Give messages when samples or taxa are dropped

mikemc / speedyseq

Speedy versions of phyloseq functions

https://mikemc.github.io/speedyseq/

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Give messages when samples or taxa are dropped #36

Open mikemc opened 4 years ago

mikemc commented 4 years ago

Examples of cases where it seems worth it to message() the user when samples or taxa are dropped include

Overwriting sample data with sample_data(ps) <- can silently drop samples
Similar for tax_table(), otu_table(), etc
tax_glom() with default params will drop taxa with bad_empty value at that rank

mikemc commented 4 years ago

Another case is when phyloseq() is called - currently at error is given only if no samples or taxa match. However, to improve this and some of the cases above would require rewriting core parts of phyloseq.