ancombc2 with pairwise comparisons of more than 3 groups

[NThie]

Hello! I think I have run into a problem with the ancombc2() function, because it seems like the pairwise comparison can only take 3 levels.

I am trying to run the following code, in which AIV has 2 levels (pos/neg) and locs has 4 levels (loc1/loc2/loc3/loc4):

output <- ancombc2(data = data, assay_name = "counts", tax_level = "Phylum",
                 fix_formula = "AIV_inf + locs", rand_formula = NULL,
                 p_adj_method = "bonferroni", pseudo = 1, pseudo_sens = TRUE,
                 prv_cut = 0.10, lib_cut = 1000, s0_perc = 0.05,
                 group = "locs", struc_zero = TRUE, neg_lb = FALSE,
                 alpha = 0.01, n_cl = 1, verbose = TRUE,
                 global = TRUE, pairwise = TRUE, dunnet = TRUE, trend = FALSE,
                 iter_control = list(tol = 1e-5, max_iter = 20, verbose = FALSE),
                 em_control = list(tol = 1e-5, max_iter = 100),
                 lme_control = lme4::lmerControl(), 
                 mdfdr_control = list(fwer_ctrl_method = "bonferroni", B = 100), 
                 trend_control = NULL)

But this gives me the following error message:

Error in names(y) <- c(colnames(x), combn_name) : 
  'names' attribute [6] must be the same length as the vector [4]

However, if I run the same code with only 3 levels in "locs" (loc1/loc2/loc3) the function does work properly and gives me all the expected results. So it does seem like it cannot take more than 3 levels - does that make sense or is there any way that I can adjust this in the function?

Thank you!

[NThie]

This question was already answered in issue #113, the same solution worked for me :)