# Plotting Paths of Infection Intensities for `twinSIR`

Models

`twinSIR_intensityplot.Rd`

`intensityplot`

methods to plot the evolution of the total infection
intensity, its epidemic proportion or its endemic proportion over time.
The default `plot`

method for objects of class `"twinSIR"`

is just a wrapper for the `intensityplot`

method.
The implementation is illustrated in Meyer et al. (2017, Section 4),
see `vignette("twinSIR")`

.

## Usage

```
# S3 method for twinSIR
plot(x, which = c("epidemic proportion", "endemic proportion",
"total intensity"), ...)
# S3 method for twinSIR
intensityplot(x, which = c("epidemic proportion", "endemic proportion",
"total intensity"), aggregate = TRUE, theta = NULL,
plot = TRUE, add = FALSE, rug.opts = list(), ...)
# S3 method for simEpidata
intensityplot(x, which = c("epidemic proportion", "endemic proportion",
"total intensity"), aggregate = TRUE, theta = NULL,
plot = TRUE, add = FALSE, rug.opts = list(), ...)
```

## Arguments

- x
an object of class

`"twinSIR"`

(fitted model) or`"simEpidata"`

(simulated`twinSIR`

epidemic), respectively.- which
`"epidemic proportion"`

,`"endemic proportion"`

, or`"total intensity"`

. Partial matching is applied. Determines whether to plot the path of the total intensity \(\lambda(t)\) or its epidemic or endemic proportions \(\frac{e(t)}{\lambda(t)}\) or \(\frac{h(t)}{\lambda(t)}\).- aggregate
logical. Determines whether lines for all individual infection intensities should be drawn (

`FALSE`

) or their sum only (`TRUE`

, the default).- theta
numeric vector of model coefficients. If

`x`

is of class`"twinSIR"`

, then`theta = c(alpha, beta)`

, where`beta`

consists of the coefficients of the piecewise constant log-baseline function and the coefficients of the endemic (`cox`

) predictor. If`x`

is of class`"simEpidata"`

, then`theta = c(alpha, 1, betarest)`

, where 1 refers to the (true) log-baseline used in the simulation and`betarest`

is the vector of the remaining coefficients of the endemic (`cox`

) predictor. The default (`NULL`

) means that the fitted or true parameters, respectively, will be used.- plot
logical indicating if a plot is desired, defaults to

`TRUE`

. Otherwise, only the data of the plot will be returned. Especially with`aggregate = FALSE`

and many individuals one might e.g. consider to plot a subset of the individual intensity paths only or do some further calculations/analysis of the infection intensities.- add
logical. If

`TRUE`

, paths are added to the current plot, using`lines`

.- 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 and`quiet`

is set to`TRUE`

. Note that the argument`x`

of the`rug()`

function, which contains the locations for the`rug`

is fixed internally and can not be modified. The locations of the rug are the time points of infections.- ...
For the

`plot.twinSIR`

method, arguments passed to`intensityplot.twinSIR`

. For the`intensityplot`

methods, further graphical parameters passed to the function`matplot`

, e.g.`lty`

,`lwd`

,`col`

,`xlab`

,`ylab`

and`main`

. Note that the`matplot`

arguments`x`

,`y`

,`type`

and`add`

are implicit and can not be specified here.

## Value

numeric matrix with the first column `"stop"`

and as many rows as there
are `"stop"`

time points in the event history `x`

. The other
columns depend on the argument `aggregate`

: if `TRUE`

, there
is only one other column named `which`

, which contains the values of

`which`

at the respective `"stop"`

time points. Otherwise, if

`aggregate = FALSE`

, there is one column for each individual, each of
them containing the individual `which`

at the respective `"stop"`

time points.

## References

Meyer, S., Held, L. and Höhle, M. (2017):
Spatio-temporal analysis of epidemic phenomena using the R package
surveillance.
*Journal of Statistical Software*, **77** (11), 1-55.
doi:10.18637/jss.v077.i11

## See also

`twinSIR`

for a description of the intensity model, and
`simulate.twinSIR`

for the simulation of epidemic data
according to a `twinSIR`

specification.

## Examples

```
data("hagelloch")
plot(hagelloch)
# a simplistic twinSIR model
fit <- twinSIR(~ household, data = hagelloch)
# overall total intensity
plot(fit, which = "total")
# overall epidemic proportion
epi <- plot(fit, which = "epidemic", ylim = c(0, 1))
head(epi)
# add overall endemic proportion = 1 - epidemic proportion
ende <- plot(fit, which = "endemic", add = TRUE, col = 2)
legend("topleft", legend = "endemic proportion", lty = 1, col = 2, bty = "n")
if (surveillance.options("allExamples")) {
# individual intensities
tmp <- plot(fit, which = "total", aggregate = FALSE,
col = rgb(0, 0, 0, alpha = 0.1),
main = expression("Individual infection intensities " *
lambda[i](t) == Y[i](t) %.% (e[i](t) + h[i](t))))
# return value: matrix of individual intensity paths
str(tmp)
# plot intensity path only for individuals 3 and 99
matplot(x = tmp[,1], y = tmp[,1+c(3,99)], type = "S",
ylab = "Force of infection", xlab = "time",
main = expression("Paths of the infection intensities " *
lambda[3](t) * " and " * lambda[99](t)))
legend("topright", legend = paste("Individual", c(3,99)),
col = 1:2, lty = 1:2)
}
```