ssa.plot {GillespieSSA}R Documentation

Simple plotting of ssa output

Description

Provides basic functionally for simple and quick time series plot of simulation output from ssa.

Usage

ssa.plot(        out = stop("requires simulation output object"),
                file = "ssaplot",
                  by = 1,
           plot.from = 2,
             plot.to = dim(out$data)[2],
             plot.by = 1,
          show.title = TRUE,
         show.legend = TRUE)

Arguments

out data object returned from ssa.
file name of the output file (only applicable if plot.device!="x11".
by time increment in the plotted time series
plot.from first population to plot the time series for (see note)
plot.to last population to plot the time series for (see note)
plot.by increment in the sequence of populations to plot the time series for (see note)
show.title boolean object indicating if the plot should display a title
show.legend boolean object indicationg if the legend is displayed

Note

The options by, plot.from, plot.to, and plot.by can be used to plot a sparser sequense of data points. To plot the population sizes using a larger time interval the by option can be set, e.g. to plot only every 10th time point by=10. To plot only specific populations the plot.from, plot.to, and plot.by options can be set to subset the state vector. Note that the indexing of the populations is based on the (t,X) vector, i.e. the first column is the time vector while the first population is index by 2 and the last population by N+1. Display of a plot title above the plot and legend is optional (and are set with the arguments {{{show.title}}} and {{{show.legend}}}. Above the plot panel miscellaneous information for the simulation are displayed, i.e. method, elapsed wall time, number of time steps executed, and the number of time steps per data point.

See Also

GillespieSSA-package, ssa

Examples

## Not run: 
## Define the Kermack-McKendrick SIR model abd run once unsing the Direct method
parms <- c(beta=.001, gamma=.100)
x0 <- c(S=500, I=1, R=0)                      # Initial state vector
nu <- matrix(c(-1,0,1,-1,0,1),nrow=3,byrow=T) # State-change matrix
a  <- c("beta*S*I", "gamma*I")                # Propensity vector
tf <- 100                                     # Final time
simName <- "Kermack-McKendrick SIR"
out <- ssa(x0,a,nu,parms,tf,method="D",simName,verbose=TRUE,consoleInterval=1)
## End(Not run)

## Not run: 
## Basic ssa plot
ssa.plot(out) 
## End(Not run)

## Not run: 
# Plot only the infectious class
ssa.plot(out,plot.from=3,plot.to=3)
## End(Not run)

## Not run: 
## Multipanel plot using different SSA methods
layout(matrix(seq(4),ncol=4,byrow=TRUE))

## Using the Direct method
ssa.plot(out)

## Run and plot results using the ETL method
out <- ssa(x0,a,nu,parms,tf=100,method="ETL,simName="Kermack-McKendrick SIR")
ssa.plot(out,show.title=FALSE,show.legend=FALSE)

## Run and plot results using the BTL method
out <- ssa(x0,a,nu,parms,tf=100,method="BTL,simName="Kermack-McKendrick SIR")
ssa.plot(out,show.title=FALSE,show.legend=FALSE)

## Run and plot results using the OTL method
out <- ssa(x0,a,nu,parms,tf=100,method="OTL,simName="Kermack-McKendrick SIR")
ssa.plot(out,show.title=FALSE,show.legend=FALSE)
## End(Not run)

[Package GillespieSSA version 0.5-3 Index]