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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...
Uninstall / re-install PRIMER
If you need to move the PRIMER software to a new machine (or re-image the machine), first uninsta...
(Leschenault estuarine fish, W Australia)
Veale L et al 2014 J Fish Biol 85: 1320-1354 describe trawl sampling for nearshore estuarine fish...
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...
Expanded RELATE test (Exe nematodes)
As an example of Tools>Expand Samples on a data matrix (or Tools>Expand on a resemblance matrix, ...
Other Model Matrix options
The conclusion is, of course, consistent with the different, but closely-related, ordered ANOSIM ...
Seriation with replication
Return to the macrofaunal data set from the Ekofisk oilfield, with workspace Ekofisk ws last save...
2-way RELATE for seriation
A new feature in PRIMER 7 parallels that discussed for the BEST analysis of the previous section,...
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...
RELATE on resemblance matrices
The BEST routine in the previous section introduced the concept of measuring how closely related ...
Missing data in linkage trees
Note that LINKTREE is able to tolerate some missing data in the abiotic matrix – the piecemeal fo...
SIMPROF test in LINKTREE
Low values of B% correspond to samples which are rather close together on the MDS plot and the qu...
LINKTREE (Messolongi lagoons data
Continuing the lagoon diatom study, having first selected (highlighting then Select>Highlighted) ...
Non-metric, non-linear, non-additive
The Analyse>Cluster>LINKTREE routine has a number of features that are designed to mesh to the PR...
Linkage trees – rationale
Another technique for linking sample patterns based on assemblage data to a suite of environmenta...