I struggled a little bit to get the output of est.R0() in a tidy format and ended up writing a very small wrapper.
Is this the plot we want here? Another option would be to have two rows on the plot and a column by region. The first row would be the observed data by region and the second row would be the Reff estimates. It's quite simple to generate with the patchwork package.
What should I use for the generation time? I used the example from R0 docs but it's probably not what we want.
There seems to be a dip in Reff after the first day. Is this a statistical artifact? If so, we should probably filter it out.
I struggled a little bit to get the output of
est.R0()in a tidy format and ended up writing a very small wrapper.