plot.excess_nimue_simulation: Add some adjustments for excess data in plotting nimue...

In mrc-ide/squire.page: Functions used in global-lmic-reports-orderly and other repos

Add some adjustments for excess data in plotting nimue simulations.

Description

Add some adjustments for excess data in plotting nimue simulations.

Usage

## S3 method for class '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.

mrc-ide/squire.page documentation built on May 27, 2023, 11:20 a.m.