campyDE: Campylobacteriosis and Absolute Humidity in Germany 2002-2011
In surveillance: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena

campyDE

R Documentation

Campylobacteriosis and Absolute Humidity in Germany 2002-2011

Description

Weekly number of reported campylobacteriosis cases in Germany, 2002-2011, together with the corresponding absolute humidity (in g/m^3) that week. The absolute humidity was computed according to the procedure by Dengler (1997) using the means of representative weather station data from the German Climate service.

Usage

data(campyDE)

Format

A data.frame containing the following columns

date: Date instance containing the Monday of the reporting week.
case: Number of reported cases that week.
state: Boolean indicating whether there is external knowledge about an outbreak that week
hum: Mean absolute humidity (in g/m^3) of that week as measured by a single representative weather station.
l1.hum-l5.hum: Lagged version (lagged by 1-5) of the hum covariate.
newyears: Boolean indicating whether the reporting week corresponds to the first two weeks of the year (TRUE) or not (FALSE). Note: The first week of a year is here defined as the first reporting week, which has its corresponding Monday within new year.
christmas: Boolean indicating whether the reporting week corresponds to the last two weeks of the year (TRUE) or not (FALSE). Note: This are the first two weeks before the newyears weeks.
O104period: Boolean indicating whether the reporting week corresponds to the W21-W30 period of increased gastroenteritis awareness during the O104:H4 STEC outbreak.

Source

The data on campylobacteriosis cases have been queried from the Survstat@RKI database of the German Robert Koch Institute (https://survstat.rki.de/).

Data for the computation of absolute humidity were obtained from the German Climate Service (Deutscher Wetterdienst), Climate data of Germany, available at https://www.dwd.de.

A complete data description and an analysis of the data can be found in Manitz and Höhle (2013).

References

Manitz, J. and Höhle, M. (2013): Bayesian outbreak detection algorithm for monitoring reported cases of campylobacteriosis in Germany. Biometrical Journal, 55(4), 509-526.

Examples

# Load the data
data("campyDE")

# O104 period is W21-W30 in 2011
stopifnot(all(campyDE$O104period == (
  (campyDE$date >= as.Date("2011-05-23")) &
  (campyDE$date < as.Date("2011-07-31"))
)))

# Make an sts object from the data.frame
cam.sts <- sts(epoch=campyDE$date, observed=campyDE$case, state=campyDE$state)

# Plot the result
plot(cam.sts)

surveillance documentation built on Oct. 2, 2024, 1:08 a.m.