Cleaning up the repository

[AaronGullickson]

I would like to clean up some stuff in the repository in the interests of reproducibility and clarity.

• Delete everything not being used right now. There is no need to keep old scripts lying around. They will still be back in the commit history so nothing is lost. Deleting would include:
  • all of the old scripts
  • the entire figures_tables directory
  • all the data that we are not actually using
• I don't quite understand where the dataset we are using is coming from. I think the original data are from here, but these don't include an RData file that I can see. If there was additional processing to get from their data to the one we load in then it should be tracked in the project, or the provenance of the RData file should be properly documented.
• I would like to split the current analysis file into an organize_data and analysis script just to keep those two separate parts of the workflow distinct.
• rename scripts "analysis"

[AaronGullickson]

Oh forgot one:

• Add a check_packages.R to do proper package dependency management.

[AaronGullickson]

This is now complete.