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PRIMER v6

PRIMER v6. Non-metric Multidimensional Analysis Analysis of Similarities Similarity Percentages. Non-Metric Multidimensional Analysis (NMDS). used for visualization of similarities or dissimilarities in data. map of samples in 2D or 3D. NMDS.

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PRIMER v6

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  1. PRIMER v6 Non-metric Multidimensional AnalysisAnalysis of SimilaritiesSimilarity Percentages

  2. Non-Metric Multidimensional Analysis(NMDS) • used for visualization of similarities or dissimilarities in data • map of samples in 2D or 3D

  3. NMDS • Distances between sample points represent dissimilarity between communities • Requires no/few assumptions • Complex algorithm, but simple to interpret 3 1 2

  4. NMDS - steps • Data entry (& transformations) -type in raw data -import from Excel -import from previous analysis

  5. NMDS - steps 2. Similarity or dissimilarity matrix - Bray-Curtis dissimilarity; distance

  6. NMDS - steps • 3. Perform non-parametric regression -Shepard diagram

  7. NMDS - steps 4. Measure goodness of fit (calculate stress = distances of points in plot from regression line) jkdjk-djk2/jkd2jk)

  8. NMDS - steps 5. Perturb the configuration – in direction of decreasing stress 6. Repeat until no further decrease in stress (global minimum vs. local minimum)

  9. NMDS - notes • Stress should low: < 0.05 excellent < 0.1 good < 0.2 should be checked < 0.3 near random • Usually lower stress with higher dimensionality

  10. NMDS - notes • Shepard diagram – outliers ** no absolute scales, no units ** only relative distance apart is meaningful

  11. ANALYSIS OF SIMILARITY(ANOSIM) • approximate analog of ANOVA tests • Null hypo. = no assemblage differences

  12. ANOSIM • Multiple options: - one-way layout - two-way crossed layout - two way crossed (no replicates) - two-way nested

  13. ANOSIM - steps • Compute R-stat • Re-compute R under different configurations of sample labels • Calculate significance level

  14. ANOSIM - notes • Operates on resemblance matrix • Minimal assumptions

  15. SIMILIRITY PERCENTAGES(SIMPER) • After differences are shown, move on to interpretation of differences • Compares contributions of species to differences between communities (samples) • Calculates percent contributions

  16. SIMPER

  17. PRIMER EXAMPLE COMMUNITY STRUCTURE OF ROCKY INTERTIDAL SHORES FACTORS: • Shore (Tor Bay vs. Sea Shore) • Elevation (high vs. low)

  18. QUESTIONS?

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