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Though PRIMER 7 does not attempt to replicate all the facilities available in graphics presentation software, there are a large number of graphics options available to modify dendrograms, many of them shared in a consistent interface for ordinations and other ...

Assemblage data on 140 species of free-living marine nematodes at 19 sites (labelled 1-19) in the inter-tidal soft sediments of the Exe estuary, UK, is in data file C:\Examples v7\Exe nematodes\ Exe nematode abundance(.pri); the entries are averaged counts ove...

The dendrogram is displayed in a plot window, and a separate Results window gives a detailed list of the precise similarities at which the groups combine, for this agglomerative method. This also now gives the cophenetic correlation (0.958 here), which is a Pe...

Returning to the main point of the previous example, the production of the dendrogram, note that printing or saving dendrograms (and other plots) in a variety of formats is seen in Section 7, but one easy thing to do with any PRIMER plot is to Edit>Copy it to ...

When the active window is a plot, levels of a factor can be displayed in place of sample labels and/or represented by differing symbols, with an accompanying symbol key, using the Graph> Sample Labels & Symbols menu. (Alternatively, the same choices result fro...

Label font sizes, typeface, colours etc can be changed with the (Labels:Data font) button, and sizes of symbols increased or decreased from the default value of 100 by changing (Size: 100), again in the Symbol area of the Sample Labels & Symbols tab – one of t...

Still in the Graph Options dialog box, take the Titles tab and edit the main and sub-title content as shown below, also altering title font sizes and types: (Main title:Font>Size:150) & (Sub title:Font> Colour:[choose black] & [Italic check box off]). From the...

Finally, on the General tab (also reached directly from Graph>General), thicken up all lines with (Line width: 1.5) , increase the size of all fonts with (Overall font scale: 140), remove the display of the calculation history (transformation, similarity measu...

Unlike Graph>Samples Labels & Symbols or Graph>General, which take you to the Graph Options dialog box, which is displayed in consistent format for these and other appropriate tabs (Titles, X axis, Y axis, Keys), the Graph>Special menu item takes you to a spec...

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 inter-secting, 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 ...