Table of Contents

• Citation
• Summary
  • Introduction
  • New Statistical Methods in P8
  • New Tools & Utilities in P8
• 1. Expanded summary statistics
  • 1.1 Expansion from P7 to P8
  • 1.2 Definitions of statistics
  • 1.3 Biotic data: summary stats
  • 1.4 Split summary stats results by groups
  • 1.5 Environmental data: summary stats
• 2. Empirical distributions
  • 2.1 What is an empirical distribution?
  • 2.2 Example: Empirical distributions of oyster sizes
• 3. Dot plots and Violin plots
  • 3.1 Plots of empirical densities
  • 3.2 Example: Dotplot of oyster sizes
  • 3.3 Example: Violin plot of kelp holdfast volumes
• 4. Univariate non-parametric methods
  • 4.1 Wilcoxon signed-rank test
  • 4.2 Example: Plankton hauls
  • 4.3 Mann-Whitney U test
  • 4.4 Example: Snapper in marine reserves
  • 4.5 Kruskal-Wallis test
  • 4.6 Example: A bivalve species from Ekofisk
  • 4.7 Kolmogorov-Smirnov test
  • 4.8 Example: Sizes of oysters
  • 4.9 Test of Association
  • 4.10 Example: Ekofisk diversity
  • 4.11 Example: Associations between species
• 5. New PERMANOVA Design file
  • Overview of new 'Design' options and tools
• 6. Allow heterogeneous dispersions in PERMANOVA
  • 6.1 Overview - Allow heterogeneity
  • 6.2 ANOVA in a nutshell
  • 6.3 The Behrens-Fisher problem (BFP)
  • 6.4 Multivariate Behrens-Fisher problem
  • 6.5 Solutions to the multivariate BFP
  • 6.6 Example: one-way PERMANOVA allowing heterogeneity
  • 6.7 Heterogeneity in more complex designs
  • 6.8 Example: two-way crossed PERMANOVA allowing heterogeneity
• 7. Finite factors
  • 7.1 Overview - Finite factors
  • 7.2 Dichotomy: fixed vs random factors
  • 7.3 Not a dichotomy: a progression from fixed to random
  • 7.4 Example: environmental impact on molluscs
  • 7.5 Broader implications for detecting impact
• 8. Specifying Subject/Whole-plot error in PERMANOVA
  • 8.1 Designs lacking replication
  • 8.2 Example: Split-plot - Woodstock vegetation
  • 8.3 Example: Repeated measures - Victorian avifauna
• 9. Group covariates
  • 9.1 Why group covariables together?
  • 9.2 Periodic and cyclical models
  • 9.3 Example: Annual monthly cycles - B.C. macroalgae
• 10. Centroid plots
  • 10.1 Ordinations for multi-factor designs
  • 10.2 Main effects plot
  • 10.3 Interaction plot
  • 10.4 Example: NZ fish assemblages
• 11. Residual distances
  • 11.1 What are 'residual' distances?
  • 11.2 Example: Plankton (revisited)
• 12. Control charts
  • 12.1 Overview - Control charts
  • 12.2 Classical univariate control chart
  • 12.3 Classical multivariate control chart
  • 12.4 Bivariate normal example: NZ fish
  • 12.5 Dissimilarity-based multivariate control chart
  • 12.6 Additional notes on implementing control charts
  • 12.7 Example: Birds from Grand Forks
• 13. New standardisation options
  • 13.1 Overview
  • 13.2 Analysing cumulative standardised data
  • 13.3 Example: Mussel sizes in the Gulf of Alaska
  • 13.4 Example: Gulf of Maine invertebrates - functional resemblance
• 14. Create ordered groups
  • 14.1 Overview
  • 14.2 Example: NE Pacific groundfish vs depth
• 15. Other new tools & utilities
  • 15.1 New default colour palette
  • 15.2 New selection options
  • 15.3 Re-name levels of a factor (or indicator)
  • 15.4 Add customised values/labels to graphical axes
  • 15.5 Split data sheet by factor/indicator
  • 15.6 Line plots for samples
  • 15.7 Output group-level stats from dispersion (or variability) weighting
  • 15.8 Output diagnostic plots from CAP
  • 15.9 New diagnostics for PCA/PCO plots
• 16. Means plots
  • 16.1 A plot of means with error bars
  • 16.2 Example: Fal biota (one-way case)
  • 16.3 Example: Okura macrofauna (two-way nested case)
  • 16.4 Example: Leschenault fish (two-way crossed case)
  • 16.5 Example: New Zealand snapper (three-way case)
• References