stsplot_spacetime: Map of Disease Incidence

In jimhester/surveillance: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena

Description

For each period (row) or for the overall period of the observed matrix of the "sts" object, a map showing the counts by region is produced. It is possible to redirect the output into files, e.g. to generate an animated GIF.

Usage

stsplot_spacetime(x, type, legend = NULL, opts.col = NULL, labels = TRUE,
                  wait.ms = 250, cex.lab = 0.7, verbose = FALSE,
                  dev.printer = NULL, ...)

Arguments

x	an object of class "sts".
type	a formula (see stsplot). For a map aggregated over time (no animation), use observed ~ 1 | unit, otherwise observed ~ 1 | unit * time.
legend	An object of type list containing the following items used for coloring dxposition increments in x direction dyposition increments in y direction xposition in x yposition in y onceBoolean - if TRUE then only shown once If NULL then a default legend is used.
opts.col	A list containing the two elements ncolorsNumber of colors to use for plotting use.colorBoolean if TRUE then colors will be used in the palette, otherwise grayscale
labels	Boolean whether to add labels
wait.ms	Number of milliseconds to wait between each plot
cex.lab	cex of the labels
verbose	Boolean whether to write out extra information
dev.printer	Either NULL, which means that plotting is only to the screen otherwise a list with elements device, extension, width and height. This options is more or less obsolete - nowadays it's better to us the animation package to generate output to files.
...	Extra arguments sent to the plot function.

Note

The animate.sts method provides a re-implementation and supersedes this function!

Author(s)

Michael Höhle

See Also

Other stsplot types, and animate.sts for the new implementation.

Examples

data("ha.sts")
print(ha.sts)

## map of total counts by district
plot(ha.sts, type=observed ~ 1 | unit)
## only show a sub-period total for two selected districts
plot(ha.sts[1:20,1:2], type=observed ~ 1 | unit)

## Not run: 
# space-time animation
plot(aggregate(ha.sts,nfreq=13), type= observed ~ 1 | unit * time)

#Configure a png device printer to save the frames
dev.printer <- list(device=png, extension=".png", width=640, height=480,
                    name=file.path(tempdir(),"berlin"))

#Do the animation (without extra sleeping time between frames)
plot(aggregate(ha.sts,nfreq=13), type = observed ~ 1 | unit * time,
     wait.ms=0, dev.printer=dev.printer)

#Use ImageMagick (you might have to adjust the path to 'convert')
system(paste("convert -delay 50 ",dev.printer$name,
           "*.png ", dev.printer$name, "-animated.gif",sep=""))

## End(Not run)

jimhester/surveillance documentation built on May 19, 2019, 10:33 a.m.