epidata_plot | R Documentation |
Functions for plotting the evolution of epidemics. The plot
methods for class
es "epidata"
and
"summary.epidata"
plots the numbers of susceptible, infectious and
recovered (= removed) individuals by step functions along the time axis. The
function stateplot
shows individual state changes along the time axis.
## S3 method for class '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 class 'epidata'
plot(x, ...)
stateplot(x, id, ...)
x |
an object inheriting from class |
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
|
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).
|
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 |
legend.opts |
if this is a list (of arguments for the
|
do.axis4 |
logical indicating if the final numbers of susceptible and removed
individuals should be indicated on the right axis. The default |
panel.first |
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. |
rug.opts |
either a list of arguments passed to the function |
which.rug |
By default, tick marks are drawn at the time points of infections.
Alternatively, one can choose to mark only |
id |
single character string or factor of length 1 specifying the individual for
which the |
... |
For |
plot.summary.epidata
(and plot.epidata
) invisibly returns the
matrix used for plotting, which contains the evolution of the three
counters.
stateplot
invisibly returns the function, which was plotted,
typically of class "stepfun"
, but maybe of class "function"
,
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.
Sebastian Meyer
summary.epidata
for the data, on which the plots are based.
animate.epidata
for the animation of epidemics.
data("hagelloch")
(s <- summary(hagelloch))
# rudimentary stateplot
stateplot(s, id = "187")
# evolution of the epidemic
plot(s)
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