Description Usage Format Details Source References See Also Examples

`imdepi`

contains data on the spatio-temporal location of 636
cases of invasive meningococcal disease (IMD) caused by the two most
common meningococcal finetypes in Germany, B:P1.7-2,4:F1-5 (of
serogroup B) and C:P1.5,2:F3-3 (of serogroup C).

1 | ```
data("imdepi")
``` |

`imdepi`

is an object of class
`"epidataCS"`

(a list with components `events`

,
`stgrid`

, `W`

and `qmatrix`

).

The `imdepi`

data is a simplified version of what has been
analyzed by Meyer et al. (2012). Simplification is with respect to the
temporal resolution of the `stgrid`

(see below) to be used in
`twinstim`

's endemic model component.
In what follows, we describe the elements `events`

,
`stgrid`

, `W`

, and `qmatrix`

of `imdepi`

in
greater detail.

`imdepi$events`

is a `"SpatialPointsDataFrame"`

object (ETRS89 projection, i.e. EPSG code 3035, with unit ‘km’)
containing 636 events, each with the following entries:

- time:
Time of the case occurrence measured in number of days since origin. Note that a U(0,1)-distributed random number has been subtracted from each of the original event times (days) to break ties (using

`untie(imdepi_tied, amount=list(t=1))`

).- tile:
Tile ID in the spatio-temporal grid (

`stgrid`

) of endemic covariates, where the event is contained in. This corresponds to one of the 413 districts of Germany.- type:
Event type, a factor with levels

`"B"`

and`"C"`

.- eps.t:
Maximum temporal interaction range for the event. Here set to 30 days.

- eps.s:
Maximum spatial interaction range for the event. Here set to 200 km.

- sex:
Sex of the case, i.e. a factor with levels

`"female"`

and`"male"`

. Note: for some cases this information is not available (`NA`

).- agegrp:
Factor giving the age group of the case, i.e. 0-2, 3-18 or >=19. Note: for one case this information is not available (

`NA`

).- BLOCK, start:
Block ID and start time (in days since origin) of the cell in the spatio-temporal endemic covariate grid, which the event belongs to.

- popdensity:
Population density (per square km) at the location of the event (corresponds to population density of the district where the event is located).

There are further auxiliary columns attached to the events' data
the names of which begin with a . (dot): These are created during
conversion to the `"epidataCS"`

class and are necessary for
fitting the data with `twinstim`

, see the description of the
`"epidataCS"`

-class.
With `coordinates(imdepi$events)`

one obtains the (x,y) locations
of the events.

The district identifier in `tile`

is indexed according to
the German official municipality key (
“Amtlicher Gemeindeschlüssel”). See
https://de.wikipedia.org/wiki/Amtlicher_Gemeindeschl%C3%BCssel
for details.

The data component `stgrid`

contains the spatio-temporal grid of
endemic covariate information. In addition to the usual bookkeeping
variables this includes:

- area:
Area of the district

`tile`

in square kilometers.- popdensity:
Population density (inhabitants per square kilometer) computed from DESTATIS (Federal Statistical Office) information (Date: 31.12.2008) on communities level (LAU2) aggregated to district level (NUTS3).

We have actually not included any time-dependent covariates here, we
just established this grid with a (reduced -> fast) temporal
resolution of *monthly* intervals so that we can model endemic
time trends and seasonality (in this discretized time).

The entry `W`

contains the observation window as a
`"SpatialPolygons"`

object, in this case the
boundaries of Germany. It was obtained as
`stateD <- rgeos::gUnaryUnion(districtsD)`

,
where `districtsD`

represents Germany's districts as at
2009-01-01, simplified by the “modified Visvalingam” algorithm
(level 6.6%) available at https://MapShaper.org (v. 0.1.17).
The objects `districtsD`

and `stateD`

are contained in
`system.file("shapes", "districtsD.RData", package="surveillance")`

.

The entry `qmatrix`

is a *2 x 2* identity matrix
indicating that no transmission between the two finetypes can occur.

IMD case reports: German Reference Centre for Meningococci at the Department of Hygiene and Microbiology, Julius-Maximilians-Universität Würzburg, Germany (https://www.hygiene.uni-wuerzburg.de/meningococcus/). Thanks to Dr. Johannes Elias and Prof. Dr. Ulrich Vogel for providing the data.

Shapefile of Germany's districts as at 2009-01-01: German Federal Agency for Cartography and Geodesy, Frankfurt am Main, Germany, https://gdz.bkg.bund.de/.

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

the data class `"epidataCS"`

, and function
`twinstim`

for model fitting.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 | ```
data("imdepi")
# Basic information
print(imdepi, n=5, digits=2)
# What is an epidataCS-object?
str(imdepi, max.level=4)
names(imdepi$events@data)
# => events data.frame has hidden columns
sapply(imdepi$events@data, class)
# marks and print methods ignore these auxiliary columns
# look at the B type only
imdepiB <- subset(imdepi, type == "B")
#<- subsetting applies to the 'events' component
imdepiB
# select only the last 10 events
tail(imdepi, n=10) # there is also a corresponding 'head' method
# Access event marks
str(marks(imdepi))
# there is an update-method which assures that the object remains valid
# when changing parameters like eps.s, eps.t or qmatrix
update(imdepi, eps.t = 20)
# Summary
s <- summary(imdepi)
s
str(s)
# Step function of number of infectives
plot(s$counter, xlab = "Time [days]",
ylab = "Number of infectious individuals",
main = "Time series of IMD assuming 30 days infectious period")
# distribution of number of potential sources of infection
opar <- par(mfrow=c(1,2), las=1)
for (type in c("B","C")) {
plot(100*prop.table(table(s$nSources[s$eventTypes==type])),
xlim=range(s$nSources), xlab = "Number of potential epidemic sources",
ylab = "Proportion of events [%]")
}
par(opar)
# a histogram of the number of events along time (using the
# plot-method for the epidataCS-class, see ?plot.epidataCS)
opar <- par(mfrow = c(2,1))
plot(imdepi, "time", subset = type == "B", main = "Finetype B")
plot(imdepi, "time", subset = type == "C", main = "Finetype C")
par(opar)
# Plot the spatial distribution of the events in W
plot(imdepi, "space", points.args = list(col=c("indianred", "darkblue")),
axes = TRUE, lwd = 2)
title(xlab = "x [km]", ylab = "y [km]")
## Not run:
# or manually (no legends, no account for tied locations)
plot(imdepi$W, lwd=2)
plot(imdepi$events, pch=c(3,4)[imdepi$events$type], cex=0.8,
col=c("indianred", "darkblue")[imdepi$events$type], add=TRUE)
## End(Not run)
## Not run:
# Show a dynamic illustration of the spatio-temporal dynamics of the
# spread during the first year of type B with a step size of 7 days
animate(imdepiB, interval=c(0,365), time.spacing=7, sleep=0.1)
## End(Not run)
``` |