Fixes Phase 1 of Issue #27

[Cateline]

Description

What kind of change(s) are included?

• Feature (adds or updates new capabilities)
• Bug fix (fixes an issue).
• Enhancement (adds functionality).
• Breaking change (these changes would cause existing functionality to not work as expected).

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  @jananiravi @epbrenner

[falquaddoomi]

Thanks for your contribution! I think the overarching issue that you're running into is that the code you've added to the R folder isn't in functions and, because of that, is getting executed any time the library is loaded.

The code you're adding also appears to be scripts, not library functions, so I'd consider restructuring your PR as follows:

• create a folder called case_studies, and one named CARD below that
• move CARD_data, Klebsiella CARD Filtering Code.R, Klebsiella CARD Filtering Code.R and Staphylococcus_aureus_DAP_sequences4.fasta into the new CARD folder
• remove CARD_AMR_Data_Integration.R (which appears to be a duplicate of Klebsiella CARD Filtering Code.R) and Staphylococcus_aureus_DAP.R from the R folder

You can at least submit your work at this point without it throwing off the automated checks.

If you'd like to go further and integrate your code into the package, I would do the following:

1. Review the existing functions in the R folder to see how you'd write a new one
2. Add a new file, say CARD_analyses.R to the R folder
3. Create one or more functions that encapsulate what your script's functionality (e.g., downloading a dataset, loading it into a dataset, and/or returning a filtered version of a datatable), being sure to remove the print statements that you were using for debugging
4. Generally, R packages shouldn't include library() calls, so you should either add #' @importFrom <package> <symbol1> <symbol2> (etc.) lines to your function's docstring, or use fully-qualified references, e.g. <library>::<method>() when calling a method from a specific library.

Hope that helps!

[falquaddoomi]

I'd suggest removing the changes to this file from your PR. You can do so via git checkout main -- MolEvolvR.Rproj to revert it to what it was before your PR, then add and commit that original version.

[falquaddoomi]

This file should likewise be removed from the PR, since it appears your scripts download it. You can run git rm --cached broadstreet-v3.3.0.tar.bz2 to remove it from the repo without removing your local copy of it.

[falquaddoomi]

This is likely what's causing that error you saw before about infinite recursion. Since the package is already being run by devtools::check(), running this within the package code is causing it to start a check within the check (and within that check, repeat ad infinitum...) You definitely don't need to call this within code that's part of the package.