Adding script to calculate daily EIP from temps
Fiddly changes to calculate_daily_eip.R
Added a comment
Refactored some parameter data structures

This commit does not change model output.  Six arrays have been replaced with
two vectors, and now we have a struct for time-varying parameters.  Removed
explicit reference to their being four serotypes.  Also replaced lots of i+1's
and i++'s with ++i's.