R scripts File Description composition_data_analysis.R Generates Aitchison, PhILR heirarchical cluster dendrogram, ordination plots. Upset plot. Taxonomy barchart ordered by metadata category. Adonis and phylofactor analysis dada2_processing.3.6.1.R Dada2 pipeline modified to work on lab computer (R v3.6.1, QIIME2) deseq.R Deseq differential abundance analysis using 16S data diversityAnalyses.R Aitchison distance, Bray Curtis dissimilarity, weighted UniFrac distance ordination plots interaction_network.R Generates microbial interaction network using output from DADA2 random_forest.R Random forest classification analysis for microbiome data