EpiModel (version 0.25)

plotABM: Plot Simulations from a Stochastic Epidemic Model

Description

This function plots values of compartments in an agent-based stochastic epidemic model.

Usage

plotABM(out, compart, simlines = TRUE, simcol, simalpha,
    medline = TRUE, medcol, medlwd, qnts = NULL, qntscol,
    xlim, ylim, axs, add = FALSE, ...)

Arguments

out

list of data frames containing runs from an epidemic model

compart

compartments to plot

simlines

logical operator to plot individual simulation lines

simcol

color for simulation lines (default is black)

simalpha

transparency level for sim lines, calculated automatically if not set

medline

logical operator to plot median of individual simulations at each timestep

medcol

color for median line

medlwd

line width for median line

qnts

plots polygon of simulation quantiles, with argument taking the quantile range. For 95% interval, set to 0.95.

qntscol

color for polygon

xlim

x-axis limits for plot, set to max of time if not set

ylim

y-axis limits for plot, calculated automatically if not set

axs

axis type (see par for details), default at 'i'

add

if TRUE then adds lines to existing plot

...

additional arguments to pass to plot

See Also

epiABM

Examples

out <- epiABM(type='SI', s.num=500, i.num=1, beta=0.2, cont=0.2, nsteps=500, nsims=20)

par(mar=c(3,3,1,1), mgp=c(2,1,0))
plotABM(out, 'i.num', simlines=TRUE, medline=TRUE, qnts=0.5)

# Plotting multiple compartment values
plotABM(out, 'i.num', simlines=FALSE, medline=TRUE, medcol=1, qnts=0.5, axs='r')
plotABM(out, 's.num', simlines=FALSE, medline=TRUE, medcol=2, qnts=0.5, qntscol=2, add=TRUE)