R/plot_weekahead.R

In jarad/FluSight: Utility functions for the CDC FluSight competition

#' Plots Week Ahead Forecasts
#'
#' This function allows you to plot Weak Ahead Predictions
#' @param dat Expects a data csv in the form of a CDC fluview submission see \code{FluSight} package for a minimal submission
#' @param region Specifies the region to be plotted
#' @param wk Numeric. How many weeks ahead to plot. Defaults to 1.
#' @param ilimax Numeric. Max level of ILI percentage to be plotted
#' @param plot_current Logical. Whether or not to plot current ILI level.
#' @keywords Week Ahead Prediction Plots
#' @export
#' @examples
#' plotWeekAhead()

plot_weekahead <- function(dat, region, wk=1, ilimax, years=NA, plot_current=TRUE){
  require(ggplot2)
  require(cdcfluview)
  
  d <- suppressWarnings(subset(dat, location==region & as.numeric(as.character(bin_start_incl)) <= ilimax))
  d <- d[grep("wk ahead", d$target),]
  
  if(plot_current){
      NatFluDat <- get_flu_data("national", NA, "ilinet", years=years)
      RegFluDat <- get_flu_data("hhs", 1:10, "ilinet", years=years)
      NatFluDat$REGION[NatFluDat$REGION=="X"] <- "National"
      CFluDat <- rbind(tail(RegFluDat, n=10), tail(NatFluDat, n=1))[,c("REGION","% WEIGHTED ILI")]
      if(region=="US National"){
          CurrentILIPer <- CFluDat[CFluDat$REGION=="National", "% WEIGHTED ILI"]
      }else{
          CurrentILIPer <- CFluDat[CFluDat$REGION==paste("Region", strsplit(region, " ")[[1]][3]), "% WEIGHTED ILI"]
      }
  }
  
  if(wk==1){
    p <- ggplot(data=subset(d, target=="1 wk ahead"), aes(x=as.numeric(as.character(bin_start_incl)), y=value)) + 
            geom_point() + labs(title = "1 Week Ahead", x="ILI%", y="Prob") 
  }
  
  
  if(wk==2){
    p <- ggplot(data=subset(d, target=="2 wk ahead"), aes(x=as.numeric(as.character(bin_start_incl)), y=value)) + 
             geom_point() + labs(title = "2 Week Ahead", x="ILI%", y="Prob")
  }
  
  if(wk==3){
    p <- ggplot(data=subset(d, target=="3 wk ahead"), aes(x=as.numeric(as.character(bin_start_incl)), y=value)) + 
             geom_point() + labs(title = "3 Week Ahead", x="ILI%", y="Prob") 
  }
  
  if(wk==4){
    p <- ggplot(data=subset(d, target=="4 wk ahead"), aes(x=as.numeric(as.character(bin_start_incl)), y=value)) + 
             geom_point() + labs(title = "4 Week Ahead", x="ILI%", y="Prob")
  }
  
  if(plot_current)
      p <- p + geom_vline(aes(xintercept = as.numeric(as.character(CurrentILIPer))))
  
  return(p)
}