14. Further matching of multivariate patterns (RELATE, 2STAGE, BEST + MVDISP)
RELATE on resemblance matrices
The BEST routine in the previous section introduced the concept of measuring how closely related ...
Model matrix construction
Model matrices corresponding to more complicated structures than simple seriation or cyclicity ne...
RELATE hypothesis test
A permutation test can be applied to the matching coefficient $\rho$ between any two resemblance ...
Seriation (Phuket coral transects)
The Phuket coral-reef assemblages at equi-spaced positions down an onshore-offshore gradient (tr...
RELATE test on two biotic arrays
Given the breakdown of the serial gradient structure for 1987, is it now the case that the patter...
2-way RELATE for seriation
A new feature in PRIMER 7 parallels that discussed for the BEST analysis of the previous section,...
Seriation with replication
Return to the macrofaunal data set from the Ekofisk oilfield, with workspace Ekofisk ws last save...
Other Model Matrix options
The conclusion is, of course, consistent with the different, but closely-related, ordered ANOSIM ...
Expanding an (abiotic) data matrix
A RELATE test could equally well have been carried out between the Ekofisk community pattern and...
Expanded RELATE test (Exe nematodes)
As an example of Tools>Expand Samples on a data matrix (or Tools>Expand on a resemblance matrix, ...
Expand Samples or Expand resemblances
The Exe environment matrix does not seem (from Plots>Draftsman Plot or Histogram Plot) to contain...
Model matrix for 2D Euclidean; Cyclicity (Sea-loch macrofauna)
The other two Model Matrix options are (Type•Cyclicity (factor as cycles)) and (Type•Euclidean 2D...
2-way RELATE for cyclicity
A 2-way RELATE version of the above test where there are no replicates, and the cyclic factor und...
(Leschenault estuarine fish, W Australia)
Veale L et al 2014 J Fish Biol 85: 1320-1354 describe trawl sampling for nearshore estuarine fish...
Rationale for 2nd stage MDS
As seen above, the $\rho$ statistic, which rank correlates the elements of two similarity matrice...
Aggregation & transforms (Morlaix macrofauna)
Chapter 10 of CiMC gives several examples of aggregating species matrices to higher taxa – using ...
Second-stage nMDS (Morlaix macrofauna)
The illustration below has calculated all combinations of species (sp), genus (gn) and family (fm...
2STAGE for resemblance coefficients (Clyde study)
The technique of 2nd stage plots has also been used (Clarke KR, Somerfield PJ, Chapman MG 2006, J...
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 displaying ‘interactions’
A very different way of using 2nd stage matrices is best accessed through the alternative entry o...
(Phuket coral transect)
Open the workspace Phuket ws, of coral cover for the Ko Phuket transect A, in C:\Examples v7\ Phu...
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...
(Tees Bay macrofauna)
The workspace Tees ws was saved in Section 9; if not available open the data Tees macrobenthic ab...
(Calafuria macroalgae experiment)
The Calafuria macroalgal recolonisation experiment monitored the same physical rock patches over ...
Other BEST applications
Another situation employing rank correlation ($\rho$) between two resemblance matrices is the BES...
BVStep stepwise selection
There is one fundamental problem with applying BEST (Bio-Env) in many of the above scenarios: the...
Species sets ‘explaining’ the overall pattern
The main application area for the BVStep routine introduced by Clarke KR & Warwick RM 1998, Oecol...
BVStep (Morlaix macrofauna)
Re-open the Morlaix ws workspace in C:\Examples v7\Morlaix macrofauna from earlier in this sectio...
BVStep starting and stopping options
On B-C on 4rt, Analyse>BEST>(Method•BVSTEP) & (Worksheet: 4rt data), taking the defaults for all ...
BVStep from random starts
Starting the iterative search process from a blank species list is certainly not guaranteed to ge...
Multivariate dispersion MVDISP
One of the few multivariate routines not so far met is Analyse>MVDISP, applied to a resemblance m...
(Mesocosm experiment, Solberg¬strand copepods)
The illustration used here is a simple 1-way design of 3 mesocosm treatments: Control (C), Low (L...