Code in Alpha.r was used to produce alpha-diversity results: Figure S7. Can also be applied to create Table S9.
Code in BetaDiversity.r was used to create Beta diversity ordination plots, Permanova, and multivariate analysis: Figure 4 Figure S8 Can also be applied to create Fig S11.
Code in NST2.r was used to create stochasticity figures and tables: Figure 3 Table S5
Code in Phylosymbiosis.r includes PACo analysis, LIPA, global measures of phylosymbiosis, and DPCoA plot: Figure 5A-C Table S6 Figure 5D Table S7 Table S8 Figure S10