# Simulation of a Self-Exciting Spatio-Temporal Point Process

`twinstim_simulation.Rd`

The function `simEpidataCS`

simulates events of a self-exciting
spatio-temporal point process of the `"twinstim"`

class.
Simulation works via Ogata's modified thinning of the conditional
intensity as described in Meyer et al. (2012). Note that simulation is
limited to the spatial and temporal range of `stgrid`

.

The `simulate`

method for objects of class
`"twinstim"`

simulates new epidemic data using the model and
the parameter estimates of the fitted object.

## Usage

```
simEpidataCS(endemic, epidemic, siaf, tiaf, qmatrix, rmarks,
events, stgrid, tiles, beta0, beta, gamma, siafpars, tiafpars,
epilink = "log", t0 = stgrid$start[1], T = tail(stgrid$stop,1),
nEvents = 1e5, control.siaf = list(F=list(), Deriv=list()),
W = NULL, trace = 5, nCircle2Poly = 32, gmax = NULL, .allocate = 500,
.skipChecks = FALSE, .onlyEvents = FALSE)
# S3 method for class 'twinstim'
simulate(object, nsim = 1, seed = NULL, data, tiles,
newcoef = NULL, rmarks = NULL, t0 = NULL, T = NULL, nEvents = 1e5,
control.siaf = object$control.siaf,
W = data$W, trace = FALSE, nCircle2Poly = NULL, gmax = NULL,
.allocate = 500, simplify = TRUE, ...)
```

## Arguments

- endemic
see

`twinstim`

. Note that type-specific endemic intercepts are specified by`beta0`

here, not by the term`(1|type)`

.- epidemic
see

`twinstim`

. Marks appearing in this formula must be returned by the generating function`rmarks`

.- siaf
see

`twinstim`

. In addition to what is required for fitting with`twinstim`

, the`siaf`

specification must also contain the element`simulate`

, a function which draws random locations following the spatial kernel`siaf$f`

. The first argument of the function is the number of points to sample (say`n`

), the second one is the vector of parameters`siafpars`

, the third one is the type indicator (a character string matching a type name as specified by`dimnames(qmatrix)`

). With the current implementation there will always be simulated only one location at a time, i.e.`n=1`

. The predefined siaf's all provide simulation.- tiaf
e.g. what is returned by the generating function

`tiaf.constant`

or`tiaf.exponential`

. See also`twinstim`

.- qmatrix
see

`epidataCS`

. Note that this square matrix and its`dimnames`

determine the number and names of the different event types. In the simplest case, there is only a single type of event, i.e.`qmatrix = diag(1)`

.- rmarks
function of single time (1st argument) and location (2nd argument) returning a one-row

`data.frame`

of marks (named according to the variables in`epidemic`

) for an event at this point. This must include the columns`eps.s`

and`eps.t`

, i.e. the values of the spatial and temporal interaction ranges at this point. Only`"numeric"`

and`"factor"`

columns are allowed. Assure that factor variables are coded equally (same levels and level order) for each new sample.For the

`simulate.twinstim`

method, the default (`NULL`

) means sampling from the empirical distribution function of the (non-missing) marks in`data`

restricted to events in the simulation period (`t0`

;`T`

]. If there are no events in this period, e.g., if simulating beyond the original observation period,`rmarks`

will sample marks from all of`data$events`

.- events
`NULL`

or missing (default) in case of an empty prehistory, or a`SpatialPointsDataFrame`

containing events of the prehistory (-Inf;`t0`

] of the process (required for the epidemic to start in case of no endemic component in the model). The`SpatialPointsDataFrame`

must have the same`proj4string`

as`tiles`

and`W`

). The attached`data.frame`

(data slot) must contain the typical columns as described in`as.epidataCS`

(`time`

,`tile`

,`eps.t`

,`eps.s`

, and, for type-specific models,`type`

) and all marks appearing in the`epidemic`

specification. Note that some column names are reserved (see`as.epidataCS`

). Only events up to time`t0`

are selected and taken as the prehistory.- stgrid
see

`as.epidataCS`

. Simulation only works inside the spatial and temporal range of`stgrid`

.- tiles
object inheriting from

`"SpatialPolygons"`

with`row.names`

matching the`tile`

names in`stgrid`

and having the same`proj4string`

as`events`

and`W`

. This is necessary to sample the spatial location of events generated by the endemic component.- beta0,beta,gamma,siafpars,tiafpars
these are the parameter subvectors of the

`twinstim`

.`beta`

and`gamma`

must be given in the same order as they appear in`endemic`

and`epidemic`

, respectively.`beta0`

is either a single endemic intercept or a vector of type-specific endemic intercepts in the same order as in`qmatrix`

.- epilink
a character string determining the link function to be used for the

`epidemic`

linear predictor of event marks. By default, the log-link is used. The experimental alternative is`epilink = "identity"`

. Note that the identity link does not guarantee the force of infection to be positive. If this leads to a negative total intensity (endemic + epidemic), the point process is not well defined and simulation cannot proceed.- t0
`events`

having occurred during (-Inf;`t0`

] are regarded as part of the prehistory \(H_0\) of the process. For`simEpidataCS`

, by default and also if`t0=NULL`

, the beginning of`stgrid`

is used as`t0`

. For the`simulate.twinstim`

method,`NULL`

means to use the fitted time range of the`"twinstim"`

`object`

.- T, nEvents
simulate a maximum of

`nEvents`

events up to time`T`

, then stop. For`simEpidataCS`

, by default, and also if`T=NULL`

,`T`

equals the last stop time in`stgrid`

(it cannot be greater) and`nEvents`

is bounded above by 10000. For the`simulate.twinstim`

method,`T=NULL`

means to use the same same time range as for the fitting of the`"twinstim"`

`object`

.- W
see

`as.epidataCS`

. When simulating from`twinstim`

-fits,`W`

is by default taken from the original`data$W`

. If specified as`NULL`

,`W`

is generated automatically via`unionSpatialPolygons(tiles)`

. However, since the result of such a polygon operation should always be verified, it is recommended to do that in advance.

It is important that`W`

and`tiles`

cover the same region: on the one hand direct offspring is sampled in the spatial influence region of the parent event, i.e., in the intersection of`W`

and a circle of radius the`eps.s`

of the parent event, after which the corresponding tile is determined by overlay with`tiles`

. On the other hand endemic events are sampled from`tiles`

.- trace
logical (or integer) indicating if (or how often) the current simulation status should be

`cat`

ed. For the`simulate.twinstim`

method,`trace`

currently only applies to the first of the`nsim`

simulations.- .allocate
number of rows (events) to initially allocate for the event history; defaults to 500. Each time the simulated epidemic exceeds the allocated space, the event

`data.frame`

will be enlarged by`.allocate`

rows.- .skipChecks,.onlyEvents
these logical arguments are not meant to be set by the user. They are used by the

`simulate`

-method for`"twinstim"`

objects.- object
an object of class

`"twinstim"`

.- nsim
number of epidemics (i.e. spatio-temporal point patterns inheriting from class

`"epidataCS"`

) to simulate. Defaults to 1 when the result is a simple object inheriting from class`"simEpidataCS"`

(as if`simEpidataCS`

would have been called directly). If`nsim > 1`

, the result will be a list the structure of which depends on the argument`simplify`

.- seed
an object specifying how the random number generator should be initialized for simulation (via

`set.seed`

). The initial state will also be stored as an attribute`"seed"`

of the result. The original state of the`.Random.seed`

will be restored at the end of the simulation. By default (`NULL`

), neither initialization nor recovery will be done. This behaviour is copied from the`simulate.lm`

method.- data
an object of class

`"epidataCS"`

, usually the one to which the`"twinstim"`

`object`

was fitted. It carries the`stgrid`

of the endemic component, but also`events`

for use as the prehistory, and defaults for`rmarks`

and`nCircle2Poly`

.- newcoef
an optional named numeric vector of (a subset of) parameters to replace the original point estimates in

`coef(object)`

. Elements which do not match any model parameter by name are silently ignored. The`newcoef`

s may also be supplied in a list following the same conventions as for the`start`

argument in`twinstim`

.- simplify
logical. It is strongly recommended to set

`simplify = TRUE`

(default) if`nsim`

is large. This saves space and computation time, because for each simulated epidemic only the`events`

component is saved. All other components, which do not vary between simulations, are only stored from the first run. In this case, the runtime of each simulation is stored as an attribute`"runtime"`

to each simulated`events`

. See also the “Value” section below.- control.siaf
see

`twinstim`

.- nCircle2Poly
see

`as.epidataCS`

. For`simulate.twinstim`

,`NULL`

means to use the same value as for`data`

.- gmax
maximum value the temporal interaction function

`tiaf$g`

can attain. If`NULL`

, then it is assumed as the maximum value of the type-specific values at 0, i.e.`max(tiaf$g(rep.int(0,nTypes), tiafpars, 1:nTypes))`

.- ...
unused (arguments of the generic).

## Value

The function `simEpidataCS`

returns a simulated epidemic of class
`"simEpidataCS"`

, which enhances the class
`"epidataCS"`

by the following additional components known from
objects of class `"twinstim"`

:
`bbox`

, `timeRange`

, `formula`

, `coefficients`

,
`npars`

, `control.siaf`

, `call`

, `runtime`

.
It has corresponding `coeflist`

,
`residuals`

,
`R0`

, and
`intensityplot`

methods.

The `simulate.twinstim`

method has some additional
*attributes* set on its result:
`call`

, `seed`

, and `runtime`

.
If `nsim > 1`

, it returns an object of class
`"simEpidataCSlist"`

, the form of which depends on the value of
`simplify`

(which is stored as an attribute `simplified`

):
if `simplify = FALSE`

, then the return value is
just a list of sequential simulations, each of class
`"simEpidataCS"`

. However, if `simplify = TRUE`

, then the
sequential simulations share all components but the simulated
`events`

, i.e. the result is a list with the same components as
a single object of class `"simEpidataCS"`

, but with `events`

replaced by an `eventsList`

containing the `events`

returned
by each of the simulations.

The `stgrid`

component of the returned `"simEpidataCS"`

will be truncated to the actual end of the simulation, which might
be \(<T\), if the upper bound `nEvents`

is reached during
simulation.

CAVE: Currently, `simplify=TRUE`

in `simulate.twinstim`

ignores that multiple simulated epidemics
(`nsim > 1`

) may have different `stgrid`

time ranges. In a `"simEpidataCSlist"`

, the `stgrid`

shared
by all of the simulated epidemics is just the `stgrid`

returned by the *first* simulation.

## Note

The more detailed the polygons in `tiles`

are the slower is
the algorithm. You are advised to sacrifice some shape
details for speed by reducing the polygon complexity,
for example via the `mapshaper`

JavaScript library wrapped by
the R package rmapshaper, or via
`simplify.owin`

.

## References

Douglas, D. H. and Peucker, T. K. (1973):
Algorithms for the reduction of the number of points required to
represent a digitized line or its caricature.
*Cartographica: The International Journal for Geographic
Information and Geovisualization*, **10**, 112-122

Meyer, S., Elias, J. and Höhle, M. (2012):
A space-time conditional intensity model for invasive meningococcal
disease occurrence. *Biometrics*, **68**, 607-616.
doi:10.1111/j.1541-0420.2011.01684.x

## See also

The function `simEndemicEvents`

is a faster alternative
for endemic-only models, only returning a
`"SpatialPointsDataFrame"`

of simulated events.

The `plot.epidataCS`

and `animate.epidataCS`

methods for plotting and animating continuous-space epidemic data,
respectively, also work for simulated epidemics (by inheritance),
and `twinstim`

can be used to fit
spatio-temporal conditional intensity models also to simulated data.

## Examples

```
data("imdepi", "imdepifit")
## load borders of Germany's districts (originally obtained from
## the German Federal Agency for Cartography and Geodesy,
## https://gdz.bkg.bund.de/), simplified by the "modified Visvalingam"
## algorithm (level=6.6%) using MapShaper.org (v. 0.1.17):
load(system.file("shapes", "districtsD.RData", package="surveillance"))
if (surveillance.options("allExamples")) {
plot(districtsD)
plot(stateD, add=TRUE, border=2, lwd=2)
}
## simulate 2 realizations (over a short period, for speed)
## considering events from data(imdepi) before t=31 as prehistory
## IGNORE_RDIFF_BEGIN
mysims <- simulate(imdepifit, nsim=2, seed=1, data=imdepi,
tiles=districtsD, newcoef=c("e.typeC"=-1),
t0=31, T=if (interactive()) 180 else 45, # for CRAN
simplify=TRUE)
## IGNORE_RDIFF_END
## plot both simulations using the plot-method for simEpidataCSlist's
mysims
plot(mysims, aggregate="time")
## extract the second realization -> object of class simEpidataCS
mysim2 <- mysims[[2]]
summary(mysim2)
plot(mysim2, aggregate="space")
### compare the observed _cumulative_ number of cases in the first 90 days to
nsim <- 20
### simulations from the fitted model
sims <- simulate(imdepifit, nsim=nsim, seed=1, data=imdepi, t0=0, T=90,
tiles=districtsD, simplify=TRUE)
## extract cusums
getcsums <- function (events) {
tapply(events$time, events@data["type"],
function (t) cumsum(table(t)), simplify=FALSE)
}
csums_observed <- getcsums(imdepi$events)
csums_simulated <- lapply(sims$eventsList, getcsums)
## plot it
plotcsums <- function (csums, ...) {
mapply(function (csum, ...) lines(as.numeric(names(csum)), csum, ...),
csums, ...)
invisible()
}
plot(c(0,90), c(0,35), type="n", xlab="Time [days]",
ylab="Cumulative number of cases")
plotcsums(csums_observed, col=c(2,4), lwd=3)
legend("topleft", legend=levels(imdepi$events$type), col=c(2,4), lwd=1)
invisible(lapply(csums_simulated, plotcsums,
col=adjustcolor(c(2,4), alpha.f=0.5)))
if (FALSE) { # \dontrun{
### Experimental code to generate 'nsim' simulations of 'nm2add' months
### beyond the observed time period:
nm2add <- 24
nsim <- 5
### The events still infective by the end of imdepi$stgrid will be used
### as the prehistory for the continued process.
origT <- tail(imdepi$stgrid$stop, 1)
## extend the 'stgrid' by replicating the last block 'nm2add' times
## (i.e., holding "popdensity" constant)
stgridext <- local({
gLast <- subset(imdepi$stgrid, BLOCK == max(BLOCK))
gAdd <- gLast[rep(1:nrow(gLast), nm2add),]; rownames(gAdd) <- NULL
newstart <- seq(origT, by=30, length.out=nm2add)
newstop <- c(newstart[-1], max(newstart) + 30)
gAdd$start <- rep(newstart, each=nlevels(gAdd$tile))
gAdd$stop <- rep(newstop, each=nlevels(gAdd$tile))
rbind(imdepi$stgrid, gAdd, make.row.names = FALSE)[,-1]
})
## create an updated "epidataCS" with the time-extended 'stgrid'
imdepiext <- update(imdepi, stgrid = stgridext)
newT <- tail(imdepiext$stgrid$stop, 1)
## simulate beyond the original period
simsext <- simulate(imdepifit, nsim=nsim, seed=1, t0=origT, T=newT,
data=imdepiext, tiles=districtsD, simplify=TRUE)
## Aside to understand the note from checking events and tiles:
# marks(imdepi)["636",] # tile 09662 is attributed to this event, but:
# plot(districtsD[c("09678","09662"),], border=1:2, lwd=2, axes=TRUE)
# points(imdepi$events["636",])
## this mismatch is due to polygon simplification
## plot the observed and simulated event numbers over time
plot(imdepiext, breaks=c(unique(imdepi$stgrid$start),origT),
cumulative=list(maxat=330))
for (i in seq_along(simsext$eventsList))
plot(simsext[[i]], add=TRUE, legend.types=FALSE,
breaks=c(unique(simsext$stgrid$start),newT),
subset=!is.na(source), # have to exclude the events of the prehistory
cumulative=list(offset=c(table(imdepi$events$type)), maxat=330, axis=FALSE),
border=NA, density=0) # no histogram
abline(v=origT, lty=2, lwd=2)
} # }
```