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.
speedyseq is so damn fast compared to
phyloseq
, and for anywhere that we usetax_glom
will have significant advantages, including in the beta diversity vignette. It would also be pretty cool to promotespeedyseq
, because not everyone knows about it, and I wish more people did!Could we make it a
Suggests
and replacelibrary(phyloseq)
withlibrary(speedyseq)
inbeta_diversity.Rmd
and anywhere else that usesphyloseq::tax_glom()
? If you load speedyseq first it also loads phyloseq, but you access speedyseq's versions of all functions by default.