Inconsistency in ancombc2 help regarding argument pseudo #326
Description
When reading the help sheet of the function ancombc2, in Usage, you can see that it is written "pseudo = 0", meaning this is the default option. Regardless, in Arguments section, it is explained that the default value for pseudo is 1. Is this an error? In any case, I have made tests and it seems that the working value when you omit this argument is pseudo = 0. If I am right, maybe this could be corrected in future versions for the tool improvement.
Moreover, I don't understand why the method can be performed without adding pseudocounts (pseudo = 0). In the same argument help of pseudo, it is stated that pseudo argument is " a small positive value added to all counts before log transformation to avoid numerical issues caused by log(0)". But, when pseudo = 0, there is no numerical issues despite having log(0)!!! And I have checked that there are zeroes in my microbiome data.
Additionally, results vary when using pseudo = 0 and pseudo = 1. In this case, why does it differ? Which option is better?
Thank in advance.