Function / object naming conventions

[andrechalom]

Currently, we have the functions time and history, which clash with stats::time and stats::history. We need to come up with better names to rename those functions and avoid namespace clashes.

Also, it is a good design practice to determine standard naming conventions for the functions and othe relevant objects in the package.

[piklprado]

Sure. I'll try to keep the new names as mnemonic and informative as time and history are. Maybe time_ellapsed and trajectories ?

[piklprado]

Also, we have to change the name of ls.m that can conflict with ls S3 methods.

[andrechalom]

I will hold this issue while waiting for the open PRs to be merged.

[andrechalom]

Changing the following:

• time() to elapsed_time() - avoids namespace clash
• history() to trajectories() - avoids namespace clash
• Interaction() to interaction_matrix() - lowercase; avoids namespace clash; also may become more self-explanatory
• ls.m() to ls_migration() - changed dot to underscore for standardization; also reduces namespace clashes with S3 methods; increased the function name in the hope that it will become more self-explanatory

We could change things like diagPlots() to diag_plots() - changed camelCase to underscores, as it is more readable. But I don't think that's necessary.

I'm leaving Init_Community and GillesComFromFile/GillesComToFile as uppercase because these are very special function in the way that they handles directly with the underlying constructor.

All of these changed already on master branch.

[andrechalom]

OK, can we close this?

[piklprado]

Ok! Can you merge into dev please?

[andrechalom]

You have already merged this changes on d090452