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This concept of taxonomic distinctness can be carried over from a diversity index to a dissimilarity coefficient. Two measures are given under Analyse>Resemblance>(Measure•Other: ✓Taxonomic P/A). Both are presence/absence measures only, indicated by the plus s...

Assemblage data from 93 groundfish species, those that could be reliably sampled and identified in beam-trawl surveys by research vessels from several countries surrounding NW European shelf waters, were analysed by Rogers SI, Clarke KR, Reynolds JD 1999, J An...

Note the alternative means of supplying the variable information, to these dissimilarity measures and the biodiversity indices of Section 15, which is now available in PRIMER 7. In the Variable Relationship dialog box, Type•Resemblance>Details now requires spe...

The introduction above of the concept of ‘distances’ among species raises the issue of how best to compute species similarities – or more generally variable associations – taking the menu option of Analyse>Resemblance>(Analyse between•Variables). Several signi...

One context in which resemblances between variables is often of primary interest is in dealing with environmental variables, biomarkers, morphology etc. Concepts of ignoring joint absences do not apply – in fact zero no longer necessarily means absence (e.g. $...

Use of a correlation matrix between all pairs of variables as input to a multivariate ordination (say), in which points denote variables rather than samples (so that highly correlated variables are placed close together), either requires one of the absolute co...

Returning to the main purpose of resemblance measures, to describe similarity among samples, an important new feature in PRIMER 7, not offered in earlier versions, is that resemblance measures will now be calculated in the presence of missing cells (identified...

File>Save Resem As will save a resemblance matrix in internal binary PRIMER v7 (*.sid) format, though the previous v6 and v5 binary formats (also *.sid) are other options – as is the early DOS text format (*.sim) – all likely to be of limited utility now. More...

PRIMER 7 now carries out a wider range of clustering methods than previously: a) hierarchical agglomerative clustering using one of four linkage methods – single, complete, group average (UPGMA) and flexible beta (a standard WPGMA extension); b) hierarchical (...

All of the clustering methods are able to exploit ‘similarity profile’ (SIMPROF) permutation tests, e.g. for stopping rules for divisive methods or choice of number of groups k in a ‘flat’ clustering. SIMPROF test sequences look for statistically significant e...

The dendrogram itself is rapidly calculated, at least for the agglomerative methods, since no search procedure is involved, and it can thus be constructed for very large numbers of samples – but the SIMPROF routine is highly compute-intensive, given the typica...

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 ...

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...