This repository contains our R code for gut microbiome and FA analysis. The file microbiomefa.Rmd is the main analysis while different helper functions are defined in separate R files.
The code calculates
- cross-sectional microbial diversity (alpha and beta) at species level
- draws cross-sectional PCoA plots at species level
- checks cross-sectional associations between top bacterial genera and FA
- Cox models for participants that don't have FA at baseline
- associations between top genera and FA
- associations between baseline PCA-axes and FA
- associations between baseline alpha diversity and FA