Chapter 12: Causality - community experiments in the field and laboratory

12.1 Introduction

In Chapter 11 we have seen how both the univariate and multivariate community attributes can be c...

12.2 `Natural experiments’

It is doubtful whether so called natural experiments deserve to be called ‘experiments’ at all, a...

12.3 Field experiments

Field manipulative experiments include, for example, caging experiments to exclude or include pre...

12.4 Laboratory experiments

More or less natural communities of some components of the biota can be maintained in laboratory ...

0.1 Introduction

0.2 Acknowledgements

0.3 Citing this book

1.1 Introduction

1.2 Univariate techniques

1.3 Example: Frierfjord macrofauna

1.4 Distributional techniques

1.5 Example: Loch Linnhe macrofauna

1.6 Example: Garroch Head macrofauna

1.7 Multivariate techniques

1.8 Example: Nutrient enrichment experiment, Solbergstrand

1.9 Summary

2.1 Similarity for quantitative data matrices

2.2 Example: Loch Linnhe macrofauna

2.3 Presence/absence data

2.4 Species similarities

2.5 Dissimilarity coefficients

2.6 More on resemblance measures

3.1 Cluster analysis

3.2 Hierarchical agglomerative clustering

3.3 Example: Bristol Channel zooplankton

3.4 Recommendations

3.5 Similarity profiles (SIMPROF)

3.6 Binary divisive clustering

3.7 k-R clustering (non-hierarchical)

4.1 Ordinations

4.2 Principal components analysis

4.3 Example: Garroch Head macrofauna

4.4 PCA for environmental data

4.5 Example: Dosing experiment, Solbergstrand mesocosm

5.1 Other ordination methods

5.2 Non-metric multidimensional scaling (MDS)

5.3 Diagnostics: Adequacy of MDS representation

5.4 EXAMPLE: Dosing experiment, Solbergstrand

5.5 Example: Celtic Sea zooplankton

5.6 Example: Amoco-Cadiz oil spill, Morlaix

5.7 MDS strengths and weaknesses

5.8 Further nMDS/mMDS developments

5.9 Example: Okura estuary macrofauna

5.10 Example: Messolongi lagoon diatoms

5.11 Recommendations

6.1 Univariate tests and multivariate tests

6.2 ANOSIM for the one-way layout

6.3 Example: Frierfjord macrofauna

6.4 Example: Indonesian reef-corals

6.5 ANOSIM for two-way layouts

6.6 Example: Clyde nematodes (2-way nested case)

6.7 Example: Eaglehawk Neck meiofauna (two-way crossed case)

6.8 Example: Mesocosm experiment (two-way crossed case with no replication)

6.9 Example: Exe nematodes (no replication and missing data)

6.10 ANOSIM for ordered factors

6.11 Example: Ekofisk oil-field macrofauna

6.12 Two-way ordered ANOSIM designs

6.13 Example: Phuket coral-reef time series

6.14 Three-way ANOSIM designs

6.15 Example: King Wrasse fish diets, WA

6.16 Example: NZ kelp holdfast macrofauna

6.17 Example: Tees Bay macrofauna

6.18 Recommendations

7.1 Species clustering

7.2 Type 2 and type 3 SIMPROF tests

7.3 Example: Amoco-Cadiz oil spill

7.4 Shade plots

7.5 Example: Bristol Channel zooplankton

7.6 Example: Garroch Head macrofauna

7.7 Example: Ekofisk oil-field macrofauna

7.8 Species contributions to sample (dis)similarities – SIMPER

7.9 Example: Tasmanian meiofauna

7.10 Bubble plots (plus examples)

8.1 Univariate measures

8.2 Graphical/distributional plots

8.3 Examples: Garroch Head and Ekofisk macrofauna

8.4 Examples: Loch Linnhe and Garroch Head macrofauna

8.5 Multivariate tools used on univariate data

8.6 Example: Plymouth particle-size data

8.7 Multiple diversity indices

9.1 Introduction

9.2 Univariate case

9.3 Multivariate case

9.4 Recommendations