R/geom_bands.R

In EpiModel: Mathematical Modeling of Infectious Disease Dynamics

#' @title ggplot2 Geom for Quantile Bands
#'
#' @description Plots quantile bands given a data.frame with stochastic model
#'              results from \code{\link{icm}} or \code{\link{netsim}}.
#'
#' @param mapping Standard aesthetic mapping \code{aes()} input for ggplot2.
#' @param lower Lower quantile for the time series.
#' @param upper Upper quantile for the time series.
#' @param alpha Transparency of the ribbon fill.
#' @param ... Additional arguments passed to \code{stat_summary}.
#'
#' @details
#' This is a wrapper around \code{ggplot::stat_summary} with a ribbon geom as
#' aesthetic output.
#'
#' @export
#' @keywords plot
#'
#' @examples
#' param <- param.icm(inf.prob = 0.2, act.rate = 0.25)
#' init <- init.icm(s.num = 500, i.num = 1)
#' control <- control.icm(type = "SI", nsteps = 250, nsims = 5)
#' mod1 <- icm(param, init, control)
#' df <- as.data.frame(mod1)
#' df.mean <- as.data.frame(mod1, out = "mean")
#'
#' library(ggplot2)
#' ggplot() +
#'    geom_line(data = df, mapping = aes(time, i.num, group = sim),
#'    alpha = 0.25, lwd = 0.25, color = "firebrick") +
#'    geom_bands(data = df, mapping = aes(time, i.num),
#'               lower = 0.1, upper = 0.9, fill = "firebrick") +
#'    geom_line(data = df.mean, mapping = aes(time, i.num)) +
#'    theme_minimal()
#'
geom_bands <- function(mapping, lower = 0.25, upper = 0.75, alpha = 0.25, ...) {
  stat_summary(mapping,
               geom = "ribbon",
               fun.min = function(x) quantile(x, lower),
               fun.max = function(x) quantile(x, upper),
               alpha = alpha, ...)
}