2.2.3. Diversity computation
Diversity computations were carried out with the R vegan package (version 2.5-5) (Oksanen et al., 2019). Shannon diversity index was calculated with the diversity function. The richness was calculated from rarefied counts (rarefy function, random subsamples of the size of the sample with the lowest number of reads). For the computation of inter-sample diversity (beta-diversity), the matrices were generated from the rarefied abundances.
If the “Bray-Curtis dissimilarity ” option is selected on the query page, the abundances are normalized using the Hellingermethod from the decostand function and a dissimilarity matrix is produced with the vegdist function.
For the ”Jaccard index ” option, the abundance matrix is transformed into a presence/absence matrix (0 and 1). The distance matrix is calculated with the vegdist function using the Jaccard option.
Based on these matrices, a nMDS is performed with the metaMDSfunction. The stress value shown on the graph indicates how similar the distances between samples in the ordination space are to the original distances. The closer the stress value is to 0, the more similar the distances are.
The “With environmental vectors ” button plots an additional nMDS graphic with projections of variable vectors. The script uses theenvfit function to fit environmental vectors or factors onto an ordination. The data projections onto vectors have a maximum correlation with corresponding environmental variables and the factors show the averages of factor levels. The variables with a percentage of missing data higher than 15 are removed.