Interesting, and timely, article on using R to analyse COVID-19 incidence data collated by John Hopkins University.
It makes use of two epidemiology packages.
earlyRfor estimation of infectiousness, as measured by the reproduction number (R), in the early stages of an outbreak.EpiEstimfor estimating the time varying instantaneous reproduction number during epidemics
These packages, and many more, are part of the R Epidemics Consortium (RECON). They
[…] gather experts in data science, modelling methodology, public health, and software development to create the next generation of analytics tools for informing the response to disease outbreaks, health emergencies and humanitarian crises, using the R software and other free, open-source resources.
