surveillance: epidata_plot – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

epidata_plot

Plotting the Evolution of an Epidemic

Description

Functions for plotting the evolution of epidemics. The plot methods for classes "epidata" and "summary.epidata" plots the numbers of susceptible, infectious and recovered (= removed) individuals by step functions along the time axis. The function stateplot shows individual state changes along the time axis.

Usage

## S3 method for class 'summary.epidata'
plot(x,
     lty = c(2, 1, 3), lwd = 2,
     col = c("#1B9E77", "#D95F02", "#7570B3"), col.hor = col, col.vert = col,
     xlab = "Time", ylab = "Number of individuals",
     xlim = NULL, ylim = NULL, legend.opts = list(), do.axis4 = NULL,
     panel.first = grid(), rug.opts = list(),
     which.rug = c("infections", "removals", "susceptibility", "all"), ...)
## S3 method for class 'epidata'
plot(x, ...)

stateplot(x, id, ...)

Arguments

`x`	an object inheriting from class `"epidata"` or `"summary.epidata"`. In the former case, its summary is calculated and the function continues as in the latter case. The `plot` method for class `"epidata"` is a simple wrapper for `plot.summary.epidata` implemented as `plot(summary(x, ...))`.
`lty, lwd`	vectors of length 3 containing the line types and widths, respectively, for the numbers of susceptible, infectious and removed individuals (in this order). By default, all lines have width 1 and the line types are dashed (susceptible), solid (infectious) and dotted (removed), respectively. To omit the drawing of a specific line, just set the corresponding entry in `lty` to 0. The vectors are recycled if necessary. For information about the different `lty` and `lwd` codes, see the help pages of `par`.
`col, col.hor, col.vert`	vectors of length 3 containing the line colors for the numbers of susceptible, infectious and removed individuals (in this order). `col.hor` defines the color for the horizontal parts of the step function, whilst `col.vert` defines the color for its vertical parts. The argument `col` is just short for `col.hor = col` and `col.vert = col`. The default `col` vector corresponds to `brewer.pal("Dark2",n=3)` from the RColorBrewer package. The vectors are recycled if necessary. For information about the possible values of `col`, see the help pages of `par`.
`xlab, ylab`	axis labels, default to "Time" and "Number of individuals", respectively.
`xlim, ylim`	the x and y limits of the plot in the form `c(xmin, xmax)` and `c(ymin, ymax)`, respectively. By default, these are chosen adequately to fit the time range of the epidemic and the number of individuals.
`legend.opts`	if this is a list (of arguments for the `legend` function), a legend will be plotted. The defaults are as follows: `x`: `"topright"` `inset`: `c(0,0.02)` `legend`: `c("susceptible", "infectious", "removed")` `lty`,`lwd`,`col`: same as the arguments `lty`, `lwd`, and `col.hor` of the main function `bty`: `"n"`
`do.axis4`	logical indicating if the final numbers of susceptible and removed individuals should be indicated on the right axis. The default `NULL` means `TRUE`, if `x` represents a SIR epidemic and `FALSE` otherwise, i.e. if the epidemic is SI, SIS or SIRS.
`panel.first`	an expression to be evaluated after the plot axes are set up but before any plotting takes place. By default, a standard grid is drawn.
`rug.opts`	either a list of arguments passed to the function `rug` or `NULL` (or `NA`), in which case no `rug` will be plotted. By default, the argument `ticksize` is set to 0.02, `col` is set to the color according to `which.rug` (black if this is `"all"`), and `quiet` is set to `TRUE`. Note that the argument `x`, which contains the locations for the `rug` is fixed internally and can not be modified. The argument `which.rug` (see below) determines the locations to mark.
`which.rug`	By default, tick marks are drawn at the time points of infections. Alternatively, one can choose to mark only `"removals"`, `"susceptibilities"` (i.e. state change from R to S) or `"all"` events.
`id`	single character string or factor of length 1 specifying the individual for which the `stateplot` should be established.
`...`	For `plot.summary.epidata`: further graphical parameters passed to `plot`, `lines` and `axis`, e.g. `main`, `las`, `cex.axis` (etc.) and `mgp`. For `plot.epidata`: arguments passed to `plot.summary.epidata`. For `stateplot`: arguments passed to `plot.stepfun` or `plot.function` (if `id` had no events during the observation period). By default, `xlab="time"`, `ylab="state"`, `xlim=attr(x,"timeRange")`, `xaxs="i"` and `do.points=FALSE`.

Value

plot.summary.epidata (and plot.epidata) invisibly returns the matrix used for plotting, which contains the evolution of the three counters.
stateplot invisibly returns the function, which was plotted, typically of class "stepfun", but maybe of class "function", if no events have been observed for the individual in question (then the function always returns the initial state). The vertical axis of stateplot can range from 1 to 3, where 1 corresponds to Susceptible, 2 to Infectious and 3 to Removed.

Author(s)

Sebastian Meyer

Examples

data("hagelloch")
(s <- summary(hagelloch))

# rudimentary stateplot
stateplot(s, id = "187")

# evolution of the epidemic
plot(s)

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