Open ffinger opened 4 years ago
Yes, definitely agreed! This is what I am currently using - quasi-Poisson actually. I was not aware of EpiNow .. there is some duplication there, and I am not sure how to handle this going forward. incidence
should be about data handling and plots really, and reforms we discussed before were aiming at moving fitting to a separate package.
yes, if there is overdispersion quasipoisson or negative binomial regression would be best.
Related issue I just posted: https://github.com/epiforecasts/EpiNow/issues/75
The way the exponential growth rate is estimated here currently (in
fit()
) is to use a log-linear model (linear model similar tolm(log(incidence) ~ date)
. For the log to work you need to remove the 0s or replace them with a small positive value.A better way to estimate the growth rate would be to use a Poisson glm of the incident cases (
glm(incidence ~ date, family = poisson)
or similar). In addition to the more appropriate error model for count data this can handle 0s in the data natively.Here are some references: https://besjournals.onlinelibrary.wiley.com/doi/10.1111/j.2041-210X.2010.00021.x https://bmcmedinformdecismak.biomedcentral.com/articles/10.1186/1472-6947-12-147
And here is how this is done in the R0 package, where you can chose between poisson and log-linear models, with a default to poisson (https://github.com/cran/R0/blob/master/R/est.R0.EG.R):