• A preliminary choice of data transformation from the original counts to proportions was made, although the authors could have chosen to take logarithms, variance stabilizing transformations10 (here proportions replaced the original counts), choose between	log, rlog, subsample, prop, orig (5)
• Nine points were dropped from the study as they were considered outliers; of course the authors could have chosen to	.. leave out 0, 1, 2,..,9, + criteria (100)
• Certain taxa were filtered out as they were considered too rare or unlabeled. filter taxa	… remove rare taxa, ie threshold at 0.01%, 1%, 2%,… (10)
• A distance was chosen (Jensen-Shannon, JSD) to quantify similarities between samples. Distances	… 40 choices in vegan/phyloseq (40)
• An ordination method and number of coordinates has to be chosen. Ordination and axes	… MDS, NMDS, DCA, k=2,3,4,5.. (16)
• A clustering method and a number of clusters is chosen	… PAM, KNN, hclust … (16)
• The authors chose an underlying continuous variable, an alternative could have been a linear or curved latent variable or group of variables.	latent variable choices… (4)