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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 tre...

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...

PRIMER therefore includes a number of S extrapolators – attempts to predict the true total number of species that would be observed as the number of samples tends to infinity (the asymptote of the species accumulation curve), assuming that a closed community i...

For this final section, we consider only cases in which the samples form a 1-way layout, i.e. there is a single (a priori defined) factor whose levels divide the data into groups, the samples in a group being considered replicates of that factor level. This fa...

Ordination means plots are therefore a vital tool for interpretation but, in relation to their univariate counterparts, they lack one useful feature – the ability to get an approximate feel for the uncertainty in our knowledge of position of each mean point on...

The construction of approximate regions is approached through bootstrap averages. We only have one observed mean from n replicates for a particular group – leaving aside how that is calculated for the moment. What we need, for a plausible region estimate, is e...

These averages can then be used to generate a bootstrap region for each of the g groups – at its simplest by displaying the full set of b$\times$g averages in a 2-d (or 3-d) ordination. Here is the first obvious approximation therefore, namely that a 2- or 3-d...

The Analyse>Bootstrap Averages routine allows both metric and non-metric options for the MDS ordination of the bootstrap average regions. However, mMDS is the recommended choice, and the default. The motivation for constructing a region plot for the group mean...

Though hopefully the above gives the motivation and an idea of the way the region estimates are constructed, the most important instruction of this Section is to read Chapter 18 of CiMC! The detailed reasoning and information it gives will not be repeated here...

These b bootstrap averages for each of the g groups are then displayed in a low-d mMDS space and you have control of whether to display any or all of: the b$\times$g bootstraps (✓Bootstrap averages); the overall averages for each group (✓Group averages); the s...

The diet study for 7 species of W Australian fish, with a variable number of dietary samples from each, has been seen several times now. In Section 3 we selected a subset of just the 3 congeneric species, Sillago schomburgkii (10 samples), S. bassensis (14) an...

None of the above is necessary in order to create the means plot with regions based on bootstrap averages – it was included purely to note the initial steps the routine takes, under the automatic m option, in order to determine the mMDS dimensionality in which...

The above study was not an example given in Chapter 18 of CiMC and was therefore discussed in detail, but bootstrap average regions are given and interpreted for three other data sets there, and we shall end just by showing a region plot from one of those, for...