Plotting the Evolution of an Epidemic
Functions for plotting the evolution of epidemics. The
"summary.epidata" plots the numbers of susceptible, infectious and
recovered (= removed) individuals by step functions along the time axis. The
stateplot shows individual state changes along the time axis.
# S3 method for summary.epidata plot(x, lty = c(2, 1, 3), lwd = 2, col = c("#1B9E77", "#D95F02", "#7570B3"), col.hor = col, col.vert = col, xlab = "Time", ylab = "Number of individuals", xlim = NULL, ylim = NULL, legend.opts = list(), do.axis4 = NULL, panel.first = grid(), rug.opts = list(), which.rug = c("infections", "removals", "susceptibility", "all"), ...) # S3 method for epidata plot(x, ...) stateplot(x, id, ...)
an object inheriting from class
"summary.epidata". In the former case, its summary is calculated and the function continues as in the latter case. The
plotmethod for class
"epidata"is a simple wrapper for
- lty, lwd
vectors of length 3 containing the line types and widths, respectively, for the numbers of susceptible, infectious and removed individuals (in this order). By default, all lines have width 1 and the line types are dashed (susceptible), solid (infectious) and dotted (removed), respectively. To omit the drawing of a specific line, just set the corresponding entry in
ltyto 0. The vectors are recycled if necessary. For information about the different
lwdcodes, see the help pages of
- col, col.hor, col.vert
vectors of length 3 containing the line colors for the numbers of susceptible, infectious and removed individuals (in this order).
col.hordefines the color for the horizontal parts of the step function, whilst
col.vertdefines the color for its vertical parts. The argument
colis just short for
col.hor = coland
col.vert = col. The default
colvector corresponds to
brewer.pal("Dark2",n=3)from the RColorBrewer package. The vectors are recycled if necessary. For information about the possible values of
col, see the help pages of
- xlab, ylab
axis labels, default to "Time" and "Number of individuals", respectively.
- xlim, ylim
the x and y limits of the plot in the form
c(ymin, ymax), respectively. By default, these are chosen adequately to fit the time range of the epidemic and the number of individuals.
if this is a list (of arguments for the
legendfunction), a legend will be plotted. The defaults are as follows:
c("susceptible", "infectious", "removed")
same as the arguments
col.horof the main function
logical indicating if the final numbers of susceptible and removed individuals should be indicated on the right axis. The default
xrepresents a SIR epidemic and
FALSEotherwise, i.e. if the epidemic is SI, SIS or SIRS.
an expression to be evaluated after the plot axes are set up but before any plotting takes place. By default, a standard grid is drawn.
either a list of arguments passed to the function
NA), in which case no
rugwill be plotted. By default, the argument
ticksizeis set to 0.02,
colis set to the color according to
which.rug(black if this is
quietis set to
TRUE. Note that the argument
x, which contains the locations for the
rugis fixed internally and can not be modified. The argument
which.rug(see below) determines the locations to mark.
By default, tick marks are drawn at the time points of infections. Alternatively, one can choose to mark only
"susceptibilities"(i.e. state change from R to S) or
single character string or factor of length 1 specifying the individual for which the
stateplotshould be established.
plot.summary.epidata: further graphical parameters passed to
plot.epidata: arguments passed to
stateplot: arguments passed to
idhad no events during the observation period). By default,
plot.epidata) invisibly returns the
matrix used for plotting, which contains the evolution of the three
stateplot invisibly returns the function, which was plotted,
typically of class
"stepfun", but maybe of class
if no events have been observed for the individual in question (then the
function always returns the initial state). The vertical axis of
stateplot can range from 1 to 3, where 1 corresponds to
Susceptible, 2 to Infectious and 3 to Removed.