Since the peaks of the epidemic happen in winter, near the transition between calendar years, we define the reference period for the annual incidence from August 1st of year /N/ to August 1st of year /N+1/. We label this period as year /N+1/ because the peak is always located in year /N+1/. The very low incidence in summer ensures that the arbitrariness of the choice of reference period has no impact on our conclusions.
This R function computes the annual incidence as defined above:
#+BEGIN_SRC R :results silent :exports both
...
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@@ -241,4 +244,4 @@ Finally, a histogram clearly shows the few very strong epidemics, which affect a
#+BEGIN_SRC R :results output graphics :file annual-inc-hist.png :exports both
hist(annnual_inc$incidence, breaks=10, xlab="Annual incidence", ylab="Number of observations", main="")