add Rt estimation function

[vpnagraj]

we have some scratch code to estimate the effective reproduction number:

https://github.com/signaturescience/focustools/blob/master/scratch/re-estimation.R

let's roll that into a function in the focustools package

[vpnagraj]

tabling this feature for now ... we can reopen down the line if we want to include something like this (most likely not until we sort out compartmental models #28 )