use speedyseq instead of phyloseq

[adw96]

speedyseq is so damn fast compared to phyloseq, and for anywhere that we use tax_glom will have significant advantages, including in the beta diversity vignette. It would also be pretty cool to promote speedyseq, because not everyone knows about it, and I wish more people did!

Could we make it a Suggests and replace library(phyloseq) with library(speedyseq) in beta_diversity.Rmd and anywhere else that uses phyloseq::tax_glom()? If you load speedyseq first it also loads phyloseq, but you access speedyseq's versions of all functions by default.

[svteichman]

Addressed in this pull request.