surveillance: plot.disProg – R documentation

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plot.disProg

Plot Generation of the Observed and the Defined Outbreak States of a (Multivariate) Time Series

Description

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

Usage

## S3 method for class 'disProg'
plot(x, title = "", xaxis.years=TRUE, startyear = x$start[1],
    firstweek = x$start[2], as.one=TRUE, same.scale=TRUE, ...)

  plot.disProg.one(x, title = "", xaxis.years=TRUE, quarters=TRUE, 
    startyear =  x$start[1], firstweek = x$start[2], ylim=NULL, xlab="time",
    ylab="No. infected",type="hh",lty=c(1,1),col=c(1,1), 
    outbreak.symbol = list(pch=3, col=3), legend.opts=list(x="top", 
    legend=c("Infected", "Outbreak"), lty=NULL,pch=NULL,col=NULL), ...)

Arguments

`x`	object of class `disProg`
`title`	plot title
`xaxis.years`	if `TRUE`, the x axis is labeled using years
`quarters`	add quarters to the plot
`startyear`	year to begin the axis labeling (the year where the oldest data come from). This arguments will be obsolete in `sts`.
`firstweek`	number of the first week of January in the first year (just for axis labeling grounds)
`as.one`	if `TRUE` all individual time series are shown in one plot
`same.scale`	if `TRUE` all plots have same scale
`ylim`	range of y axis
`xlab`	label of the x-axis
`ylab`	label of the y-axis
`type`	line type of the observed counts (should be `hh`)
`lty`	line type of the observed counts
`col`	color of the observed count lines
`outbreak.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 An further arguments to the `legend` function are just provided as additional elements of this list, e.g. `horiz=TRUE`.
`...`	arguments passed to `plot.disProg.one`. From there, further arguments are passed to `matplot`.

Value

a plot showing the number of infected and the defined alarm status for a time series created by simulation or given in data either in one single plot or in several plots for each individual time series.

Author(s)

M. Höhle with contributions by A. Riebler and C. Lang

Examples

# Plotting of simulated data
disProgObj <- sim.pointSource(p = 0.99, r = 0.5, length = 208,
                              A = 1, alpha = 1, beta = 0, phi = 0,
                              frequency = 1, state = NULL, K = 5)
# plot the simulated disease with the defined outbreaks
plot(disProgObj)
title <- "Number of Infected and Defined Outbreak Positions for Simulated Data"
plot(disProgObj, title = title)
plot(disProgObj, title = title, xaxis.years=TRUE,
     startyear = 1999, firstweek = 13)
plot(disProgObj, title = title, xaxis.years=TRUE,
     startyear = 1999, firstweek = 14)

# Plotting of measles data
data(measles.weser)
# one plot
plot(measles.weser, title = "measles cases in the district Weser-Ems",
     xaxis.years=TRUE, startyear= 2001, firstweek=1)
# plot cases for each "Kreis" 
plot(measles.weser, same.scale=TRUE, as.one=FALSE)

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