-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)
-it adds tests for contrastsTest() to increase code coverage
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) -it adds tests for
contrastsTest()to increase code coverage