Quality Control -- Report Making Function

[kweav]

Description

This pull request is for issue #3, functionalizing the steps of QC.

Type of change

• Bug fix (non-breaking change which fixes an issue) -- there were a few bugs that have been fixed in setting up data
• New feature (non-breaking change which adds functionality) -- the QC steps are functionalized, producing all of the plots and tables of the original code. These still need to be output in a produced report.
• This change requires a documentation update -- each step of the QC is its own function and those headers as well as descriptions in the getting_started.Rmd vignette of loading data and running qc need fleshed out further.

How Has This Been Tested?

The run_qc() function was added to the getting_started.Rmd vignette and ran without error. The filter was saved in and accessible from the gimap_dataset variable.

Checklist:

While I have performed a self-review of my code, and commented it, more comments and additions to the documentation are necessary. Tests are also necessary

[cansavvy]

This is a good amount of code for one PR. How about we work on getting this merged and don't worry about the report Rmd until a next PR? You have it well set up for that!

Looks very cool! Let me know when you are ready for me to help/review!

[cansavvy]

@kweav Thanks for doing all this excellent work! I have some ideas and thoughts here. Happy to talk through this in a meeting if you'd like, or if you want me to commit some changes myself I can do that too. Whatever you prefer!

But excellent job infusing the science in the code and being super thoughtful about this! Really appreciate how much you've been digging in here!

Now that you have a basis of what's going on here my comments are just about polishing things a bit to the next stages! Really excited about this!

[kweav]

Thanks for the feedback -- I think I added responses to everything.

[kweav]

I've made several additions and edits to the code in order to incorporate most of this feedback. I've also verified that the code runs without error. Could we review these changes, merge this pull request, and open another for next steps?

[cansavvy]

I thought I asked this somewhere but can't find it. Did we get to the bottom of whether this needs to be given as a list like this? I generally like simplifying the structures we are asking users to supply for arguments so it is more easy for them supply the argument.

[cansavvy]

This is passing checks and although we need to do some more iterative work on it, I think this is good enough for us to merge and put this behind us. I will file issues on what we need to iteratively work on from here.

[cansavvy]

Let's merge it!