plot.epi.data.frame: Plot Epidemic Model Results From a Netsim Data.Frame

Description

This function is a wrapper around plot.netsim accepting a data.frame obtain with as.data.frame(netsim_object).

Usage

# S3 method for epi.data.frame
plot(
  x,
  y = NULL,
  sims = NULL,
  legend = NULL,
  mean.col = NULL,
  qnts.col = NULL,
  sim.lwd = NULL,
  sim.col = NULL,
  sim.alpha = NULL,
  popfrac = FALSE,
  qnts = 0.5,
  qnts.alpha = 0.5,
  qnts.smooth = TRUE,
  mean.line = TRUE,
  mean.smooth = TRUE,
  add = FALSE,
  mean.lwd = 2,
  mean.lty = 1,
  xlim = NULL,
  ylim = NULL,
  main = NULL,
  xlab = NULL,
  ylab = NULL,
  sim.lines = FALSE,
  grid = FALSE,
  leg.cex = 0.8,
  ...
)

Arguments

x

A data.frame obtain with as.data.frame(netsim_object).

y

Output compartments or flows from netsim object to plot.

sims

If type="epi" or "formation", a vector of simulation numbers to plot. If type="network", a single simulation number for which to plot the network, or else "min" to plot the simulation number with the lowest disease prevalence, "max" for the simulation with the highest disease prevalence, or "mean" for the simulation with the prevalence closest to the mean across simulations at the specified time step.

legend

If TRUE, plot default legend.

mean.col

Vector of any standard R color format for mean lines.

qnts.col

Vector of any standard R color format for polygons.

sim.lwd

Line width for simulation lines.

sim.col

Vector of any standard R color format for simulation lines.

sim.alpha

Transparency level for simulation lines, where 0 = transparent and 1 = opaque (see adjustcolor function).

popfrac

If TRUE, plot prevalence of values rather than numbers (see details).

qnts

If numeric, plot polygon of simulation quantiles based on the range implied by the argument (see details). If FALSE, suppress polygon from plot.

qnts.alpha

Transparency level for quantile polygons, where 0 = transparent and 1 = opaque (see adjustcolor function).

qnts.smooth

If TRUE, use a loess smoother on quantile polygons.

mean.line

If TRUE, plot mean of simulations across time.

mean.smooth

If TRUE, use a loess smoother on the mean line.

add

If TRUE, new plot window is not called and lines are added to existing plot window.

mean.lwd

Line width for mean lines.

mean.lty

Line type for mean lines.

xlim

the x limits (x1, x2) of the plot. Note that x1 > x2 is allowed and leads to a ‘reversed axis’.

The default value, NULL, indicates that the range of the finite values to be plotted should be used.

ylim

the y limits of the plot.

main

a main title for the plot, see also title.

xlab

a label for the x axis, defaults to a description of x.

ylab

a label for the y axis, defaults to a description of y.

sim.lines

If TRUE, plot individual simulation lines. Default is to plot lines for one-group models but not for two-group models.

grid

If TRUE, a grid is added to the background of plot (see grid for details), with default of nx by ny.

leg.cex

Legend scale size.

...

Additional arguments to pass.