surveillance: plot.survRes – R documentation

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plot.survRes

Plot a survRes object

Description

Plotting a (multivariate) survRes object. The internal 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, ...)

  plot.survRes.one(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 specifying 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`.
`...`	arguments passed to `plot.survRes.one`. From there, further arguments are passed to `matplot`.

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))

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