Refactoring the code

[kkdey]

1. We have a working code for Issue 1 and Issue 3 models and they seem to be working. However it is important to check if the code can be refactored to gain computation efficiency.
2. We aim to vectorize and parallelize the code as much as possible
3. We also plan to fix the dimensionality issue between the simulated allele freq matrix and the allele freq matrix inside the main code. Right now we are doing f_known = t(freq_mat)...We want to change it so that freq_mat and f_known have same dimensions
4. Write comments in the code...for easier handling in future.