plot.epi.data.frame: Plot Epidemic Model Results From a Netsim Data.Frame
In EpiModel: Mathematical Modeling of Infectious Disease Dynamics

plot.epi.data.frame

R Documentation

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 class '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.