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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 pla...

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...

The Explorer tree not only makes it easy to navigate the sequence of steps taken in an analysis but also, importantly, reflects the program’s internal knowledge of the inter-relationships among data, resemblance sheets and plot windows. It uses this structure ...

From the Explorer tree for the above illustration, you can see that workspace has been saved as Bristol Channel ws, with every row below this representing a window in the workspace, whether open or not. It is important to appreciate that whilst you can close d...

Understanding the Explorer tree, however, is the key to managing your work pattern in PRIMER. In the above workspace, click on the successive entries. After the workspace name ( Bristol Channel ws) two data matrices have clearly been opened into the workspa...

In the display of the Explorer tree at the beginning of this section, the SIMPROF1 window was prefaced by the rolled-up icon , and it is necessary to click on this to expand the branch below this point, replacing the rolled-up icon with one indicating t...

Met briefly in Section 1 and again above, renaming or deleting windows in the Explorer tree is an essential part of keeping a workspace navigable and understandable, especially since workspaces for many real analyses can become voluminous! Renaming is accompli...

The name of a window can also be changed as part of the process of saving it, as a file external to the workspace: if the file is given a different name in the act of saving it, then that new name will also replace the existing entry in the Explorer tree. Howe...

Closing the second PRIMER desktop and returning to the original Bristol Channel ws workspace, note the other options for saving a dendrogram or any plot file with File>Save Graph As>(Save as type: $\text{\hspace{3mm}}$ ). The vector format Windows Enhanced M...

Certain graphs, such as MDS ordinations (Section 8) or Cluster dendrograms, can be validly rotated in an infinity of ways (effectively), after the results window is generated, perhaps to align them better with a previous run under different transformation or c...

It is not permitted to edit directly the information in a results window. This tells you what operation or analysis was actually carried out, and what the outcome was, and should remain immutable, to avoid confusion if the workspace is revisited later. Natural...

Direct printing from PRIMER is also possible for analysis endpoints such as results windows, all graphics windows, and notes (but not data sheets or resemblance matrices, which are generally too large and unwieldy for easy printing – selections of them are bes...

The concept of a Multi-plot is a new feature in PRIMER 7. This construction has already been met in Section 4 where histograms of all selected environmental variables, using frequencies calculated over the samples, were presented in a single multi-plot window ...