geom_bands: ggplot2 Geom for Quantile Bands

In EpiModel: Mathematical Modeling of Infectious Disease Dynamics

ggplot2 Geom for Quantile Bands

Description

Plots quantile bands given a data.frame with stochastic model results from icm or netsim.

Usage

geom_bands(mapping, lower = 0.25, upper = 0.75, alpha = 0.25, ...)

Arguments

mapping	Standard aesthetic mapping aes() input for ggplot2.
lower	Lower quantile for the time series.
upper	Upper quantile for the time series.
alpha	Transparency of the ribbon fill.
...	Additional arguments passed to stat_summary.

Details

This is a wrapper around ggplot::stat_summary with a ribbon geom as aesthetic output.

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()

EpiModel documentation built on Oct. 12, 2024, 1:06 a.m.