EpiModel (version 0.25)

plotDCM: Plot Values from a Compartmental Epidemic Model

Description

This function plots values from an deterministic compartment epidemic model.

Usage

plotDCM(out, compart, run, plt, comp.lwd, alpha, leg,
    leg.name, leg.cex, xlim, ylim, axs, add = FALSE, ...)

Arguments

out

list of data frames containing runs from an epidemic model

compart

compartments to plot

run

run number for multiple compartment plots

plt

palette to use from RColorBrewer palettes. The default is 'Spectral' for single compartment plots and 'Set1' for multiple compartment plots.

comp.lwd

line width for compartments

alpha

transparency level for colors, where 0 = transparent and 1 = opaque

leg

type of legend to plot. Values are 'n' for none, 'full' for full legend, and 'lim' for limited legend.

leg.name

character string to use for legend, calculated automatically if not supplied

leg.cex

legend size

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 main plot

See Also

epiDCM, display.brewer.all

Examples

out <- epiDCM(type='SIR', s.num=1000, i.num=1, r.num=0,
              beta=0.2, cont=1:10, nu=1/3,
              b=0.011, ms=0.01, mi=0.03, mr=0.01,
              dt=500, verbose=TRUE)

par(mar=c(3.5,3,1,1), mgp=c(2,1,0))
plotDCM(out, compart='s.prev', plt='Greys')
plotDCM(out, compart='i.num', leg='lim', alpha=0.5, xlim=c(0,200), axs='r')

plotDCM(out, compart=c('s.num','r.num'), run=5, leg='full')
plotDCM(out, compart=c('s.num','r.num'), run=2, alpha=0.3, add=TRUE)