Restructure everything to a package

[lboel]

Here I will lay out the steps to convert the current code base to a relatively clean package structure:
First Version:

• Just move scripts/script<1-3> to functions in /R folder and make the runner script accept something like: a4d::step_1,a4d::step_2,a4d::step_3
• change our workflow to call devtools::install() instead of load_all()

[lboel]

@pmayd

[pmayd]

@lboel but we have to replace all function calls with a4d::, have we not? Like the fix functions etc. So basically everywhere where we were able to call a function from the /R folder because it was available thanks to load_all should now be called with a4d:: in front of it, or not? Or is this not necessary because we are inside the package and this is only relevant like in the main script where I want to call a function from outside?

[pmayd]

@lboel what do you think about changing the main functions into handling a single file instead of inside getting a list of files?
I think having three main steps as a pipeline for a SINGLE file will simplify the code and we can more easily test a single file with the pipeline by just executing this function.
This would mean to refactor at least the two first scripts to accept a file and move the list.files functionality outside and iterate over the list from outside. This is also in preparation of parallelising the loops more easily as we can directly use parallel loop versions...

I guess this comment is not really helpful after all as I think we need to do this anyway and this was the idea from the beginning but yeahg...

[pmayd]

Decided to put this on hold for now in favor of more high priority issues

• have to fix log problems first before going forward with this