
    
    
    
  )
  
  
  
  
  ###ANCOVA analysis table###
  output$analysis1<-renderPrint(
    
    
    if (input$menu1=='Otter') {anova(otters.model)}
    else if (input$menu1=='Diet'){
      if (input$select_conti=='Age' & input$select_covar=='Gender'){anova(diet.model2)}
      else if (input$select_conti=='Height' & input$select_covar=='Gender'){anova(diet.model3)}
      else if (input$select_conti=='Pre-diet Weight' & input$select_covar=='Gender'){anova(diet.model4)}
      else if (input$select_conti=='Age' & input$select_covar=='Diet'){anova(diet.model5)}
      else if (input$select_conti=='Height' & input$select_covar=='Diet'){anova(diet.model6)}
      else if (input$select_conti=='Pre-diet Weight' & input$select_covar=='Diet'){anova(diet.model7)}
    }
    else if (input$menu1=='Random'){
      A<-'A'
      B<-'B'
      
      a<-input$inter1
      b<-input$inter2
      
      slope1<-input$slope1
      slope2<-input$slope2
      
      def <- defData(varname = "inter", dist = "nonrandom", formula = a, id = "id")
      
      def<- defData(def,varname = "slope", dist = "nonrandom", formula = slope1, id = "slope")
      def <- defData(def, varname = "X", dist = "uniform", formula = "10;20")
      def <- defData(def, varname = "Y", formula = "inter + X * slope", variance = 11)
      
      def2<- defData(varname = "inter", dist = "nonrandom", formula = b, id = "id")
      
      def2 <- defData(def2,varname = "slope", dist = "nonrandom", formula = slope2, id = "slope")
      def2<- defDataAdd(def2, varname = "X", dist = "uniform", formula = "10;20")
      def2 <- defDataAdd(def2, varname = "Y", formula = "inter + X * slope", variance = 11)
      
      
      dt <- genData(input$sample, def)
      dt2<-genData(input$sample,def2)
      
      names(dt2)[1]<-'id'
      
      dt$cov<-'A'
      dt2$cov<-'B'
      
      comb<-rbind(dt,dt2)
      
      
      aov.model<-lm(Y~X+cov+cov:X,data=comb)
      
      ##testing passing the model
      rand$rand_mod<-anova(aov.model)[3,"Pr(>F)"]
      
      anova(aov.model)
      
      
    }
    
    
  )
  
  
  #####get p values for each interaction 
  
  var<-reactiveValues(p=NULL)
  observe({
    
    # if (is.null(input$menu1)){
    #   return()
    # }
    # 
    # isolate({
    #   var$p<-as.numeric(anova(otters.model)[3,"Pr(>F)"])
    #  
    # })
    
    
    if (input$menu1=='Otter') {var$p<-as.numeric(anova(otters.model)[3,"Pr(>F)"])}
    else if (input$menu1=='Diet'){
      if (input$select_conti=='Age' & input$select_covar=='Gender'){var$p<-as.numeric(anova(diet.model2)[3,"Pr(>F)"])}
      else if (input$select_conti=='Height' & input$select_covar=='Gender'){var$p<-as.numeric(anova(diet.model3)[3,"Pr(>F)"])}
      else if (input$select_conti=='Pre-diet Weight' & input$select_covar=='Gender'){var$p<-as.numeric(anova(diet.model4)[3,"Pr(>F)"])}
      else if (input$select_conti=='Age' & input$select_covar=='Diet'){var$p<-as.numeric(anova(diet.model5)[3,"Pr(>F)"])}
      else if (input$select_conti=='Height' & input$select_covar=='Diet'){var$p<-as.numeric(anova(diet.model6)[3,"Pr(>F)"])}
      else if (input$select_conti=='Pre-diet Weight' & input$select_covar=='Diet'){var$p<-as.numeric(anova(diet.model7)[3,"Pr(>F)"])}
    }
    else if (input$menu1=='Random'){var$p<-as.numeric(rand$rand_mod)}
  })
  
  output$p<-renderUI(
    if (var$p<=0.05){
      h4(strong('P-value for this interaction is',signif(var$p,4),'.' ,br(),'Since the p-value is smaller than 0.05
                (α=0.05), there is a statistically significant interaction between these two variables.'))}
    else {h4(strong('P-value for this interaction is',signif(var$p,4),'.' ,br(),'Since the p-value is greater than 0.05
                    (α=0.05), there is NOT a statistically significant interaction between these two variables.'))}
    )
  
  
  
  
  
  ######################################  Bank B #############################################################
  numbers <- reactiveValues(strong = c(), moderate = c(), insig = c(), index = c(), question = data.frame())
  
  observeEvent(input$go,{
    numbers$strong = sample(1:12,1)
    numbers$moderate = sample(13:24,1)
    numbers$insig= sample(25:36,1)
    
    
    numbers$index =c("A","B","C")
    numbers$question = cbind(bank[c(numbers$strong,numbers$moderate,numbers$insig),],numbers$index)
    
  })
  
  observeEvent(input$new,{
    numbers$strong = sample(1:12,1)
    numbers$moderate = sample(13:24,1)
    numbers$insig= sample(25:36,1)
    
    
    numbers$index = c("A","B","C")
    numbers$question = cbind(bank[c(numbers$strong,numbers$moderate,numbers$insig),],numbers$index)
    
    updateRadioButtons(session, 'radio1','',c('A','B','C'),selected='',inline=TRUE)
    updateRadioButtons(session,"radio2", '',c('A','B','C'),selected='',inline=TRUE)
    updateRadioButtons(session, "radio3", '',c('A','B','C'),selected='',inline=TRUE)
  })
  
  observeEvent(input$tabs,{
    numbers$strong = sample(1:12,1)
    numbers$moderate = sample(13:24,1)
    numbers$insig= sample(25:36,1)
    
    
    numbers$index = c("A","B","C")
    numbers$question = cbind(bank[c(numbers$strong,numbers$moderate,numbers$insig),],numbers$index)
    
  })
  
  output$plot1 <- renderUI({
    img(src = numbers$question[numbers$question[5] == "A",4], width = "100%", height = "107%", style = "text-align: center")
  })
  
  # output$table1 <- renderUI({
  #   img(src = numbers$question[numbers$question[5] == "A",3], width = "100%", height = "100%", style = "text-align: center")
  # })
  
  output$plot2 <- renderUI({
    img(src = numbers$question[numbers$question[5] == "B",4], width = "100%", height = "107%", style = "text-align: center")
  })
  
  # output$table2 <- renderUI({
  #   img(src = numbers$question[numbers$question[5] == "B",3], width = "100%", height = "100%", style = "text-align: center")
  # })
  
  output$plot3 <- renderUI({
    img(src = numbers$question[numbers$question[5] == "C",4], width = "100%", height = "107%", style = "text-align: center")
  })
  
  # output$table3 <- renderUI({
  #   img(src = numbers$question[numbers$question[5] == "C",3], width = "100%", height = "100%", style = "text-align: center")
  # })
  
  #######randomize the table######
  
  index2 <- reactiveValues(index2 = 3)
  
  observeEvent(input$new,{index2$index2 <- sample(1:4,1, replace=TRUE, prob=NULL)
  })
  
  observeEvent(input$reset,{index2$index2 <- sample(1:4,1, replace=TRUE, prob=NULL)
  })
  
  output$table1<-renderUI({
    if (index2$index2==1){img(src = numbers$question[numbers$question[5] == "A",3], width = "105%", height = "105%", style = "text-align: center")}
    else if (index2$index2==2){img(src = numbers$question[numbers$question[5] == "B",3], width = "105%", height = "105%", style = "text-align: center")}
    else if (index2$index2==3){img(src = numbers$question[numbers$question[5] == "C",3], width = "105%", height = "105%", style = "text-align: center")}
    else if (index2$index2==4){img(src = numbers$question[numbers$question[5] == "A",3], width = "105%", height = "105%", style = "text-align: center")}
  })
  
  output$table2<-renderUI({
    if (index2$index2==1){img(src = numbers$question[numbers$question[5] == "B",3], width = "105%", height = "105%", style = "text-align: center")}
    else if (index2$index2==2){img(src = numbers$question[numbers$question[5] == "C",3], width = "105%", height = "105%", style = "text-align: center")}
    else if (index2$index2==3){img(src = numbers$question[numbers$question[5] == "A",3], width = "105%", height = "105%", style = "text-align: center")}
    else if (index2$index2==4){img(src = numbers$question[numbers$question[5] == "C",3], width = "105%", height = "105%", style = "text-align: center")}
  })
  
  output$table3<-renderUI({
    if (index2$index2==1){img(src = numbers$question[numbers$question[5] == "C",3], width = "105%", height = "105%", style = "text-align: center")}
    else if (index2$index2==2){img(src = numbers$question[numbers$question[5] == "A",3], width = "105%", height = "105%", style = "text-align: center")}
    else if (index2$index2==3){img(src = numbers$question[numbers$question[5] == "B",3], width = "105%", height = "105%", style = "text-align: center")}
    else if (index2$index2==4){img(src = numbers$question[numbers$question[5] == "B",3], width = "105%", height = "105%", style = "text-align: center")}
  })
  
  
  
  ####letter for the plot
  output$a<-renderUI(h4('A'))
  output$b<-renderUI(h4('B'))
  output$c<-renderUI(h4('C'))
  #####buttons####
  
  observeEvent(input$submitA,{
    updateButton(session,"submitA",disabled = TRUE)
  })
  observeEvent(input$new,{
    updateButton(session,"submitA",disabled = FALSE)
  })
  
  observeEvent(input$submitA,{
    updateButton(session,"new",disabled = FALSE)
  })
  
  observeEvent(input$new,{
    updateButton(session,"new",disabled = TRUE)
  })
  
  
  observeEvent(input$new, {
    reset("radio1")
  })
  
  
  ###################check answers#####
  
  summationC<-reactiveValues(correct1 = c(0), started=FALSE)
  
  observeEvent(input$submitA,{
    observeEvent(input$new,{
      output$answer1 <- renderUI({
        img(src = NULL,width=30)
      })
    })
    observe({
      output$answer1 <- renderUI({
        if (!is.null(input$radio1)){
          if (index2$index2==1 &input$radio1 == 'A'){
            img(src = "check.png",width=30)
          }
          else if (index2$index2==2 &input$radio1 == 'B') {img(src = "check.png",width=30)}
          else if (index2$index2==3 &input$radio1 == 'C'){img(src = "check.png",width=30)}
          else if (index2$index2==4 &input$radio1 == 'A'){img(src = "check.png",width =30)}
          else{
            img(src = "cross.png",width=30)
          }
        }
      })
    })
  })
  
  
  observeEvent(input$submitA,{
    observeEvent(input$new,{
      output$answer2 <- renderUI({
        img(src = NULL,width=30)
      })
    })
    observe({
      output$answer2 <- renderUI({
        if (!is.null(input$radio2)){
          if (index2$index2==1 &input$radio2 == 'B'){
            img(src = "check.png",width=30)
            
          }
          else if (index2$index2==2 &input$radio2 == 'C') {img(src = "check.png",width=30)}
          else if (index2$index2==3 &input$radio2 == 'A'){img(src = "check.png",width=30)}
          else if (index2$index2==4 &input$radio2 == 'C'){img(src = "check.png",width=30)}
          else{
            img(src = "cross.png",width=30)
          }
        }
      })
    })
  })
  
  observeEvent(input$submitA,{
    observeEvent(input$new,{
      output$answer3 <- renderUI({
        img(src = NULL,width=30)
      })
    })
    observe({
      output$answer3 <- renderUI({
        if (!is.null(input$radio3)){
          if (index2$index2==1 &input$radio3 == 'C'){
            img(src = "check.png",width=30)
          }
          else if (index2$index2==2 &input$radio3 == 'A') {img(src = "check.png",width=30)}
          else if (index2$index2==3 &input$radio3 == 'B'){img(src = "check.png",width=30)}
          else if (index2$index2==4 &input$radio3 == 'B'){img(src = "check.png",width=30)}
          else{
            img(src = "cross.png",width=30);
            
          }
        }
      })
    })
  })
  
  
  #####count correct answer ########
  summationC<-reactiveValues(correct1 = c(0),total=c(), started=FALSE)
  
  observeEvent(input$submitA,{
    for (i in input$radio1){
      summationC$total = c(summationC$total,1)
      if (index2$index2==1 &input$radio1 == 'A'){
        summationC$correct1 = c(summationC$correct1,1)
      }
      else if (index2$index2==2 &input$radio1 == 'B') { summationC$correct1 = c(summationC$correct1,1)}
      else if (index2$index2==3 &input$radio1 == 'C'){summationC$correct1 = c(summationC$correct1,1)}
      else if (index2$index2==4 &input$radio1 == 'A'){summationC$correct1 = c(summationC$correct1,1)}
      else{
        summationC$correct1 = c(summationC$correct1,0)}
      
    }
    
    for (i in input$radio2){
      summationC$total = c(summationC$total,1)
      if (index2$index2==1 &input$radio2 == 'B'){
        
        summationC$correct1 = c(summationC$correct1,1)
        
      }
      else if (index2$index2==2 &input$radio2 == 'C') {summationC$correct1 = c(summationC$correct1,1)}
      else if (index2$index2==3 &input$radio2 == 'A'){summationC$correct1 = c(summationC$correct1,1)}
      else if (index2$index2==4 &input$radio2 == 'C'){summationC$correct1 = c(summationC$correct1,1)}
      else{
        
        summationC$correct1 = c(summationC$correct1,0)}
    }
    
    
    for (i in input$radio3){
      summationC$total = c(summationC$total,1)
      if (index2$index2==1 &input$radio3 == 'C'){
        i
        summationC$correct1 = c(summationC$correct1,1)
      }
      else if (index2$index2==2 &input$radio3 == 'A') {summationC$correct1 = c(summationC$correct1,1)}
      else if (index2$index2==3 &input$radio3 == 'B'){summationC$correct1 = c(summationC$correct1,1)}
      else if (index2$index2==4 &input$radio3 == 'B'){ summationC$correct1 = c(summationC$correct1,1)}
      else{
        
        summationC$correct1 = c(summationC$correct1,0)}
    }
  })
  
  
  
  output$correctC <- renderPrint({
    if (sum(c(summationC$correct1))==0) {cat("You have earned 0 points")}
    else{
      cat("You have earned",sum(c(summationC$correct1)),'points')}
  })
  
  
  ###########timer####################
  
  # Initialize the timer, 60 seconds, not active.
  timer <- reactiveVal(60)
  active <- reactiveVal(FALSE)
  
  # Output the time left.
  output$timeleft <- renderText({
    paste("Time left: ", seconds_to_period(timer()))
  })
  
  
  ########show up the scoreing panel and popup####
  
  
  # observer that invalidates every second. If timer is active, decrease by one.
  observe({
    invalidateLater(1000, session)
    isolate({
      if(active())
      {
        timer(timer()-1)
        if(timer()<1)
        {
          active(FALSE)
          shinyalert('Count Down Complete','Click to see your score',
                     type = "success")
          
          output$scoreBox <- renderValueBox({
            valueBox(
              paste0(sum(c(summationC$correct1))), "Totel Score", icon = icon("list"),
              color = "purple"
            )
          })
          
          output$percentBox <- renderValueBox({
            if (sum(c(summationC$correct1))==0){valueBox(
              paste0('0%'), "Accuracy", icon = icon("thumbs-up", lib = "glyphicon"),
              color = "light-blue"
            )}
            else{
              valueBox(
                paste0(round(sum(c(summationC$correct1))/sum(c(summationC$total))*100,digit=1),'%'), "Accuracy", icon = icon("thumbs-up", lib = "glyphicon"),
                color = "light-blue"
              )}
          })
          
          output$timeBox <- renderValueBox({
            valueBox(
              paste0(input$seconds,'s'), "Time Used", icon = icon("time",lib = "glyphicon"),
              color = "maroon"
            )
          })
          
          
        }
        
      }
    })
  })
  
  
  
  
  
  
  
  
  
  # observers for actionbuttons
  observeEvent(input$start_timer, {active(TRUE)})
  #observeEvent(input$stop, {active(FALSE)})
  observeEvent(input$start_timer, {timer(input$seconds)})
  observeEvent(input$reset, {timer(input$seconds);active(FALSE)
    output$scoreBox<-NULL; 
    output$percentBox<-NULL;
    output$timeBox<-NULL;
    summationC$correct1 <- c(0); summationC$total=c()
  })
  
  
  ##closing for ui DON'T DELET####  
    })