Spurious and indirection correlations pairwise halla?

[andrewGhazi]

I believe in that instance they are accounting for additional covariates by first regressing them out using a mixed-effects model. Then HAllA was run on the matrices of residuals instead of the matrices of raw data.

So in your example, you’d run a mixed effects model to regress out the effect of the environment variable that you think might cause confounding.

Given how dataset-specific this modelling would need to be, HAllA doesn’t include the functionality to run the model and extract the residuals. You can see more discussion about this type of process in this thread:

Adjusting for covariates in HAllA

Dear all I would like to perform HAllA on a two datasets (both of which quantitative variables). However, I also have qualitative covariates that I would like to adjust for prior to HAllA. I read the manuscript for Lloyd-Price et al. 2019 and some other manuscripts out there, and it says that the dataset needs to first be “residualized” based on a linear mixed effects model from the differential abundance analysis, and the HAllA tutorial mentions that any covariates need to be regressed out usi…