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The order of samples on the (by default) x axis of a dendrogram is to a large extent arbitrary, since all arrangements of samples along the axis, which do not lead to vertical and horizontal lines intersecting, are equally satisfactory displays – think of the ...

As discussed at the start of this section, if you have set SIMPROF running, with the (✓SIMPROF test) check box, you will find that calculating the dendrogram takes some while – the timing bar on the Status Bar at the bottom of the PRIMER desktop (turning green...

PRIMER 7 now automatically displays the levels of a numeric factor in increasing order in a plot key, but note that it makes no attempt to order non-numeric levels alphabetically, instead keying them in the order in which they are met in the factor sheet, whic...

Zooming is invoked by Graph>Zoom In or Zoom Out from the main menu, or by clicking on the Zoom in or out icons on the Tool Bar. The cursor changes to or when over the plot, and left-clicking zooms one step in or out. To leave the plot in i...

The similarity profile test (SIMPROF), Clarke KR, Somerfield PJ, Gorley RN 2008, J Exp Mar Biol Ecol 366: 56-69, is a permutation test of the null hypothesis that a specified set of samples, which are not a priori divided into groups, contain no multivariate s...

Densities from 24 species of zooplankton at 57 sites in the Bristol Channel and Severn Estuary, collected by double-oblique net hauls, are in C:\Examples v7\BC zooplankton\BC zooplankton density(.pri). The sampling sites were defined as a grid (Fig 3.2, CiMC),...

In addition to the dendrogram plot itself, Analyse>CLUSTER (like all analysis routines) produces a separate Results window (here CLUSTER1) which firstly lists the conditions under which the analysis was run (e.g. whether on a selection of the matrix, with what...

SIMPROF can be run directly using Analyse>SIMPROF, rather than as part of another analysis such as CLUSTER (above), UNCTREE or kRCLUSTER (later this section) or LINKTREE (see Section 13). In that case, the active window must be the data sheet, the rectangular ...

The first dialog box from running Analyse>SIMPROF, however, is of a new option to PRIMER 7, a choice of 4 types of SIMPROF test, which cover all 2 $\times$ 2 combinations of analysing samples or variables and permuting within samples or variables. The default,...

From the Bristol Channel zooplankton transformed data matrix Data1, select (say) the samples of the first of the four groups (a) produced by the above series of SIMPROF tests under CLUSTER, by Select>Samples>(•Factor levels)>(Factor name: SprofGps)>Levels>(Inc...

As in all permutation tests in PRIMER v7 (e.g. in ANOSIM, RELATE, BEST etc.), a further output from Analyse>SIMPROF is thus a histogram of the values of the test statistic ($\pi$, here) for the null hypothesis conditions, under permutation, with the real value...

There are four possible Cluster mode choices within the Analyse>Cluster>CLUSTER dialog box, distinguished by the way they redefine the among-group dissimilarities at each proposed step of the agglomerative process. The linkage options are: •Single (/nearest ne...

Now re-run Analyse>Cluster>CLUSTER>(Cluster mode•Single linkage), creating the SIMPROF factor Single and run again with (Cluster mode•Complete linkage), giving factor Complete. The respective cophenetic correlations $\rho$ for the four linkage methods are: 0.7...

Note that the plots above required a certain amount of juxtaposition of different font sizes for titles, axis titles, x-axis labels, keys etc., away from the default values (usually 100). Changing Graph> General>(Overall font scale: 100) is sometimes a good pl...

Two new clustering methods are introduced towards the end of Chapter 3 in CiMC, the first still a hierarchical clustering method leading to a tree diagram, but a divisive rather than agglomerative algorithm in which all samples start off in a single group and ...

Using the Bristol Channel zooplankton workspace which should still be open, and with active sheet the Bray-Curtis similarities on fourth-root transformed data, run Analyse>Cluster>UNCTREE> (Min group size: 1)&(Min split size: 4)&(Number of restarts: 50)&(Min s...

Note how each node is now lettered so that information about the R value for that split can be displayed in the text pane underneath the tree, and also in the accompanying results window (right). The lettering size in the tree can be increased (as it has been ...

PRIMER 7 also provides a choice of representations of the tree structure, using either the A% or the B% axis scale. In general, the layout shown above is to be preferred, because the regular spacing of the sample axis allows non-numeric labels and/or symbols t...

Another new introduction in PRIMER 7 is a form of non-hierarchical (flat) clustering, the analogue of the k-means method in traditional cluster analysis. The latter is a widely-used technique based on Euclidean distances in the variable space of the original d...

It will have been obvious from performing the worked examples of the previous sections that the structure of all calculations in the current workspace is stored and displayed in logical fashion, on the left of the PRIMER desktop, in the Explorer tree. This lis...