Kris Sankaran

Hi @sundamiguel. I think it's worth clarifying the role of alpha: it’s the False Discovery Rate (FDR) control rate within a single family of hypothesis. An FDR control rate of...

Hi Yogesh, I think the point is that `abund_ranks` should be a matrix type (you can check this using `str(abund_ranks)`. In this case, you can get an ordination directly from...

Hi Yogesh, There is no "automatic" answer for this (it's probably better to build intuition about the influence of different choices, anyways), but you can refer to the last paragraph...

In some analysis, having zeros turn into nonzero values can be problematic. For example, this would cause problems for any procedures expecting some sort of zero-inflation. However, for the hierarchical...

Hi @chloelulu, this is a somewhat subtle transformation of the data. I think it's worth thinking through each step carefully. The first step is a rank-transformation on the abundance matrix....

Hi @Ninahuadiy. I think once we noticed the outliers in the figure, we looked those coordinates up in the original `out.wuf.log` object, ordering rows by their value on Axis 2,...

Mhm, each column is an RSV. But it's not actually hard to see which RSV dominates samples. For example, once you know sample `F15D165` is an outlier, you can identify...

Hm, the use for `select_ggplot` might not be entirely obvious -- did you brush over points and click "add points" before clicking done? Otherwise, it will print an empty data...

I think part of the issue is that if the installation fails, it fails silently, because of the `ignore.stdout = TRUE` and `ignore.stderr = TRUE` on line 44 of `updateR.R`:...

Hi @AndreaCirilloAC I just created a pull request. In my case printing the error message helped me update my system so that the terminal installation (and hence this package) worked....