surveillance: sts_animate – R documentation

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sts_animate

Animated Maps and Time Series of Disease Counts or Incidence

Description

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/incidence), 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,
        population = NULL, at = 10, ...,
        timeplot = list(pos = 1, size = 0.3, fill = TRUE),
        sleep = 0.5, verbose = interactive(), draw = TRUE)

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 `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/incidence over time should be plotted. The cumulative incidence is relative to the population from the first time point `tps[1]` throughout the whole animation, while `cumulative=FALSE` computes the incidence from the current population numbers.
`population,at,...`	arguments for `stsplot_space`.
`timeplot`	if a list and package gridExtra is available, a time series chart of the counts along the selected time points `tps` will be plotted next to the map. The list elements determine both the positioning of this plot (`pos`, `size`, and `fill`) and its appearance. The default `pos=1` and `size=0.3` arguments put the time series plot below the map, using 30% of the total plot height. The logical value `fill` indicates whether to make the panel as big as possible (default: TRUE). An alternative to `fill=FALSE` is to manually specify an `aspect` (ratio) value in `timeplot`. Other list elements are arguments for the internal (and currently undocumented) function `stsplot_timeSimple`. For example, `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), and the boolean `as.Date` determines whether dates should be put on the x-axis (instead of the `tps` indexes).
`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)`.

Value

(invisibly) a list of the length(tps) sequential plot objects. These are of class "gtable" (from gtable) if the timeplot is included, otherwise of class "\code{trellis".

Author(s)

Sebastian Meyer

References

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

Examples

data("measlesWeserEms")

## animate the weekly counts of measles (during 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),
             title="Evolution of the measles epidemic in the Weser-Ems region",
             ani.width=500, ani.height=600)
    setwd(oldwd)
}

## Not run: 
## animate the weekly incidence of measles (per 100'000 inhabitants),
## and label the time series plot with dates in a specified format
animate(measlesWeserEms, tps=12:16,
        population = measlesWeserEms@map$POPULATION / 100000,
        timeplot = list(as.Date = TRUE,
                        scales = list(x = list(format = "%G/%V"))))

## End(Not run)

surveillance

Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena

v1.19.1

GPL-2

Authors

Michael H<f6>hle [aut, ths] (<https://orcid.org/0000-0002-0423-6702>), Sebastian Meyer [aut, cre] (<https://orcid.org/0000-0002-1791-9449>), Michaela Paul [aut], Leonhard Held [ctb, ths], Howard Burkom [ctb], Thais Correa [ctb], Mathias Hofmann [ctb], Christian Lang [ctb], Juliane Manitz [ctb], Andrea Riebler [ctb], Daniel Saban<e9>s Bov<e9> [ctb], Ma<eb>lle Salmon [ctb], Dirk Schumacher [ctb], Stefan Steiner [ctb], Mikko Virtanen [ctb], Wei Wei [ctb], Valentin Wimmer [ctb], R Core Team [ctb] (A few code segments are modified versions of code from base R)

Initial release

2021-03-30