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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 community samples. Howeve...

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...

Save and close Tasmania ws and, as a last example, open the recently closed N Sea ws workspace. On the Normalised biomarkers sheet, run Analyse>SIMPER>(Design•One way>Factor A: Site) & (Measure•Euclidean distance), unchecking the box which truncates the listin...

Both the Edit (see Section 1) and Tools main menus carry out ‘housekeeping’ manipulations on a dataset (or a resemblance or variable information sheet, such as an aggregation file). The operations are usually rather straightforward, and with an obvious outcome...

Tools>Average and Sum operate in the same way on data sheets. For example, when (Samples• Averages for factor: area) & (Variables•No averaging) is selected, they average (or sum) across all samples with the same level of the specified factor, separately for ea...

So far we have only seen variable information sheets, containing taxonomic (or other) hierarchies (*.agg files), used in calculating specialised forms of resemblance which exploit the relatedness of species in the samples being compared (Section 5). More signi...

Use the open aggregation file, Groundfish taxonomy, to show the smaller set of Tools items (Tree, Check, Duplicate) available when the active window is of variable information. Tools>Duplicate has been seen previously for worksheets and plots (in Sections 3 an...

The other Tools menu item for aggregation sheets is distinctive to this case, namely Tools>Tree; it simply displays the hierarchical structure of an aggregation file in the same way as the Explorer tree, in a left-hand panel. Successive clicking on the ic...

Tools>Duplicate operates in the same way whether the active window is a data array, resemblance matrix, variable information sheet or plot. In the case of a Graph window, Duplicate is the only specific option offered on the Tools menu, and there are no choices...

The nematode and copepod datasheets from 16 samples at a Tasmanian sand-flat (C:\Examples v7\ Tasmania meiofauna) were seen in both the previous two sections, in workspace Tasmania ws, but if the latter is not available open Tasmania nematodes and Tasmania cop...

Occasionally, use of strict label names does not give the this desired outcome, and the default behaviour can be changed to force PRIMER to consider an identical label, but in a different matrix, to be treated as a different name. For example, this might be ne...