stsplot_space: Map of Disease Incidence During a Given Period

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

Description

This is the plot variant of type=observed~unit for "sts" objects, i.e., plot(stsObj, type=observed~unit, ...) calls the function documented below. It produces an spplot where regions are color-coded according to disease incidence (either absolute counts or relative to population) during a given time period.

Usage

stsplot_space(x, tps = NULL, map = x@map, population = NULL,
              main = NULL, labels = FALSE, at = 10, col.regions = NULL,
              colorkey = list(space = "bottom", labels = list(at=at)),
              total.args = NULL,
              gpar.missing = list(col = "darkgrey", lty = 2, lwd = 2),
              sp.layout = NULL,
              xlim = bbox(map)[1, ], ylim = bbox(map)[2, ], ...)

Arguments

x	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. The possibility of specifying a matrix is, e.g., useful to plot mean counts of simulations from simulate.hhh4.
tps	a numeric vector of one or more time points. The unit-specific sum over all time points tps is plotted. The default tps=NULL means cumulation over the whole time period 1:nrow(x).
map	an object inheriting from "SpatialPolygons" representing the ncol(x) regions. By default the map slot of x is queried (which might be empty and is not applicable if x is a matrix of counts).
population	an optional numeric vector of population numbers in the ncol(x) regions. If given, incidence values instead of absolute counts are plotted.
main	a main title for the plot. If NULL and x is of class "sts", the time range of tps is put as the main title.
labels	determines if and how the regions of the map are labeled, see layout.labels.
at	either a number of levels (default: 10) for the categorization (color-coding) of counts, or specific break points to use, or a named list of a number of levels ("n"), a transformer ("trafo") of class "trans" defined by package scales, and optional further arguments for pretty. The default is the square root transformation (sqrt_trans). Note that the intervals given by at are closed on the left and open to the right, i.e., if specifying at manually as a vector of break points, make sure that max(at) is larger than the maximum observed count.
col.regions	a vector of fill colors of length length(at)-1. By default (NULL), a “heat” palette is generated using colorspace::heat_hcl (if available) or heat.colors.
colorkey	a list describing the color key, see levelplot. The default list elements will be updated by the provided list using modifyList.
total.args	an optional list of arguments for grid.text to have the overall number/incidence of cases printed at an edge of the map. The default settings are list(label="Overall: ", x=1, y=0), and total.args=list() will use all of them.
gpar.missing	list of graphical parameters for sp.polygons applied to the regions of map, which are not part of x. Such extra regions won't be plotted if !is.list(gpar.missing).
sp.layout	optional list of additional layout items, see spplot.
xlim,ylim	numeric vectors of length 2 specifying the axis limits.
...	further arguments for spplot.

Value

a lattice plot of class "trellis", but see spplot.

Author(s)

Sebastian Meyer

See Also

the central stsplot-documentation for an overview of plot types, and animate.sts for animations of "sts" objects.

Examples

data("measlesWeserEms")

# default plot: total region-specific counts over all weeks
plot(measlesWeserEms, type=observed~unit)

# compare with old implementation
plot(measlesWeserEms, type=observed~1|unit)

# plot incidence with region labels
plot(measlesWeserEms, type=observed~unit,
     population=measlesWeserEms@map$POPULATION / 100000,
     labels=list(labels="GEN", cex=0.7, font=3))

# counts in the first week of the second year only (+ display overall)
plot(measlesWeserEms, type=observed~unit, tps=53, total.args=list())

# if we had only observed a subset of the regions
plot(measlesWeserEms[,5:11], type = observed~unit,
     gpar.missing = list(col="gray", lty=4))

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