6. Clustering methods (CLUSTER, SIMPROF, UNCTREE, kRCLUSTER)
Clustering methods & choice of linkage
PRIMER 7 now carries out a wider range of clustering methods than previously: a) hierarchical agg...
SIMPROF tests
All of the clustering methods are able to exploit ‘similarity profile’ (SIMPROF) permutation test...
SIMPROF on large matrices
The dendrogram itself is rapidly calculated, at least for the agglomerative methods, since no sea...
Modifying plots in PRIMER
Though PRIMER 7 does not attempt to replicate all the facilities available in graphics presentati...
(Exe estuary nematodes)
Assemblage data on 140 species of free-living marine nematodes at 19 sites (labelled 1-19) in the...
Cophenetic correlation
The dendrogram is displayed in a plot window, and a separate Results window gives a detailed list...
Copying & pasting plots externally
Returning to the main point of the previous example, the production of the dendrogram, note that ...
Sample labels & symbols menu/tab
When the active window is a plot, levels of a factor can be displayed in place of sample labels a...
Symbol & text sizes
Label font sizes, typeface, colours etc can be changed with the (Labels:Data font) button, and si...
Editing plot titles & scales
Still in the Graph Options dialog box, take the Titles tab and edit the main and sub-title conten...
General menu/tab & Keys tab
Finally, on the General tab (also reached directly from Graph>General), thicken up all lines with...
Special menu for slicing & orientation of dendrograms
Unlike Graph>Samples Labels & Symbols or Graph>General, which take you to the Graph Options dialo...
Rotating & condensing dendrograms
The order of samples on the (by default) x axis of a dendrogram is to a large extent arbitrary, s...
Timing bar, Stop Tasks & multi-tasking
As discussed at the start of this section, if you have set SIMPROF running, with the (✓SIMPROF te...
Ordering factor levels in keys; Point & click short-cuts
PRIMER 7 now automatically displays the levels of a numeric factor in increasing order in a plot ...
Zooming dendrograms
Zooming is invoked by Graph>Zoom In or Zoom Out from the main menu, or by clicking on the Zoom in...
SIMPROF method
The similarity profile test (SIMPROF), Clarke KR, Somerfield PJ, Gorley RN 2008, J Exp Mar Biol E...
(Bristol Channel zooplankton)
Densities from 24 species of zooplankton at 57 sites in the Bristol Channel and Severn Estuary, c...
CLUSTER results window
In addition to the dendrogram plot itself, Analyse>CLUSTER (like all analysis routines) produces ...
SIMPROF direct run
SIMPROF can be run directly using Analyse>SIMPROF, rather than as part of another analysis such a...
SIMPROF Types (1-4)
The first dialog box from running Analyse>SIMPROF, however, is of a new option to PRIMER 7, a cho...
SIMPROF on a subset of samples
From the Bristol Channel zooplankton transformed data matrix Data1, select (say) the samples of t...
Histograms of null distributions
As in all permutation tests in PRIMER v7 (e.g. in ANOSIM, RELATE, BEST etc), a further output fro...
Linkage by flexible beta method
There are four possible Cluster mode choices within the Analyse>Cluster>CLUSTER dialog box, disti...
Single and complete linkage
Now re-run Analyse>Cluster>CLUSTER>(Cluster mode•Single linkage), creating the SIMPROF factor Sin...
Limiting font size
Note that the plots above required a certain amount of juxtaposition of different font sizes for ...
Binary divisive clustering
Two new clustering methods are introduced towards the end of Chapter 3 in CiMC, the first still a...
UNCTREE options
Using the Bristol Channel zooplankton workspace which should still be open, and with active sheet...
Text pane in tree plots; A% and B% y-axis scales
Note how each node is now lettered so that information about the R value for that split can be di...
Special menu for divisive trees
PRIMER 7 also provides a choice of representations of the tree structure, using either the A% or ...
Flat-form clustering
Another new introduction in PRIMER 7 is a form of non-hierarchical (flat) clustering, the analogu...