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A useful variation of this, but one which needs more care, is to compute average body mass of each species in each sample. This is simply B/A, but needs to cater for the many cases when A (and B) are zero and a simple ratio is undefined. With active sheet Clyd...

Transforming resemblances remains in the Tools menu in PRIMER 7, since it is not an option for pre-treatment of data matrices prior to resemblance calculation (which characterises the other items on the Pre-treatment menu). Although not commonly required, it f...

Tools operations on resemblances which are discussed elsewhere are: a) Dissim and Unravel in Sections 5 & 6 – the former turns similarity into dissimilarity, or vice-versa, and the latter creates a single column of entries from unravelling rows of the triangul...

PRIMER uses the term environmental variables as a shorthand for a wide variety of data types (including biological data!), extending well beyond the archetypal case of physical or chemical measurements made on the environment surrounding an assemblage sample....

Normalisation (subtracting the mean and dividing by the standard deviation, for each variable), and subsequent selection of Euclidean distance or PCA, operates more effectively the closer the data is to approximate (multivariate) normality. The latter is not a...

PCA is an ordination method in which samples, regarded as points in the high-dimensional variable space (11-d here) are projected onto a best-fitting plane, or other low-dimensional solution – the user can specify how many principal components (new axes) are r...

Though the vector overlay has a tendency to clutter the plot, the changing contaminant load along this E-W transect of sampling sites (Fig. 1.5 in CiMC) is clear. The end points S1 and S12 lie close together and there is a strong trend from S1 to the dump cent...

The final table in the results window is headed Principal Component Scores – these can instead be sent to a new worksheet by checking (✓Scores to worksheet) in the Analyse>PCA dialog, which facilitates their further use in PRIMER. An example would be to comput...

Many of the options for manipulating PCA configurations are exactly the same as for MDS plots, covered extensively in Section 8, so will not be repeated – only features that differ will be shown. General rotation is not allowed in a PCA: directions have define...

From the Graph>Special menu, remove the vector overlay by unchecking the (✓Overlay vectors) box on the Overlays tab, and on the same tab, join the points along the transect with (✓Overlay trajectory>Trajectory numeric factor: Site#) – if the factor doesn’t exi...

Of the other options on the Graph>Special menu, overlaying groups from a CLUSTER run (which to be consistent must use Euclidean distance) is no different than for MDS ordination, in Section 8, and bubble plots likewise are executed in just the same way as for ...

As with MDS, use of Graph>Special>Main>Axes, with (Plot type•2D or •3D), allows any pairs or triples of axes to be plotted: (PC1, PC2), (PC1, PC3), (PC1, PC4), (PC2, PC3), (PC2, PC4), …; or (PC1, PC2, PC3), (PC1, PC2, PC4), … etc. By default, PCA is drawn with...

Another subtle distinction from MDS is that only a single PCA graph window is produced initially, allowing a choice between displaying a 2-d or 3-d scatter plot. This is because the PC algorithm generates just one solution, with as many PCs as requested: a 2-d...

An example where a 3-d plot is marginally more necessary is given by the biomarker data last seen for a 1-way ANOSIM test in Section 9. Re-open the N Sea ws workspace, or if not available, open N Sea flounder biomarkers from C:\ Examples v7\N Sea biomarkers. ...

The main rationale for the Analyse>BEST procedure in PRIMER is to find the best match between the multivariate among-sample patterns of an assemblage and that from environmental variables associated with those samples. The extent to which these two patterns ma...

BEST amalgamated the earlier (PRIMER 5) BIOENV and BVSTEP procedures (hence BEST = Bio-Env + Stepwise) since they had an identical purpose – to search for high matrix correlations, rank-based, between a fixed sample similarity matrix (typically from a species ...

In what is one of the very few examples of ‘moving the furniture around’ between PRIMER 7 and earlier versions, the active window for a run of Analyse>BEST is no longer the data matrix of (usually abiotic) variables, from which selections are made to best matc...

After the initial choice of Method, the next area on the BEST dialog inputs the explanatory (fitted) data worksheet and, in a new option in PRIMER 7, allows the user to specify an indicator for that sheet which groups its variables into indivisible sets. For e...

After the (✓Group variables(indicator)) check box, the next option is a Select variables/groups button, which gives the usual type of selection dialog with three panes. The default is for all the variables – for which read ‘groups of variables’ if the previous...

On the right of this main dialog box for BEST is another option new to PRIMER 7, also covered in Chapter 11 of CiMC, namely the check box (✓Within levels of factor       ). Essentially, this gives a constrained (or 2-way) BEST procedure in which the matc...