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A very different way of using 2nd stage matrices is best accessed through the alternative entry option in the dialog box for 2STAGE, namely to specify a single similarity matrix with factors defining a 2-way crossed layout of samples (e.g. of sites and times),...

Open the workspace Phuket ws, of coral cover for the Ko Phuket transect A, in C:\Examples v7\ Phuket corals, or if not available, open the data files Phuket coral cover 83-87, 88-97 and 98-00, and Tools>Merge them (as in Section 11), taking the defaults to p...

In the context of a 2-factor design, PRIMER makes a 2nd stage matrix very simple to produce but it is less easy to understand what it represents! The structure requires that the factors divide the data into a 2-way layout with no replicates in each cell; the i...

The workspace Tees ws was saved in Section 9; if not available open the data Tees macrobenthic abundance from C:\Examples v7\Tees macrobenthos and recalculate Bray-Curtis similarity on the 4th-root transformed abundances for all 192 samples (B-C all), with str...

The Calafuria macroalgal recolonisation experiment monitored the same physical rock patches over one year, having first cleared the (subtidal) rockface. Replicate patches were tracked for 8 different ‘treatments’, namely different times of year for the clearan...

Another situation employing rank correlation ($\rho$) between two resemblance matrices is the BEST (Bio-Env) routine of Section 13, where the biological similarity matrix (‘response’) describes the among-sample relationships of the full community and the secon...

There is one fundamental problem with applying BEST (Bio-Env) in many of the above scenarios: the number of variable combinations from the active matrix that must be considered in a full search increases exponentially with the number of variables. For p variab...

The main application area for the BVStep routine introduced by Clarke KR & Warwick RM 1998, Oecologia 113: 278-289, is what might be termed Bio-Bio, namely searching for subsets of species whose resemblance matrix best matches that of another (fixed) set of sp...

Re-open the Morlaix ws workspace in C:\Examples v7\Morlaix macrofauna from earlier in this section, or since this is all that is needed, just open the data file Morlaix macrofauna abundance into a clear workspace. It consists of 21 sampling times and 251 speci...

On B-C on 4rt, Analyse>BEST>(Method•BVSTEP) & (Worksheet: 4rt data), taking the defaults for all other entries (Spearman correlations, the suggested Bray-Curtis similarity, all 100 species Available for selection, and the permutation test ignored – a test of $...

Starting the iterative search process from a blank species list is certainly not guaranteed to get you to the best solution (minimum number of species which give $\rho \ge$0.95) – it is easy to get trapped in a local optimum which is not the globally best solu...

One of the few multivariate routines not so far met is Analyse>MVDISP, applied to a resemblance matrix from samples with a simple group structure (i.e. a 1-way layout, or a crossed design that can be turned into a 1-way layout by defining an appropriate combin...

The illustration used here is a simple 1-way design of 3 mesocosm treatments: Control (C), Low (L) and High (H) dose of organic enrichment applied to the surface of 12 intact sediment cores, taken from the same location into a mesocosm system, and randomly all...

PRIMER computes an extensive set of univariate diversity measures, covering most of the standard indices used in ecology. The active sheet is a data matrix for which the chosen indices are calculated for every sample. The measures are selected by ticking check...

One of the distinctive features of PRIMER is its inclusion of a suite of biodiversity measures based on the relatedness of species within a sample, e.g. the average ‘distance apart’ of any two species or individuals chosen at random from the sample (termed ave...

The range of indices available is illustrated with the macrobenthic data Clyde macrofauna counts from the Clyde sludge dump-ground study, directory C:\Examples v7\Clyde macrofauna, last seen in Section 14. Analyses so far have used only the abiotic and biomass...

For the diversity (variables) by samples matrix, Data1, Plots>Draftsman Plot>(✓Correlations to worksheet) shows that none of the indices is badly behaved, i.e. skewed, dominated by outliers, strongly curvilinear relationships etc., so no transforms seem called...

Soft-sediment macrofaunal assemblages (along with meiofauna and biomarker suites) were studied at 6 sites in Hamilton Harbour, Bermuda (labelled H2, H3, H4, H5, H6, H7) during an international IOC workshop on the effects of pollutants in sub-tropical waters (A...

In order to obtain a diversity measure which steps outside the species abundance distribution, and which could therefore potentially strike out along a different axis to the linear richness-evenness combinations shown in the MDS of the mechanistic correlations...

For the first set of measures (on the Taxdisc tab), the Taxonomy button gives a choice of whether the distances among species (or whatever the variables represent) are provided by a tree structure (•Taxonomy) or a direct distance matrix among species (•Resembl...