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A good example of how ordering of species in a shade plot can aid interpretation is seen for macro-benthic communities at different distances from the Ekofisk oilfield, last saved in Section 9 but which we have seen several times since it was introduced as the...

A Western Australian study of the dietary assemblages of a single fish species (King Wrasse) were analysed as a 3-way crossed ANOSIM design, followed by an nMDS means plot, in Section 9. The three factors were samples taken at 3 locations (j1, j2, p2), at 2 pe...

With OK to get back to the first dialog screen under Special, we now look at the options available there. (Dendrogram size 100) will increase the size of the variables dendrogram (and a samples dendrogram at the same time, if one has been selected) so that its...

A further option on the initial Special menu for a shade plot (✓3D>Opacity (0-100): 75) turns the 2-d matrix into a 3-d bar plot, also carrying across any dendrograms and sample or variable labels and symbols on the axes. The (transformed) quantities in the ce...

A final choice on the Special dialog for shade plots can be useful when planning to compare plots. Save sample order and Save variable order allow the current order (top to bottom for species and left to right for samples) to be saved to a factor or indicator ...

The time-averaged Exe nematode community data were used extensively in Section 8 to illustrate nMDS ordination, and the workspace Exe ws in C:\Examples v7\Exe nematodes should contain the data sheet Exe nematode abundance of the 19 sites, averaged over the 6 b...

The core task faced by the Special>Reorder operation is to reduce what is inevitably a high-d similarity structure, on either axis, to a 1-d representation of those samples (or species). The default for Matrix display, when no group structure is provided for t...

The final option that Reorder offers, attempting to find a useful ordering on a 1-d axis of a non-serial structure, is (Order•Nearest Neighbour) which implements a simplified travelling salesman algorithm. This is available for both samples and species axes, a...

For the final example of the options in shade plot, save and close Exe ws and return to the Bristol Channel ws used extensively in Section 6 to illustrate different clustering methods (and seen again in Section 7 – and 8, for MDS bubble plots). If not availabl...

The third item on the Wizards menu is Coherence plots. This is a combination of SIMPROF runs within a species CLUSTER analysis, to identify groups of coherent species, and Plots>Line Plot, to draw line graphs of species-standardised matrix entries (y) across s...

A Type 2 SIMPROF test is not part of a Wizards>Coherent plots run, and there is a good case for carrying out a test of its null hypothesis (H$_0$: there are no species associations at all) prior to trying to break down those associations into coherent groups, ...

Type 3 SIMPROF can be run as a single test on the species set defined by the active matrix (which could be under a selection), using Analyse>SIMPROF>(Type•Type 3), leading to similar dialog and outputs as for the Type 2 test. However, there are two important d...

For this (reduced) Loch Linnhe data matrix, e.g. with the selection of 50 species made in Data1, it is straightforward to create also a shade plot. There are, of course, differences in visual impact in the way matrix entries are represented by y axes of a line...

In order to display a shade plot carrying precisely the same information as the coherent species line plots, first save the species order in the above shade plot – in order to make it easier to compare the two shade plots – using Graph>Special>Save variable or...

A final possibility for this Loch Linnhe data is to display both horizontal and vertical divisions in a shade plot, from sets of Type 3 and Type 1 SIMPROF tests respectively. Though it might normally be preferable to display the years in their chronological or...

Save the workspace as Linnhe ws, close it and re-open the data on a suite of biomarkers (‘health’ measures) from flounder sampled at five N Sea sites S3, S5, S6, S7, S9, with 10 replicate samples (pools of fish) from each site. The workspace N Sea ws in C:\Exa...

Shade plots are an excellently succinct way of displaying the abundance (or other quantity) of all the influential species (or other taxon category), in the pre-treated state in which they are input to the multivariate analysis of the comm¬unity samples. Howev...

Re-open the Bristol Channel ws workspace from C:\Examples v7\BC zooplankton, for which the shade plot was seen a few pages ago. The BC zooplankton density sheet was 4th-root transformed (4rt density) prior to Bray-Curtis calculation (BC resem) and binary divis...

Earlier in the results window, tables are given of the contributions of each species to the Bray-Curtis similarity within each of the groups (see Chapter 7 of the methods manual for the formula). The average Bray-Curtis similarity between all pairs of sites i...

A natural extension to the 1-way SIMPER is to the 2-way crossed design, so re-open the Tasmania ws workspace of meiofaunal communities Tasmania nematodes on a sand-flat, with disturbed and undisturbed patches (factor ‘treatment’ Trt: D or U) at 4 locations (fa...