surveillance: stsplot_spacetime – R documentation

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stsplot_spacetime

Map of Disease Incidence

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 once`Boolean` - 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.color`Boolean` 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` (default), which means that plotting is only to the screen, or a list with elements `device`, `extension`, `width`, `height`, and `name` (with defaults `png`, `".png"`, `640`, `480`, and `"Rplot"`, respectively) to `dev.print` the plots to files (only works in interactive sessions). This option is more or less obsolete since the animation package provides better features for 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

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)

#print the frames to a png device
#and do the animation without extra sleeping between frames
imgname <- file.path(tempdir(), "berlin")
plot(aggregate(ha.sts,nfreq=13), type = observed ~ 1 | unit * time,
     wait.ms=0, dev.printer=list(name=imgname))

#Use ImageMagick (you might have to adjust the path to 'convert')
system(paste0("convert -delay 50 ", imgname,
              "*.png ", imgname, "-animated.gif"))

## 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