First, Maaslin2 is a really really wonderful tool!
I am running an analysis with one predictor of interest and 7 categorical covariates. I’ve run maaslin2 (lm analysis method, “AST” transformation, min prevalence and abundance thresholds to filter out rare features), and a warning message comes along with the output, saying “Warning message: In var(if (is.vector(x) || is.factor(x)) x else as.double(x), na.rm = na.rm) : Calling var(x) on a factor x is deprecated and will become an error.” what would be the possible causes?
Thank you for your feedback. This warning looks like it is letting us know that soon the way we phrased something in the source code will no longer work. I will add this to our development document for a patch in the next release. Thank you for sharing it with us. I do not believe that this will change anything about how MaAsLin is currently running… but if you want to share your data (or a minimally reproducible/blinded dataset) I am happy to take a closer look.