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