README.md

I modified your code slightly to use the rCharts syntax. You will need to install the dev branch of rCharts from github to run this application.

devtools::install_github("rCharts", "ramnathv", ref = "dev")
shiny::runGist('7074303')

I made three changes to your code:

1. Replaced library(rHighcharts) with library(rCharts) in both ui.R and server.R
2. Replaced Line 7 in server.R with a <- Highcharts$new() to make use of rCharts class.
3. Replaced renderChart with renderChart2 which is a modified version of renderChart and will eventually replace it.

server.R

require(rCharts)
shinyServer( function( input , output )
{
  output$myPlot <- renderChart2( 
{
  
  a <- Highcharts$new()
  readFileName <- paste( input$region, input$disease, "2002-2011weekly.csv" )
  mydata = read.csv(readFileName)
  dataMatrix <-  as.matrix(mydata)[1:52,-1]
  dataMatrix2 <- dataMatrix
  numYears <- ncol(dataMatrix)
  if (input$incubation == 2)
  {
    for (r in 2:52 ){
      for (c in 1:numYears ){
        dataMatrix[r, c] <- dataMatrix2[r ,c]+dataMatrix2[r-1, c]
      }       
    }
  }
  L <- input$L 
  degree <-  as.numeric(input$degree)
  includeObs <-  array( TRUE , dim=dim(dataMatrix) )
  limitArray <-  getLimits( dataMatrix , includeObs , L , degree )
  LCL <-  limitArray[,1]
  CL  <-  limitArray[,2]
  UCL <-  limitArray[,3]
  if ( input$its == "Yes" ) 
  {
    for (week in 1:52)
    { 
      for (j in 1:numYears)
      {
        if ( dataMatrix[week,j] > UCL[week] )   { includeObs[week,j] <- FALSE }
      }
    }
    limitArray <-getLimits( dataMatrix , includeObs , L , degree )
    LCL <-  limitArray[,1]
    CL  <-  limitArray[,2]
    UCL <-  limitArray[,3]
  }
  ymax <- max( dataMatrix )
  ymax <- 1.1*max( c(ymax,UCL))
  cat( "ymax =")
  cat( ymax )
  a$title(text = paste(input$disease,as.character(input$year)))
  a$xAxis(title = list(text= "Week"))
  a$yAxis(title = list(text= paste("Counts in",as.character(input$year))))
  a$plotOptions(line = list(marker = list(symbol='circle', radius=2)))
  a$data(name = "Disease Counts", dataMatrix[,as.numeric(input$year)-2001] , 
         type="line", color="blue" )                
  a$data(name="LCL", c(LCL,LCL[52]) , type="line", color="red")
  a$data(name="UCL", c(UCL,UCL[52]) , type="line", color="red" )
  
  return(a)
  
  
} )
} )


getLimits <- function( dataMatrix , includeObs , L , degree) 
{ x = 1:52
  nyears = ncol( dataMatrix )
  cat("\n")
  if ( degree == 2 )
  {  
    xs1 = sin(2*pi*x/52);        xc1 = cos(2*pi*x/52)
    for ( week in x )
    {
      for ( j in 1:nyears )
      {
        if ( ! includeObs[week,j] ) { dataMatrix[week,j] = NA } 
      }
    }
    weeklyMeans = apply( dataMatrix[,1:nyears] , 1 , mean , na.rm=TRUE )  
    y = weeklyMeans[1:52]
    trigReg = lm( y ~ xs1 + xc1 )
    b0 = trigReg[[1]][[1]];      b1 = trigReg[[1]][[2]]
    b2 = trigReg[[1]][[3]]
    yhat = b0 + b1*xs1 + b2*xc1
    yhat = pmax(0,yhat)
    #    cat("yhat = ")
    #    cat(yhat)
  }
  if ( degree == 4)
  {  
    xs1 = sin(2*pi*x/52);        xc1 = cos(2*pi*x/52)
    xs2 = sin(4*pi*x/52);        xc2 = cos(4*pi*x/52)
    for ( week in x )
    {
      for ( j in 1:nyears )
      {
        if ( ! includeObs[week,j] ) { dataMatrix[week,j] = NA } 
      }
    }
    weeklyMeans = apply( dataMatrix[,1:nyears] , 1 , mean , na.rm=TRUE )  
    y = weeklyMeans[1:52]
    trigReg = lm( y ~ xs1 + xc1 + xs2 + xc2 )
    b0 = trigReg[[1]][[1]];      b1 = trigReg[[1]][[2]]
    b2 = trigReg[[1]][[3]];      b3 = trigReg[[1]][[4]]
    b4 = trigReg[[1]][[5]]
    yhat = b0 + b1*xs1 + b2*xc1 + b3*xs2 + b4*xc2
    yhat = pmax(0,yhat)
    #    cat("yhat = ")
    #    cat(yhat) 
  }
  LCL = rep(0,52)
  CL  = rep(0,52)
  UCL = rep(0,52)
  for ( week in 1:52 )
  {
    LCL[week] = max( 0, yhat[week]-L*sqrt(yhat[week]) )
    CL[week]  = yhat[week]
    UCL[week] = yhat[week]+L*sqrt(yhat[week])
  }
  return( cbind(LCL,CL,UCL) )
}

State Pertussis 2002-2011weekly.csv

ui.R

library( shiny )
library(rCharts)

shinyUI(
  pageWithSidebar(
    headerPanel("Disease Surveillance"),
    sidebarPanel(
      selectInput( "disease" , "Choose the disease:" ,
                   choices=c("Pertussis","Q Fever","Ehr","Ecoli O157") ) ,
      sliderInput( "L" , label="Factor for Control Limits",
                   min=2 , max=6 , value=3 , step=0.2 , animate=T) ,
      selectInput( "year" , "Choose the year:" ,
                   choices=c("2002","2003","2004","2005","2006",
                             "2007","2008","2009","2010","2011") ) ,
      selectInput( "region" , "Select the region:",
                   choices=c("State","Eastern")) ,
      selectInput("incubation", "Select surveillance period (weeks):", 
                  choices=c("1","2"), selected="1"),
      selectInput( "degree" , "How many terms in the trigonometric
                   regression?" , choices=c("2","4")) ,
      selectInput( "its" , 
                   "Do you want to recompute limits after excluding 
                   points above limits?" , 
                   choices=c("Yes","No"))
    ),
    mainPanel( chartOutput("myPlot", "highcharts") )
  )
)

Ramnath,

Thank you for the modifications. The codes are working perfectly on the localhost. However, when I upload it on my Shiny hosting account, the charts are not shown. Do I need to upload javascript files on the hosting account, as well as the rfiles, to solve this problem?

Thank you again!