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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 occurrence 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...

PRIMER plots a range of what might be termed diversity curves, under the Plots>Geometric Class Plot and Dominance Plot menus, obtained when the active window is a data matrix, and these are described in Chapter 8 of CiMC. They display a combination of evenness...

These are essentially multiple frequency polygons, plotted on a single graph, for each sample in the active sheet, which needs to be a taxon (species) by samples array of genuine counts. If you wish to plot a single curve for each of a number of groups of samp...

Dominance plot is the convenient generic name for a family of curves also known as ranked species abundance plots, which can be computed for abundance, biomass, % cover or other biotic measure representing quantity of each taxon. For each sample, or pooled set...

Macrobenthos in soft sediments of a site in Loch Linnhe, Scotland were monitored by Pearson TH 1975, J Exp Mar Biol Ecol 20:1-41, over the period 1963-73, recording both species abundance and biomass. The data are pooled to a single sample for each year, with ...

ABC curves plot abundance and biomass k-dominance lines on the same plot, and are interpreted in the literature as indicating an undisturbed community if the biomass curve is above the abundance curve, gross disturbance if the abundance curve lies above the bi...

An attempt to run the routine with the matrices reversed, or to run it on a data type Environmental sheet, will provoke one or more warnings (e.g. Primary data not Abundance), though not usually an outright error. It is always advisable to check that Data type...

Testing for differences in ABC curves for group structures of sites, times or treatments etc., where there are replicate samples within each group, is probably best accomplished by using the W index. This is computed for every replicate and the W values are tr...

The Tikus Island, Indonesia, data on % area cover of coral communities on 10 transects in the years 1981, 83, 84, 85, 87 and 88, were first met in Section 5, with data sheet Tikus coral cover in the directory C:\Examples v7\Tikus corals. It is discussed extens...

The final set of data in this section is of a benthic study by Gage JD & Coghill GG 1977, in Coull B (ed) Ecology of marine benthos, Univ S Carolina Press, at a single site (C-12) in Loch Creran, Scotland, involving 256 contiguous cores arranged along a single...