plot.survRes: Plot a survRes object

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

Description

Plotting of a (multivariate) survRes object. The function plot.survRes.one is used as a helper function to plot a univariate time series.

Usage

  ## S3 method for class 'survRes'
plot(x, method=x$control$name, disease=x$control$data, 
  xaxis.years=TRUE,startyear = 2001, firstweek = 1, same.scale=TRUE,...)
  ## S3 method for class 'survRes.one'
plot(x, method=x$control$name, disease=x$control$data,
   domany=FALSE,ylim=NULL,xaxis.years=TRUE,startyear = 2001, firstweek = 1, 
   xlab="time", ylab="No. infected", main=NULL, type="hhs",
   lty=c(1,1,2),col=c(1,1,4), 
   outbreak.symbol = list(pch=3,col=3),alarm.symbol=list(pch=24,col=2),
   legend.opts=list(x="top",
   legend=c("Infected", "Upperbound", "Alarm", "Outbreak"),
   lty=NULL,col=NULL,pch=NULL), ...)

Arguments

x	object of class survRes
method	surveillance method to be used in title
disease	name of disease in title
xaxis.years	Boolean indicating whether to show a year based x-axis for weekly data
domany	Boolean telling the function whether it is called for a multivariate (TRUE) or univariate (FALSE) survRes object. In case of TRUE no titles are drawn.
ylim	range of y axis
startyear	year to begin the axis labeling (the year where the oldest data come from)
firstweek	number of the first week of January in the first year (just for axis labeling reasons)
xlab	label of the x-axis
ylab	label of the y-axis
main	the title of the graphics is generated from the method and disease arguments if not specified otherwise
same.scale	plot all time series with the same ylim? Defaults to true

.

type	line type of the observed counts (first two elements) and the upper bound (third element)
lty	vector of size 3 speciying the line type of the observed counts (left, right) and the upperbound line
col	vector with three elements: color of left bar and color of top bar, color of right bar, col of the upperbound line.
outbreak.symbol	list with entries pch and col specifying the plot symbol
alarm.symbol	list with entries pch and col specifying the plot symbol
legend.opts	a list containing the entries to be sent to the legend function. If no legend is requested use legend.opts=NULL. Otherwise, the following arguments are default x top legend The names infected and outbreak. lty If NULL the lty argument will be used pch If NULL the pch argument is used col If NULL the col argument is used Any further arguments to the legend function are just provided as additional elements of this list, e.g. horiz=TRUE.
...	further arguments for the function matplot. If e.g. xlab or main are provided they overwrite the default values.

Details

The plot.survRes.one is intended for internal use. At the moment none of the surveillance methods support multivariate survRes objects. New versions of the packages currently under development will handle this.

Value

none. A plot showing the number of infected, the threshold for recognizing an outbreak, the alarm status and the outbreak status is generated.

Author(s)

M. Höhle

Examples

data(ha)
ctrl <- list(range = 209:290, b = 2, w = 6, alpha = 0.005)
plot(algo.bayes(aggregate(ha), control = ctrl))

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