sts_animate: Animated Maps and Time Series of Disease Incidence
In jimhester/surveillance: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena

Description Usage Arguments Value Author(s) References See Also Examples

The animate-method for sts objects supersedes the stsplot type observed~1|unit*time implemented by the function stsplot_spacetime. Maps generated by 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.

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

`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 `map` object has to be provided explicitly (as part of `...`).
`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.
`population,at,...`	arguments for `stsplot_space`.
`timeplot`	if a list (of arguments for the internal function `stsplot_timeSimple`) and package gridExtra is available, a time series chart of the counts along the selected time points `tps` will be plotted below the map. The argument `height` gives the relative height of the time series plot (default: 0.3), and the arguments `inactive` and `active` are lists of graphical parameters (e.g., `col`) determining the appearance of the bars (e.g., default color is grey when inactive and black when active).
`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 `interactive` sessions.
`draw`	logical indicating if the produced plots at each time point should be drawn directly (the default) or not. The setting `draw = FALSE` is useful if one would like to manually arrange the plots, which are always returned invisibly in a list of length `length(tps)`.

(invisibly) a list of the length(tps) sequential plot objects of class "\code{gtable}" (if the the timeplot is active) or of class "\code{trellis" (otherwise).

Sebastian Meyer

Meyer, S. and Held, L. (2014): Power-law models for infectious disease spread. The Annals of Applied Statistics, 8 (3), 1612-1639.
DOI-Link: http://dx.doi.org/10.1214/14-AOAS743
Supplement A is available from http://www.biostat.uzh.ch/static/powerlaw/.

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

data("measlesWeserEms")

## sequential plot of the counts by region in weeks 12-16 only (for speed)
if (require("animation")) {
    oldwd <- setwd(tempdir())  # to not clutter up the current working dir
    saveHTML(animate(measlesWeserEms, tps=12:16, cumulative=FALSE),
             title="Evolution of the measles epidemic in the Weser-Ems region",
             ani.width=500, ani.height=600)
    setwd(oldwd)
}