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Visualizing sample similarities with nonmetric Multidimensional Scaling (nMDS)

b. a. a. b. b. a. c. c. c. Visualizing sample similarities with nonmetric Multidimensional Scaling (nMDS). Colin Bates. Visualizing similarities. clustering. samples. a. c. b. species. b. a. a. b. b. a. Sample similarities. c. c. c. ordination. b. a. a. b. b. a.

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Visualizing sample similarities with nonmetric Multidimensional Scaling (nMDS)

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  1. b a a b b a c c c Visualizing sample similarities with nonmetric Multidimensional Scaling (nMDS) Colin Bates

  2. Visualizing similarities clustering samples a c b species b a a b b a Sample similarities c c c ordination

  3. b a a b b a c c c ordination Why ordination? clustering Clustering dendrograms often don’t work well in ‘gradient’ situations. Ordination “maps” relationships between samples a c b

  4. Bay of Fundy seaweeds - Clustering similarity

  5. B of F seaweeds - nMDS ordination

  6. Nonmetric multidimensional scaling (nMDS) “the future of ordination is in nonmetric multidimensional scaling” – McCune & Grace, 2002 Nonmetric: no axes Multidimensional: represents relationships between multiple variables in two or three dimensions Scaling: the ratio between reality and representation

  7. How does nMDS work? nMDS uses the RANK ORDER of similarity relationships between samples: A1 is closer to A2 than it is to A3

  8. How does nMDS work? Then, nMDS tries to place points in 2 (or 3) dimensional space to represent this ranked order: A3 A1 is closer to A2 than it is to A3 A1 A2

  9. A2 A1 A3 How does nMDS work? Then, nMDS tries to place points in 2 (or 3) dimensional space to represent this ranked order: A1 is closer to A2 than it is to A3

  10. BIOL 404 mite communities A B C wet dry Moisture gradient

  11. BIOL 404 mite communities

  12. BIOL 404 mite communities

  13. BIOL 404 mite communities

  14. BIOL 404 mite communities Abundance of X87

  15. BIOL 404 mite communities - nMDS is a good exploratory tool

  16. BIOL 404 mite communities - nMDS is a good exploratory tool

  17. How accurate is the nMDS map? - Sometimes the nMDS can’t represent all relationship accurately - this is reflected by a high STRESS value

  18. How accurate is the nMDS map? - Sometimes the nMDS can’t represent all relationship accurately - this is reflected by a high STRESS value If Stress Value = 0.0 : perfect map 0.1 : decent map 0.2 : ok map 0.3 : don’t bother . . . . . . . . . . . . Distance in sim. matrix . . . . . . . . Distance on nMDS

  19. nMDS notes • nMDS is simple in concept • nMDS maps can be rotated, scaled or inverted • any similarity measure can be used for underlying matrix • when stress is high, nMDS and clustering should be used together

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