Turn phyloseq from an Imports to a Suggests

[svteichman]

This pull request does several things:

-it adds new data, specifically the sample data, otu tables, and in some cases taxonomy tables, that make up phyloseq objects used for tests and the vignette
-it removes all phyloseq objects from the data folder of the package
-it updates all examples so that they run without phyloseq and without phyloseq data objects (for bbdml(), differentialTest(), and contrastsTest(), there are examples using phyloseq wrapped in \donotrun{} tags)
-it takes all tests that use phyloseq and puts them into a single testing file, where the phyloseq objects are created from the dataframes stored in the package
-it creates a new vignette that doesn't use phyloseq (with most of the same analyses as the original vignette that does use phyloseq)

[codecov-commenter]

Codecov Report

Attention: 16 lines in your changes are missing coverage. Please review.

Comparison is base (779de75) 94.12% compared to head (cfc6ba6) 93.36%.

❗ Current head cfc6ba6 differs from pull request most recent head cc47207. Consider uploading reports for the commit cc47207 to get more accurate results

Files	Patch %	Lines
R/contrastsTest.R	35.71%	9 Missing ⚠️
R/differentialTest.R	87.50%	3 Missing ⚠️
R/clean_taxa_names.R	85.71%	1 Missing ⚠️
R/convert_phylo.R	87.50%	1 Missing ⚠️
R/otu_to_taxonomy.R	85.71%	1 Missing ⚠️
R/warn_phyloseq.R	0.00%	1 Missing ⚠️

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Additional details and impacted files

@@            Coverage Diff             @@
##             main     #171      +/-   ##
==========================================
- Coverage   94.12%   93.36%   -0.77%     
==========================================
  Files          34       35       +1     
  Lines        1158     1176      +18     
==========================================
+ Hits         1090     1098       +8     
- Misses         68       78      +10     

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