Hi,
Following the recommendations in the doc for PERMANOVA using aitchison distances (option 2):
pass an object with untransformed (or 'identity' transformed) taxa to the data argument of dist_calc() and specify dist = "aitchison".
is it ok to subset the resulting psExtra object, i-e remove certain low abundance taxa, before running dist_permanova ? I thought it would, but I realise that this procedure doesnt rcclr transform the data. I thought aitchison distance calculations were based on log-ratio transformed compositions, so I'm a bit confused. I was counting on subcompositional coherence to subset, but my (very basic) understanding of the underlying maths of compositional data may be causing my confusion.
Hi, Following the recommendations in the doc for PERMANOVA using aitchison distances (option 2):
pass an object with untransformed (or 'identity' transformed) taxa to the data argument of dist_calc() and specify dist = "aitchison".is it ok to subset the resulting psExtra object, i-e remove certain low abundance taxa, before running dist_permanova ? I thought it would, but I realise that this procedure doesnt rcclr transform the data. I thought aitchison distance calculations were based on log-ratio transformed compositions, so I'm a bit confused. I was counting on subcompositional coherence to subset, but my (very basic) understanding of the underlying maths of compositional data may be causing my confusion.
Looking forward to your input