p_susceptibility implementation for final_size R

[pratikunterwegs]

Adding functionality to handle populations with non uniform distribution of susceptibilities in current finalsize function final_size in R.

This will add a p_susceptibility (or similar) argument to final_size.

End point is a function whose functionality is in line with the proposed final_size_cpp function whose underlying Cpp code already implements heterogenous susceptibility distributions across age groups.

[BlackEdder]

I have addressed some of the problems with the contact matrix in #26 , but we need further changes in the code.

The cpp function will need to accept an r0 here:

finalsize/R/final_size_cpp.R

Line 14 in f59f61a

final_size_cpp <- function(contact_matrix, demography,

Then

finalsize/R/final_size_cpp.R

Line 27 in f59f61a

contact_matrix <- contact_matrix / (max(Re(eigen(contact_matrix)$values)))

needs to change to

contact_matrix <- r0*contact_matrix / (max(Re(eigen(contact_matrix)$values)))

The current issue is that by rescaling the contact matrix you basically set r0 to 1, which results in a final size close to 0

[pratikunterwegs]

This issue is fixed by #42