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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 calcul-ated for every sample. The measures are selected by ticking chec...

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...

Such tree structures (e.g. taxonomies) are one of a distinct worksheet type, Variable Information, slightly expanded in PRIMER 7 from the aggregation file format of PRIMER 6, but still with an *.agg extension when saved as PRIMER 7 binary format – they can al...

The other box in this Taxonomy (data) dialog can be used to alter the weights given to the various branch lengths in the tree (and includes the previous compression at the top or bottom of the tree as a special case, with those step lengths set to zero). By t...

The aggregation matrix for the NW European beam-trawl survey data on groundfish assemblages (93 species in 277 samples, from 9 sea areas) was last seen in Section 11, where it was checked for consistency. However, the workspace is now rather cluttered so open ...

The sheet Data1 of this suite of diversity indices for each of the 277 samples, split into 9 sea areas (factor area), could now be input to two new multi-plot routines in PRIMER 7, namely standard univariate box plots and means plots, treating the sea areas (1...

Wide-ranging biogeographic studies, and particularly historic data, are often restricted to simple species lists. Even where quantitative information exists, it is rarely from sampling protocols that have been standardised with respect to sampling effort over ...

Further theoretical details and discussion can be found in Chapter 17 of CiMC, which also presents analyses for the Europe groundfish data, whose workspace Groundfish ws2 should still be open. These taxonomic distinctness tests (on presence/absence data only) ...

A new option in PRIMER 7 recognises that computation time can become an issue for particular relatedness analyses when the master list is extremely large - as could happen if, for example, the world list of fish species, or the entire marine species directory ...

For an example, take the first of the 277 groundfish samples, the 0.25$^\circ$ rectangle S1. Highlight and select just this column from Groundfish density, with Select>Highlighted (this is a quantitative matrix not presence/absence, but TAXDTEST will automatic...

It is impractical to produce detailed histograms, such as those above, for each of the 277 samples, so a preferable option is just to view the 95% lower and upper limits for a range of sample sizes S, using a funnel plot so that a set of samples can be plotted...

Another option on the TAXDTEST dialogs is that the simulation of random draws from the master list, to generate histograms, funnels etc, can be constrained to match the probabilities of occurr¬ence of each species, as observed in a large set of samples definin...

The final option is to consider $\Delta^{\scriptscriptstyle +}$ and $\Lambda^{\scriptscriptstyle +}$ in combination, by plotting 95% probability contours for their joint distribution, under the null hypothesis of simple random (or frequency-based) selection fr...