surveillance: epidataCS_animate – R documentation

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epidataCS_animate

Spatio-Temporal Animation of a Continuous-Time Continuous-Space Epidemic

Description

Function for the animation of continuous-time continuous-space epidemic data, i.e. objects inheriting from class "epidataCS". There are three types of animation, see argument time.spacing. Besides the on-screen plotting in the interactive R session, it is possible and recommended to redirect the animation to an off-screen graphics device using the contributed R package animation. For instance, the animation can be watched and navigated in a web browser via saveHTML (see Examples).

Usage

## S3 method for class 'epidataCS'
animate(object, interval = c(0,Inf), time.spacing = NULL,
        nmax = NULL, sleep = NULL, legend.opts = list(), timer.opts = list(),
        pch = 15:18, col.current = "red", col.I = "#C16E41",
        col.R = "#B3B3B3", col.influence = NULL,
        main = NULL, verbose = interactive(), ...)

Arguments

`object`	an object inheriting from class `"epidataCS"`.
`interval`	time range of the animation.
`time.spacing`	time interval for the animation steps. If `NULL` (the default), the events are plotted sequentially by producing a snapshot at every time point where an event occurred. 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 snapshots. 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). If `time.spacing = NA`, then the time spacing is automatically determined in such a way that `nmax` snapshots result. In this case, `nmax` must be given a finite value.
`nmax`	maximum number of snapshots to generate. The default `NULL` means to take the value from `ani.options("nmax")` if the animation package is available, and no limitation (`Inf`) otherwise.
`sleep`	numeric scalar specifying the artificial pause in seconds between two time points (using `Sys.sleep`), or `NULL` (default), when this is taken from `ani.options("interval")` if the animation package is available, and set to 0.1 otherwise. Note that `sleep` is ignored on non-interactive devices (see `dev.interactive`), e.g., if generating an animation inside animation's `saveHTML`.
`pch, col`	vectors of length equal to the number of event types specifying the point symbols and colors for events to plot (in this order). The vectors are recycled if necessary.
`legend.opts`	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.
`timer.opts`	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.
`col.current`	color of events when occurring (new).
`col.I`	color once infectious.
`col.R`	color event has once “recovered”. If `NA`, then recovered events will not be shown.
`col.influence`	color with which the influence region is drawn. Use `NULL` (default) if no influence regions should be drawn.
`main`	optional main title placed above the map.
`verbose`	logical specifying if a (textual) progress bar should be shown during snapshot generation. This is especially useful if the animation is produced within `saveHTML` or similar.
`...`	further graphical parameters passed to the plot-method of the `SpatialPolygons-class`.

Author(s)

Sebastian Meyer with documentation contributions by Michael Höhle

Examples

data("imdepi")
imdepiB <- subset(imdepi, type == "B")

## Not run: 
# Animate the first year of type B with a step size of 7 days
animate(imdepiB, interval=c(0,365), time.spacing=7, nmax=Inf, sleep=0.1)

# Sequential animation of type B events during the first year
animate(imdepiB, interval=c(0,365), time.spacing=NULL, sleep=0.1)

# Animate the whole time range but with nmax=20 snapshots only
animate(imdepiB, time.spacing=NA, nmax=20, sleep=0.1)

## End(Not run)

# Such an animation can be saved in various ways using the tools of
# the animation package, e.g., saveHTML()
if (require("animation")) {
  oldwd <- setwd(tempdir())  # to not clutter up the current working dir
  saveHTML(animate(imdepiB, interval = c(0,365), time.spacing = 7),
           nmax = Inf, interval = 0.2, loop = FALSE,
           title = "Animation of the first year of type B events")
  setwd(oldwd)
}

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