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3.4 How does adonis2 do it?
The adonis2 function (in the vegan package in R) will provide a partitioning of the total sum of ...
17.7 Example: N Europe groundfish surveys
An investigation of the taxonomic structure of demersal fish assemblages in the North Sea, Englis...
1.2 PRIMER has some down sides
Like any software package, PRIMER has some down sides. PRIMER has a pretty specific niche As alre...
17.6 Example: UK free-living nematodes
examined 14 species lists from a range of different habitats and impacted/undisturbed UK areas (...
17.5 ‘Expected distinctness’ tests
Species master list The construction of taxonomic distinctness indices from simple species lists ...
17.4 Other relatedness measures
The remainder of this chapter deals only with data in the form of a species list for a locality (...
17.2 Average taxonomic diversity and distinctness
Two measures, which address some of the problems identified with species richness and the other d...
16.7 Second-stage interaction plots
Phuket coral-reef times series A rather different application of second-stage MDS¶ is motivated b...
16.6 Comparison of resemblance measures
S Tikus Island coral cover The use of second-stage MDS plots can be extended to also include the ...
16.5 Second-stage MDS
It is not normally a viable sampling strategy, for soft-sediment benthos at least, to use BVStep ...
16.4 Further extensions
Both BEST Bio-Env and BVStep routines can be generalised to accommodate possibilities other than ...
16.2 Matching of ordinations
The BEST (Bio-Env) technique of Chapter 11 can be generalised in a natural way, to the selection ...
15.6 Examples
Example: Tees Bay macrofauna Fig. 15.7 shows the nMDS plot for the inter-annual macrofauna sample...
15.4 Breakdown of seriation
Clear-cut zonation patterns in the form of a serial change in community structure with increasing...
15.3 Increased variability
noted that, in a variety of environmental impact studies, the variability among samples collecte...
15.2 Meta-analysis of marine macrobenthos
This method was initially devised as a means of comparing the severity of community stress betwee...
14.3 Examples 4, 5, 6 and 7
Example 4: Fish communities from coral reefs in the Maldives In the Maldive islands, compared ree...
Appendix 3: Bibliography
Addison & Clark (1990) Addison, R.F. and Clarke, K.R. (1990) ‘Biological effects o...
Running the Bootstrap Averages routine
None of the above is necessary in order to create the means plot with regions based on bootstrap ...
Output options for region plots
These b bootstrap averages for each of the g groups are then displayed in a low-d mMDS space and ...