Reproducing FHMs "skattning av det momentana reproduktionstalet"
Estimating the reproduction number of an active pandemic can be tough. However, with simple available tools one can produce estimates that potentially aren't that far from the truth.
On this problem, as for active pandemics, formating the data and tune the models is usually the problem. In this short code sample, I aim to show how one can simply reproduce number similar to what the Public Health Agency Of Sweden has publiced here https://www.folkhalsomyndigheten.se/smittskydd-beredskap/utbrott/aktuella-utbrott/covid-19/statistik-och-analyser/analys-och-prognoser/
In short, this is the code needed to replicate their results.
config <- make_config(list(mean_si = 4.8,
std_si = 2.3))
method <- "parametric_si"
res <- estimate_R(df$incidence,
method=method,
config = config)
Which will give you
for the region of Uppsala.
See the full code under /R/ and the data is found in /data/ the
figures produced can be found under /fig/.
The noisy incidence creates poor estimates, what we can do to address this we can use (all are for Uppsala, one can change region in the code)
- rolling mean on the data
- uncertainty in the gamma distribution.
- both of the above
