names of parameters in deSolve_to_denim.Rmd

[choisy]

In the deSolve code on deSolve_to_denim.Rmd, the choice of rate and scale as parameters names is very unfortunate. Use names based on classical names of SIR such as lambda for the force of infection and gamma for the recovery rate.

[quingzz]

I have updated the S -> I transition to follow the classical formulation (beta for contact rate, beta*I/N is the time varying FOI)

For I -> R, I kept the erlang distributed infectious period to demonstrate the convenience when implementing LCT in denim. The gamma parameter in the classical SIR model isn't applicable here (which refers to the rate of the exponentially distributed infectious period) so I kept the shape, rate parameter name as is.

Please correct me if I misunderstood somewhere.