Helper function to construct specific objects

[guiblanchet]

I know some of the function has imbedded in them some code to obtained the right matrices to perform the analyses.

It would be great to write these bit of code into functions that can be used by other function. An example of this would be a getTraitMatrix function that could replace code on L58-59 of fitDMC.

[KevCaz]

I agree

Related to this, we should better distinguish functions that will be part of the API and functions that won't. We could do so by having the same prefix for functions that are included in the API, for instance aln_function1() aln_function2() and keep the camel Case style for functions that are not.

[guiblanchet]

No problem with that structure.

What are you referring to when you discuss about API ?

In my opinion, the main focus should be on implementing as many methods as possible and focus on other things after.

[KevCaz]

The functions the user will use = API vs the function behind the scene to make the code better structured!