surveillance (version 1.8-0)

sts_animate: Animated Maps and Time Series of Disease Incidence

Description

The new animate-method for sts objects supersedes the stsplot type observed~1|unit*time implemented by the function stsplot_spacetime. Maps generated by the new function stsplot_space are sequentially plotted along time (optionally showing cumulative counts), with an optional time series chart below the map to track the epidemic curve. It is worth using functionality of the animation package (e.g., saveHTML) to directly export the animation into a useful format. See Meyer and Held (2014, Supplement A) for an example with the fluBYBW data.

Usage

## S3 method for class 'sts':
animate(object, tps = NULL, cumulative = FALSE, at = 10, ...,
        timeplot = list(height = 0.3), sleep = 0.5, verbose = interactive())

Arguments

object

an object of class "sts" or a matrix of counts, i.e., observed(stsObj), where especially colnames(x) have to be contained in row.names(map). If a matrix, the

tps

a numeric vector of one or more time points at which to plot the map. The default tps=NULL means the whole time period 1:nrow(object).

cumulative

logical specifying if the cumulative counts over time should be plotted.

at,...

arguments for stsplot_space.

timeplot

if a list (of arguments for the internal function stsplot_timeSimple), a time series chart of the counts along the selected time points tps will be plotted below the map. The argument height gives the rel

sleep

time to wait (Sys.sleep) between subsequent snapshots (only if dev.interactive), in seconds.

verbose

logical indicating if a txtProgressBar should be shown during generation of the animation -- which may take a while. Default is to do so in interacti

Value

• NULL (invisibly)

References

Meyer, S. and Held, L. (2014): Power-law models for infectious disease spread. Annals of Applied Statistics. In press. http://arxiv.org/abs/1308.5115{arXiv:1308.5115}. Supplement A is available from http://www.biostat.uzh.ch/static/powerlaw/.

See Also

the other plot types documented in stsplot for static time series plots and maps.

Examples

data("measlesWeserEms")

## sequential plot of the counts by region in weeks 12-16 only (for speed)
if (require("animation")) {
    saveHTML(animate(measlesWeserEms, tps=12:16, cumulative=FALSE),
             outdir = tempdir(), htmlfile = "measles.html",
             title = "Evolution of the measles epidemic in the Weser-Ems region",
             ani.width=500, ani.height=600)
}