Closed colinbrislawn closed 1 year ago
unused arguments (formula = formula, tol = tol, max_iter = max_iter, conserve = conserve)
formula ->fix_formula
tol and max_iter ->em_control = list(tol = tol, max_iter = max_iter)
conserve is not used in ancombc2(). Looks like this is built into the new function?
' @param conserve logical. whether to use a conservative variance estimator for
' the test statistic. It is recommended if the sample size is small and/or
' the number of differentially abundant taxa is believed to be large.
' Default is FALSE.
Tests still use the old ancombc() function, which I'm keeping for now to see if new results match old results.
Error in
colnames<-
(*tmp*
, value = "id") : attempt to set 'colnames' on an object with less than two dimensions
Looks like fit
object returned by ancombc2() may be different.
Hey @colinbrislawn, yeah we realized pretty early that ancombc2 was not a drop-in replacement for ancombc, so we just finished work on adding ancombc and still need to do some exploration here for ancombc2.
cc @lizgehret
@colinbrislawn yeah echoing what @ebolyen mentioned above - these two methods are actually quite different. From the README in Huang's ANCOMBC repository, it looks like ANCOM-BC2 has a manuscript in preparation, so we had discussed waiting until there was a publication before adding this new method in.
Hey @colinbrislawn are you okay if we close this one out? Once a paper is published for ancombc2, we'll definitely look into adding that as another method in composition, but I don't know if this PR makes sense to keep open since it's not just a drag and drop replacement for ancombc.
Yes, I agree that a holistic PR is needed once we are ready.
WIP, do not merge.
Simple change to method name to address warning.
This looks like an extension/improvement to
ancombc
function, but let's see if tests pass. https://github.com/FrederickHuangLin/ANCOMBC/blob/devel/R/ancombc2.R