NAs in philr output matrix

[NicolaiVe]

Hej hej,

I have a question. I ran the philr function on my phyloseq object:

OBJS1philr <- philr(x = as.matrix(otu_table(Data.c)), tree = rooted_tree,
part.weights = "enorm.x.gm.counts",
ilr.weights = "blw.sqrt",
pseudocount = 1,
abund_values = "counts")

and the output matrix contained quite a lot of NAs.

Why is that? Is there a way to change that? Or how do I handle the NAs afterwards, e.g. turning them into zeroes or a mean?

Kind regards,
Nicolai

[jsilve24]

Appologies for the delay.

I don't have enough information to answer this question. It is almost certaintly not related to PhILR but likely something specific with the Data.c or the rooted_tree you are passing in.