Refactor and breakdown: ExtractCore

[jibarozzo]

I'm adding issues I work and encounter them. They are not super priorities unless stated other wise, like hindering the analysis itself.

Code Smells

The ExtractCore functions, as it stands, has many hard coded elements. For example, line 111 of core_microbiome_function.R contains magic numbers in a row count, hard coded for a specific dataset ("glbrc"). It should be refactored to dynamic count rows for applicability to other data sets, in this case the `filtered_phyloseq.rda" with all datasets from BRCs.

For now changing magic numbers for dynamic inputs can get this working for the complete dataset.
We can later improve this by breaking down the ExtractCore function into smaller functions, eliminating duplicate and competing code for better readability and reproducibility. For example, lines 90-127 contain duplicate code and hard coded elements. When does it consider the magic number and when does it consider the whole dataset? Maybe this logic can be handle in the function signature.

To-do

• Add dynamic handling of data input.
• Breakdown lines 90-127 into community_dissimilarity function and TEST.

I've created a GitHub project to keep track of issue and mark progress on the analysis.

@B-Kristy @adina @jaejinlee83 @fandemonium

[jibarozzo]

function_refactor branch created.