Estimating R_t for Covid-19 in Madagascar

Here we estimate the time varying effective reproductive number of R_t for Covid-19 in Madagascar.

Methods

We use the methods described in here, using the R packages epiNow, epiSoon, and [epiEstim](), code available here.

The pipeline for running national and regional Rt estimates is adapted from here

There are a number of limitations and uncertainties in these methods and in estimating R_t, many of which are reviewed here.