R/casesfig.R

In cyhsuTN/COVID19: Prediction of Cases Volumne and Hospitalization by SIR Model

#' A figure for cases volumne.
#' @description To show a figure for cases volumne.
#' @import stats ggplot2
#' @importFrom reshape2 melt


#' @param showdays Input. Number of days to project.
#' @param casevolumne Input. Object from function \emph{fitSIR}.


#' @examples ## To predicte 100 days from today (dayFT=100).
#' @examples casevolumne <- fitSIR(susceptible=4119405, Infected=3733, inihos=14,
#' @examples      hosrate=2.5, hms=15, inidbt=4, mrt=14, sdis=30, dayFT=100)
#' @examples casesfig(showdays=60, casevolumne) ## show the first 60 days
#'

#' @export



casesfig <- function(showdays=60, casevolumne) {
  if (showdays > nrow(casevolumne$result) - 1) {
    showdays <- nrow(casevolumne$result) - 1
  }
  dd <- reshape2::melt(casevolumne$result[1:(showdays+1),c(1,3:4)], id=c("days.from.today"))
  levels(dd$variable) <- c("Infected", "Recovered")
  pp <- ggplot() + geom_line(data=dd, aes(x=days.from.today, y=value, colour=variable), size=1) +
    geom_point(data=dd, aes(x=days.from.today, y=value, colour=variable), size=2) +
    xlab("Date") +
    ylab("Number of people") +
    theme(axis.text=element_text(size=16), ## change size of text
          axis.title=element_text(size=18, face="bold")) + # change size of label name
    theme(legend.text=element_text(size=16)) + # change text size in legend
    theme(legend.title=element_text(size=16)) + # change title size of legend
    guides(col=guide_legend("Status")) +
    scale_colour_manual(values=c("blue","orange"))

  currentCDTDate <- function() as.Date(format(Sys.time(), tz="America/Chicago"))

  break1 <- round(seq(0,showdays,length.out=7))
  labels1 <- format(break1 + currentCDTDate(), "%b/%d")
  pp + scale_x_continuous(breaks=break1, labels=labels1) +
    theme(axis.text.x = element_text(size=14, angle=30, vjust = 0.8))

}