I am trying to run a multivariate analysis of variance test on a small set of microbial community samples. I have tried using anosim, manova, as well as the adonis functions from the vegan package and I keep coming up against similar errors of "missing values if na.rm=FALSE. I'm not sure how to resolve this since not every OTU is represented in every sample. Any tips/resources on how to format my data set before running these tests/ or to bypass this issue? I am a beginner in R and I am pretty lost.
I tried manova, anosim and adonis/adonis2 from the vegan package. My data has four categorical environmental factors as well as ~200 domain level OTUs per sample. I am hoping to run multivariate analysis between samples, as well as a paired multivariate analysis relative to one of my environmental variables.
