plot_sirplus.Rd
Flexible function to generate sirplus plots (i.e. compartment counts over time). This function allows for plotting multiple experiments, viewing the plots of different scales (e.g. log2), plotting compartments separately, adding 95% CIs, and plotting known data along side the simulations.
plot_sirplus( x, comp_remove, time_limit, ci, sep_compartments, trans, known, start_date, x_axis, plot_title, ... )
x | A seiqhrf object (or list of multiple seiqhrf objects) returned
from |
---|---|
comp_remove | Compartments to remove. Suggest c(s.num, r.num) |
time_limit | Number of steps (days) to plot. |
ci | T/F to include 95% confidence intervals in sirplus plot. |
sep_compartments | T/F use faceting to show each compartment in a separate plot, only works if plotting a single simulation. |
trans | Y-axis transformation (e.g. log2, log10). Default = none. |
known | Dataframe with known compartment numbers to plot alongside projections |
start_date | Date for day 0. Default: ymd("2020-03-21"), |
x_axis | Title for x-axis. Default: 'Days since beginning of epidemic' |
plot_title | Title for whole plot. Default: 'SEIQHRF plot' |
... | Additional parameters |
ggplot2 object