Build ModelContext constructur, revamp includes
Change model context to have ownership of the data objects' memory.
Work on using new methods
Change InitData to manage it's own memory
Start using and testing the model context framework
Move covariate matrix to model context
Write, integrate, and test basic DistanceMatrix functionality
Stub out S,E,I,R calculation methods
Add implementation for calculateS_CPU to ModelContext
Add temporary testing code to help with debugging
more testing code and a bug fix in R init function
Re-align S calculation to correspond to current R work. That is, Sostar_i is drawn from S_i, rather than S_{i-1}
Push compartment calculation to generic function, implement CPU version for S, E, I and R
Add eta functions for combined time varying and stationary covariate vector arguments
fix eta calculation, add to init
Apply eta fix to three parameter method
Add an empty container to model context class on populate for calculation purposes
Implement (but not yet test) the calculateP_SE_CPU function for model context.
Wire up full conditionals to their data sources, add in a reference to the parent model context so that full conditional sampling functions can call the requisite calculation functons on model context.
Rip out the dependency on the FullConditional superclass, becasue it is breaking everything, and I don't have internet to figure out why.