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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 Graph...

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...

That the stress is low here is also evident from the Shepard diagrams for the 2-d and 3-d solutions (possibly Graph4 & Graph6). They are scatter plots of distances between samples in the ordination against original (dis)similarities, in which the deviations of...

One can also ask how well the (Euclidean) distances among points in the nMDS plot correlate with the dissimilarities in the resemblance matrix. The former are calculated by running the ordination co-ordinates (output to Data4 and Data5 by the ✓Ordinations to w...

For the MDS run above, two of the defaults taken for options in the MDS dialog were (Minimum stress: 0.01) and (Kruskal fit scheme•1). Changing the former from 0.01 to 0.001 would decrease the lower threshold of stress at which the iteration decides that it h...

nMDS ordinations (unlike mMDS) have no meaningful axis scales for the configuration, since they use only ranks rather than original dissimilarities. There are also no defined directions for plot axes (unlike PCA, Section 12, or PCO, PERMANOVA+ add-on), so MDS ...

A new feature in PRIMER 7 is the ability to automatically reflect in the axes and rotate an MDS configuration (and rescale it, if necessary) such that it best matches the pattern of another supplied configuration. This can make it quicker and simpler to compar...

It is scarcely necessary here, with only 19 samples, to zoom in on part of the plot in order to see the detailed structure, though this is possible using the Zoom In, Zoom Out and Cancel Zoom options on the Graph menu (also accessible from the , and ...

We have seen before that, whilst the Graph>Sample Labels & Symbols and General menus are universal, having dialog boxes of the same form for all the graphics routines, the Graph>Special dialogs are specific to each routine, and this option is at its most exten...

There are a number of new diagnostic tools available in PRIMER 7 for assessing how well a low-d ordination represents the structure in the resemblance matrix. One of the simplest is to join pairs of points on the ordination which have similarity greater than s...

It is worth saying, as we start to explore the wide range of tools which can be applied to an MDS or other ordination that, although demonstrated for 2-d plots, most of the techniques are also available for 3-d configurations. This includes all joining operati...

The minimum spanning tree (MST, see CiMC for the Gower and Ross, 1969 reference) is used in the same way, to identify parts of the configuration which do not fully represent the underlying (dis)similarity matrix. All samples are connected on the ordination by ...

The 2-d ordination plot shows a clear separation of the nematode assemblages at these 19 sites into 5 groups (which CiMC, Chapter 11, shows can be related to sediment properties such as the median particle size, anoxic layer depth and interstitial salinity). A...