inst/extdata/deprecated/plot_attack_rates.R

In kylieainslie/MoreVac: Modelling Repeat Vaccination

### MoReVac - Modelling Repeat Vaccination ###
### Agent-based model of repeat vaccination in birth cohort

#' Plot multi-annual attack rates
#'
#' This function initializes the population before running the model.
#' @param dat data frame of annual attack rates. Should have two colums: Year and Attack_Rate.
#'             If by_vac=TRUE, dat should have a third column: Vac_Strategy.
#' @param by_vac logical. if TRUE then plot by vaccination strategy.
#' @param c_bands logical. Plot confidence bands or not. Must have columns named Lower and Upper.
#' @param y_max maximum value for y-axis.
#' @param no_legend logical. if TRUE legend will be suppressed.
#' @param legend_x x position of legend.
#' @param legend_y y position of legend.
#' @return plot of multi-annual attack rates with vertical dashed line indicating year of start of
#'         vaccination and a horizontal dashed line indicating mean attack rate prior to start of vaccination.
#' @keywords morevac
#' @export

plot_attack_rates <- function(dat, by_vac_strategy = FALSE, by_age_group = FALSE, c_bands = FALSE, y_max = 0.5,
                              no_legend = FALSE, legend_x = 0.95, legend_y = 0.95){
  years <- unique(dat$Year)

  if (by_vac_strategy) {
    p1 <- ggplot(data = dat, aes(x = Year, y = Attack_Rate, colour= Vac_Strategy)) +
          geom_line()
    if(c_bands){p1 <- p1 + geom_ribbon(aes(x=Year,ymin=Lower,ymax=Upper,linetype=NA, fill = Vac_Strategy),alpha=0.2)}
  } else if (by_age_group) {
    p1 <- ggplot(data = dat, aes(x = Year, y = Attack_Rate, colour= Age_Group)) +
      geom_line()
    if(c_bands){p1 <- p1 + geom_ribbon(aes(x=Year,ymin=Lower,ymax=Upper,linetype=NA, fill = Age_Group),alpha=0.2)}
  } else {
    p1 <- ggplot(data = dat, aes(x = Year, y = Attack_Rate)) +
          geom_line()
    if(c_bands){p1 <- p1 + geom_ribbon(aes(x=Year,ymin=Lower,ymax=Upper,linetype=NA),alpha=0.2)}
  }

  p1 <- p1 + xlab('Year') +
        ylab('Attack Rate') +
        scale_y_continuous(limits = c(0,y_max), expand = c(0,0))

    if (no_legend){
      p1 <- p1 + theme(panel.grid.major = element_blank(),
                     panel.grid.minor = element_blank(),
                     panel.background = element_blank(),
                     axis.line = element_line(colour = "black"),
                     legend.position = "none")
    } else {
      p1 <- p1 + theme(panel.grid.major = element_blank(),
                     panel.grid.minor = element_blank(),
                     panel.background = element_blank(),
                     axis.line = element_line(colour = "black"),
                     legend.position = c(legend_x, legend_y),
                     legend.justification = c("right", "top"),
                     legend.box.just = "right",
                     legend.margin = margin(6, 6, 6, 6),
                     legend.key = element_rect(fill = "white"))
    }

  return(p1)
}