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Input/output for diversity; Presentation of diversity information
PRIMER computes an extensive set of univariate diversity measures, covering most of the standard ...
(Mesocosm experiment, Solbergstrand copepods)
The illustration used here is a simple 1-way design of 3 mesocosm treatments: Control (C), Low (L...
Multivariate dispersion MVDISP
One of the few multivariate routines not so far met is Analyse>MVDISP, applied to a resemblance m...
BVStep from random starts
Starting the iterative search process from a blank species list is certainly not guaranteed to ge...
BVStep (Morlaix macrofauna)
Re-open the Morlaix ws workspace in C:\Examples v7\Morlaix macrofauna from earlier in this sectio...
Species sets ‘explaining’ the overall pattern
The main application area for the BVStep routine introduced by Clarke KR & Warwick RM 1998, Oecol...
BVStep stepwise selection
There is one fundamental problem with applying BEST (Bio-Env) in many of the above scenarios: the...
Other BEST applications
Another situation employing rank correlation ($\rho$) between two resemblance matrices is the BES...
(Calafuria macroalgae experiment)
The Calafuria macroalgal recolonisation experiment monitored the same physical rock patches over ...
(Tees Bay macrofauna)
The workspace Tees ws was saved in Section 9; if not available open the data Tees macrobenthic ab...
2STAGE for time series and repeated measures
In the context of a 2-factor design, PRIMER makes a 2nd stage matrix very simple to produce but i...
(Phuket coral transect)
Open the workspace Phuket ws, of coral cover for the Ko Phuket transect A, in C:\Examples v7\ Phu...
2STAGE for displaying ‘interactions’
A very different way of using 2nd stage matrices is best accessed through the alternative entry o...
Conclusions on comparing resemblance coefficients
Clarke KR, Somerfield PJ, Chapman MG 2006, J Exp Mar Biol Ecol 330: 55-80 discuss this analysis (...
2STAGE for resemblance coefficients (Clyde study)
The technique of 2nd stage plots has also been used (Clarke KR, Somerfield PJ, Chapman MG 2006, J...
Second-stage nMDS (Morlaix macrofauna)
The illustration below has calculated all combinations of species (sp), genus (gn) and family (fm...
Aggregation & transforms (Morlaix macrofauna)
Chapter 10 of CiMC gives several examples of aggregating species matrices to higher taxa – using ...
Rationale for 2nd stage MDS
As seen above, the $\rho$ statistic, which rank correlates the elements of two similarity matrice...
4.4 PCA for environmental data
The above example makes it clear that PCA is an unsatisfactory ordination method for biological d...
Principal Components Analysis
PCA is an ordination method in which samples, regarded as points in the high-dimensional variable...