EpiModel (version 0.95)

plot.epiDCM: Plot Values from a Deterministic Compartmental Epidemic Model

Description

This function plots values from an deterministic compartment epidemic model solved with epiDCM.

Usage

## S3 method for class 'epiDCM':
plot(x, y, popfrac, run, col, lwd, lty, alpha, leg, leg.name,
  leg.cex, xlim, ylim, main, axs, add = FALSE, ...)

Arguments

x

an EpiModel object of class epiDCM.

y

output compartments or flows from epiDCM object to plot.

popfrac

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

run

run number to plot for models with multiple runs; with a default of run 1.

col

color for lines, either specified as a single color in a standard R color format, or alternatively, a color palette from RColorBrewer (see details).

lwd

line width for output values.

lty

line type for output values.

alpha

transparency level for lines, where 0 = transparent and 1 = opaque (see transco).

leg

type of legend to plot. Values are "n" for no legend, "full" for full legend, and "lim" for limited legend (see details).

leg.name

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

leg.cex

legend scale size, with default of 0.8.

xlim

x-axis scale limits for plot, with default calculated based on model time steps.

ylim

y-axis scale limits for plot, with default calculated based on range of data.

main

character string for main plot title.

axs

plot axis type (see par for details), with default to "r".

add

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

...

additional arguments to pass to main plot (see plot.default).

Details

The goal of this plotting function is to facilitate plotting values from a deterministic compartmental model solved with epiDCM. Depending on the number of model runs (sensitivity analyses) and number of groups, the default plot without any options set will generally plot the disease prevalence from the model. The specific compartments or flows to plot may be set using the y parameter, and in multiple run models the specific run may also be set.

Compartment prevalences are the size of a compartment over some denominator. To plot the raw numbers from any compartment, use popfrac=FALSE; this is the default for any plots of flows. The popfrac parameter calculates and plots the denominators of all specified compartments using these rules: 1) for one-group models, the prevalence of any compartment is the compartment size divided by the total population size; 2) for two-group models, the prevalence of any compartment is the compartment size divided by the group population size.

Since epiDCM supports multiple run sensitivity models, plotting the results of such models must use a complex visual scheme for easy representation of results. This is accomplished mainly using the RColorBrewer color palettes, in which one may specify a range of linked colors using named palettes. For plot.epiDCM, one may either specify a Brewer color palette listed in display.brewer.all, or alternatively a single or vector of standard R colors (named, hexidecimal, or positive integers; see col2rgb).

There are three automatic legend types available, and the legend is automatically added by default for most plots. To shut off the legend, use leg="n". To plot a legend with values for every line, use leg="full". With sensitivity models with many runs, this is generally not visually appealing Therefore, in those cases, use leg="lim" to plot a legend limited to the highest and lowest of the varying parameters in the model. In cases where the default legend names are not helpful, one may override those names with the leg.names argument.

See Also

epiDCM, display.brewer.all, transco

Examples

# Deterministic SIR model with varying act rate
mod <- epiDCM(type="SIR", s.num=1000, i.num=1, r.num=0,
              trans.rate=0.2, act.rate=1:10, rec.rate=1/3,
              b.rate=0.011, ds.rate=0.01, di.rate=0.03,
              dr.rate=0.01, nsteps=500, verbose=TRUE)

# Plot disease prevalence by default
plot(mod)

# Plot prevalence of susceptibles
plot(mod, y="s.num", col="Greys")

# Plot number of susceptibles
plot(mod, y="s.num", popfrac=FALSE, col="Greys")

# One way to plot multiple runs of multiple compartments together
plot(mod, y=c("s.num", "i.num"), run=5, xlim=c(0,200))
plot(mod, y=c("s.num", "i.num"), run=10, alpha=0.3, leg="n", add=TRUE)