Error reported by the user

[shbrief]

The error we found should be a fixable error in their relative abundance calculation. Essentially, in their code (and example analysis provided in the manuscript) they take in reads summed at the kingdom/phylum/class/order/genus/species levels for normalization. So in general the sum of the bacterial kingdom reads should be roughly equal to sum of the phylum reads (minus those that can't be mapped to phyla level), which should be equal to sum of class reads (minus those that can't be mapped to class level), etc. etc. However, when they calculate relative abundance they simply sum all of these values, so that if a bacteria is mapped to the species level it is counted 6 times. Example chart below showing the differences between the paper and what should be the correct values. This should primarily provide incorrect estimates of effect size differences, not which taxa are actually different (unless there is substantial/variable loss of mapping down the taxonomic tree).