"sts" Objectsplot variants of type=observed~time|unit,
type=observed~time, and type=alarm~time
for "sts " objects (see the central "sts"
plot-method for
an overview of plot types).stsplot_time(x, units=NULL,
as.one=FALSE, same.scale=TRUE, par.list=list(), ...)stsplot_time1(x, k=1, ylim=NULL,
axes=TRUE, xaxis.tickFreq=list("%Q"=atChange),
xaxis.labelFreq=xaxis.tickFreq, xaxis.labelFormat="%G%OQ",
epochsAsDate=x@epochAsDate,
xlab="time", ylab="No. infected", main=NULL,
type="s", lty=c(1,1,2), col=c(NA,1,4), lwd=c(1,1,1),
outbreak.symbol=list(pch=3, col=3, cex=1, lwd=1),
alarm.symbol=list(pch=24, col=2, cex=1, lwd=1),
legend.opts=list(),
dx.upperbound=0L, hookFunc=function(){},
.hookFuncInheritance=function() {}, ...)
stsplot_alarm(x, lvl=rep(1,nrow(x)), ylim=NULL,
xaxis.tickFreq=list("%Q"=atChange),
xaxis.labelFreq=xaxis.tickFreq, xaxis.labelFormat="%G%OQ",
epochsAsDate=x@epochAsDate, xlab="time", main=NULL,
type="hhs", lty=c(1,1,2), col=c(1,1,4),
outbreak.symbol=list(pch=3, col=3, cex=1, lwd=1),
alarm.symbol=list(pch=24, col=2, cex=1, lwd=1),
cex=1, cex.yaxis=1, ...)
- x
{an object of class "sts ".}
- units
{optional integer or character vector to select the units (=columns of
observed(x)) to plot. The default is to plot all time series.
If as.one=FALSE, stsplot_time1 is called
for (k in units) with mfrow splitting (see par.list).
Note that if there are too many units, the default mfrow
setting might lead to the error figure margins too large
(meaning that the units do not fit onto a single page).}
- as.one
{logical indicating if all time series should be plotted
in a single frame (using matplot).}
- same.scale
{logical indicating if all time series should be
plotted with the same ylim. Default is to do so. Only
relevant for multivariate plots (ncol(x) > 1).}
- par.list
{a list of arguments delivered to a call of
par to set graphical parameters before plotting.
The mfrow splitting is handled per default. Afterwards,
the parameters are reverted to their original values.
Use par.list=NULL to disable the internal par call.}
- k
{the unit to plot, i.e., an element of 1:ncol(x).}
- ylim
{the y limits of the plot(s). Ignored if
same.scale=FALSE.}
- axes
{a logical value indicating whether both axes should be drawn
on the plot.}
- xaxis.tickFreq,xaxis.labelFreq,xaxis.labelFormat
{see
addFormattedXAxis.}
- epochsAsDate
{Boolean indicating whether to treat the epochs as
Date objects (or to transform them to dates such that the new x-axis
formatting is applied).
Default: Value of the epochAsDate slot of x.}
- xlab
{a title for the x axis. See plot.default.}
- ylab
{a title for the y axis. See plot.default.}
- main
{an overall title for the plot: see 'title'.}
- type
{type of plot to do.}
- lty
{vector of length 3 specifying the line type for the three
lines in the plot -- see col argument.}
- col
{Vector of length 3 specifying the color to use in the
plot. The first color is the fill color of the polygons for the
counts bars (NA for unfilled), the 2nd element denotes their
border color, the 3rd element is the color of the upperbound
plotting.}
- lwd
{Vector of length 3 specifying the line width of the three
elements to plot. See also the col argument.}
- alarm.symbol
{a list with entries pch, col,
cex and lwd specifying the appearance of the outbreak
symbol in the plot.}
- outbreak.symbol
{a list with entries pch, col,
cex and lwd specifying the appearance of the outbreak
symbol in the plot.}
- legend.opts
{a list of arguments for legend.
If missing(legend.opts) (i.e., not explicitly
specified), the default legend will only be produced if x
contains any information on outbreaks, alarms, or upperbounds.
To disable the legend, use, e.g., legend.opts=NULL.
Otherwise, the following arguments are default:
[object Object],[object Object],[object Object]
Any further arguments to the legend function are
just provided as additional elements of this list,
e.g. horiz=TRUE.
}
- dx.upperbound
{horizontal change in the plotting of the
upperbound line. Sometimes it can be convenient to offset this line
a little for better visibility.}
- lvl
{A vector of length ncol(x), which is used to
specify the hierarchy level for each time series in the sts object
for alarm plots.}
- cex
{A numerical value giving the amount by which plotting text
and symbols should be magnified relative to the default. See
par for details.}
- cex.yaxis
{The magnification to be used for y-axis annotation
relative to the current setting of cex.}
- hookFunc
{a function that is called after all the basic plotting
has be done, i.e., it is not possible to control formatting with
this function. See Examples.}
- .hookFuncInheritance
{a function which is altered by sub-classes
plot method. Do not alter this function manually.}
- ...
{further arguments for the function matplot. If
e.g. xlab or main are provided they overwrite the
default values.}
The time series plot relies on the work-horse stsplot_time1.
Its arguments are (almost) similar to plot.survRes.
NULL (invisibly).
The functions are called for their side-effects.
[object Object],[object Object]
the central stsplot-documentation for an overview of
plot types.
data("ha.sts")
print(ha.sts)
plot(ha.sts, type=observed ~ time | unit) # default multivariate type
plot(ha.sts, units=c("mitt", "pank")) # selected units
plot(ha.sts, type=observed ~ time) # aggregated over all districts
## Hook function example
hookFunc <- function() grid(NA,NULL,lwd=1)
plot(ha.sts, hookFunc=hookFunc)
## another multivariate time series example plotted "as.one"
data("measlesDE")
plot(measlesDE, units=1:2, as.one=TRUE, legend.opts=list(cex=0.8))
## more sophisticated plots are offered by package "xts"
if (require("xts")) # need version > 0.9.7 for plots of multiple time series
plot(as.xts(measlesDE))
## Use ISO8601 date formatting (see ?strptime) and no legend
data("salmNewport")
plot(aggregate(salmNewport,by="unit"), xlab="Time (weeks)",
xaxis.tickFreq=list("%m"=atChange,"%G"=atChange),
xaxis.labelFreq=list("%G"=atMedian),xaxis.labelFormat="%G")
## Formatting now also works for daily data (illustrate by artifical
## outbreak converted to sts object by linelist2sts)
set.seed(123)
exposureTimes <- as.Date("2014-03-12") + sample(x=0:25,size=99,replace=TRUE)
sts <- linelist2sts(data.frame(exposure=exposureTimes),
dateCol="exposure",aggregate.by="1 day")
## Plot it with larger ticks for days than usual
surveillance.options("stsTickFactors"=c("%d"=1, "%W"=0.33,
"%V"=0.33, "%m"=1.75, "%Q"=1.25, "%Y"=1.5, "%G"=1.5))
plot(sts,xaxis.tickFreq=list("%d"=atChange,"%m"=atChange),
xaxis.labelFreq=list("%d"=at2ndChange),xaxis.labelFormat="%d-%b",
xlab="Time (days)")
hplot
ts