Function for the animation of epidemic data, i.e. objects inheriting from
class "epidata". This only works with 1- or 2-dimensional coordinates
and is not useful if some individuals share the same coordinates
(overlapping). There are two types of animation, see argument
time.spacing. Besides the direct plotting in the R session, it is
also possible to generate a sequence of graphics files to create animations
outside R.
# S3 method for summary.epidata
animate(object, main = "An animation of the epidemic",
pch = 19, col = c(3, 2, gray(0.6)), time.spacing = NULL,
sleep = quote(5/.nTimes), legend.opts = list(), timer.opts = list(),
end = NULL, generate.snapshots = NULL, ...)# S3 method for epidata
animate(object, ...)
an object inheriting from class "epidata" or
"summary.epidata". In the former case, its summary is calculated
and the function continues as in the latter case, passing all ...
arguments to the summary.epidata method.
a main title for the plot, see also title.
vectors of length 3 specifying the point symbols and colors for
susceptible, infectious and removed individuals (in this order).
The vectors are recycled if necessary.
By default, susceptible individuals are marked as filled green circles,
infectious individuals as filled red circles and removed individuals as
filled gray circles. Note that the symbols are iteratively drawn
(overlaid) in the same plotting region as time proceeds.
For information about the possible values of pch and col, see
the help pages of points and par, respectively.
time interval for the animation steps. If NULL (the default), the
events are plotted one by one with pauses of sleep seconds. Thus,
it is just the ordering of the events, which is shown. To plot
the appearance of events proportionally to the exact time line,
time.spacing can be set to a numeric value indicating the period of
time between consecutive plots. Then, for each time point in
seq(0, end, by = time.spacing) the current state of the epidemic can
be seen and an additional timer indicates the current time
(see timer.opts below). The argument sleep will be the
artificial pause in seconds between two of those time points.
time in seconds to Sys.sleep before the next plotting
event. By default, each artificial pause is of length 5/.nTimes
seconds, where .nTimes is the number of events (infections and
removals) of the epidemic, which is evaluated in the function body.
Thus, for time.spacing = NULL the animation has a duration of
approximately 5 seconds. In the other case, sleep is the duration of
the artificial pause between two time points.
Note that sleep is ignored on non-interactive devices
(see dev.interactive)
either a list of arguments passed to the legend function or
NULL (or NA), in which case no legend will be plotted. All
necessary arguments have sensible defaults and need not be specified, i.e.
x:"topright"
legend:c("susceptible", "infectious", "removed")
pch:same as argument pch of the main function
col:same as argument col of the main function
either a list of arguments passed to the legend function or
NULL (or NA), in which case no timer will be plotted. All
necessary arguments have sensible defaults and need not be specified, i.e.
x:"bottomright"
title:"time"
box.lty:0
adj:c(0.5,0.5)
inset:0.01
bg:"white"
Note that the argument legend, which is the current time of the
animation, can not be modified.
ending time of the animation in case of time.spacing not being
NULL. By default (NULL), time stops after the last event.
By default (NULL), the animation is not saved to image files
but only shown on the on-screen device. In order to print to files,
time.spacing must not be NULL, a screen device must be
available, and there are two options:
If the framework of the animation package
should be used, i.e. the animate-call is passed as the
expr argument to one of the save* functions of the
animation package, then set
generate.snapshots = img.name, where img.name is the
base name for the generated images (the same as passed to the
save* function). The path and format (type, width, height)
for the generated images is derived from
ani.options. See the last example below.
Alternatively, generate.snapshots may be a list of arguments
passed to the function dev.print, which then is
executed at each time point of the grid defined by
time.spacing. Essentially, this is used for
saving the produced snapshots to files, e.g.
generate.snapshots =
list(device=pdf, file=quote(paste("epidemic_",sprintf(form,tp),".pdf",
sep="")))
will store the animation steps in pdf-files in the current
working directory, where the file names each end with the time point
represented by the corresponding plot. Because the variables tp
and form should only be evaluated inside the function the
file argument is quoted. Alternatively, the file name
could also make use of the internal plot index i, e.g., use
file=quote(paste("epidemic",i,".pdf",sep="")).
further graphical parameters passed to the basic call of plot, e.g.
las, cex.axis (etc.) and mgp.
Sebastian Meyer
summary.epidata for the data, on which the plot is based.
plot.epidata for plotting the evolution of an epidemic by
the numbers of susceptible, infectious and removed individuals.
The contributed R package animation.
data("hagelloch")
(s <- summary(hagelloch))
# plot the ordering of the events only
animate(s) # or: animate(hagelloch)
# with timer (animate only up to t=10)
animate(s, time.spacing=0.1, end=10, sleep=0.01,
legend.opts=list(x="topleft"))
# Such an animation can be saved in various ways using tools of
# the animation package, e.g., saveHTML()
if (interactive() && require("animation")) {
oldwd <- setwd(tempdir()) # to not clutter up the current working dir
saveHTML({
par(bg="white") # default "transparent" is grey in some browsers
animate(s, time.spacing=1, sleep=0, legend.opts=list(x="topleft"),
generate.snapshots="epiani")
}, use.dev=FALSE, img.name="epiani", ani.width=600, interval=0.5)
setwd(oldwd)
}
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