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anadat:cs:exercises:cv6

PCoA, NMDS

  1. Run PCoA on Bray-Curtis distance matrix calculated on ln(x+1) transformed species data.hint
  2. Find the proportion of variance captured by the first two axes.
  3. Calculate species scores as averages of sites' scores weighted by species abundances. hint
  4. 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
  5. Get the stress of the resulting NMDS ordination. hint
  6. Plot Shepard diagram showing the relationship between original distances and distances preserved within the ordination. hint
anadat/cs/exercises/cv6.txt · Last modified: 2017/04/18 18:15 by vitek