Vít Syrovátka

PCoA, NMDS

Run PCoA on Bray-Curtis distance matrix calculated on ln(x+1) transformed species data.hint

Use function cmdscale(), check its help to make it return eigenvalues.
Find the proportion of variance captured by the first two axes.
Calculate species scores as averages of sites' scores weighted by species abundances. hint

Use function wascores().
Run NMDS on the same distance matrix, resulting in a two-dimensional ordination. Do not allow additional data autotransformation. Increase the number of random starts to 50. hint

Use function metaMDS() and check its help for arguments.
Get the stress of the resulting NMDS ordination. hint

Just print the result returned by metaMDS().
Plot Shepard diagram showing the relationship between original distances and distances preserved within the ordination. hint

Use function stressplot().