Add some adjustments for excess data in plotting nimue simulations.

Usage

# S3 method for excess_nimue_simulation
plot(
  x,
  var_select = NULL,
  replicates = FALSE,
  summarise = TRUE,
  ci = TRUE,
  q = c(0.025, 0.975),
  summary_f = stats::median,
  x_var = "t",
  date_0 = NULL,
  particle_fit = FALSE,
  ...
)

Arguments

x: An excess_nimue_simulation object
var_select: Vector of variable names to plot (default is all)
replicates: Plot replicates
summarise: Logical, add summary line
ci: logical add confidence interval ribbon
q: Quantiles for upper and lower of interval ribbon
summary_f: Function to summarise each compartment passed to the fun argument of stat_summary
x_var: X variable to use for plotting (default is "t", but can be set to, "date", if date_0 provided), which will cause the date to be plotted rather than time.
date_0: Date of time 0 (e.g. "2020-03-01"), if specified a date column will be added
particle_fit: If the squire_simulation provided is the result of running the particle filter, do we want to just plot the fit. Default = FALSE
...: additional arguments affecting the plot produced.