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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 ...

In addition to automatic generation by certain routines, multi-plots can be created and populated by the user, to hold sets of related plots in a single composite window. File>New>(•Multi plot) gives a dialog box headed by a Graphs button which allows an order...

PRIMER 7 has a new Plots main menu, available when the active window is a data matrix. This brings together a number of standard plot formats, and more specialised ones, relevant to a range of multivariate analyses. Some are similar or identical to those in PR...

To conclude this section, it is worth remarking that care taken in structuring workspaces will often pay dividends if the analysis results need to be returned to later. An Explorer tree represents a single workspace. It can contain several starting data matric...

Chapter 5 of the CiMC methods manual describes the operation and rationale of multi-dimensional scaling (MDS) ordination, Analyse>MDS. The aim of MDS is to represent the samples as points in low-d space (often 2-d or 3-d, but PRIMER 7 will now compute MDS solu...

A further new feature of nMDS in PRIMER 7 is the ability to minimise a combination of two stress functions, equally mixed – this has potential application, for example, to combining information on a common set of samples from community matrices (typically usin...

In addition to the ability in a previous PRIMER version to Graph>Special>Overlays>(✓Overlay clusters) from a dendrogram onto a related MDS ordination, in order to judge agreement between these differing low-d displays of high-d data, PRIMER 7 now provides a wi...

The ability to display, on any ordination plot, external structure such as factors (e.g. for sites, times etc.) by Graph>Sample labels & symbols is a fundamental interpretational tool, as is the addition of time (or unidirectional space) trajectories, via Grap...

From the directory C:\Examples v7\Exe nematodes, File>Open the workspace Exe ws, last seen in Section 6, of the sediment nematode communities at 19 inter-tidal sites in the Exe estuary. If this does not exist, open the data file Exe nematode abundance(.pri) in...

As with all results windows, the MDS1 window first lists the resemblance sheet on which analysis is carried out, and whether it was under any selection on the original sample set (given as ranges of sample numbers) but the main function of this window is to re...