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(Morlaix macrofauna, Amoco-Cadiz oil spill)
Some data sets have a natural sequence to their samples, usually a time series (though this can b...
Spinning a 3-d MDS & capture in a movie file
The 3-d MDS plot box can be made to rotate horizontally, automatically (from whatever vertical pe...
Drawing verticals for 3-d plots
Whilst it is relatively easy to visualise a 3-d plot by rotation of the axes – and PRIMER 7 is no...
Rotate axes or rotate/flip data
The 3-d Exe nematode nMDS plot should be in the current workspace as Graph5 under Multiplot1 (if ...
Dendrogram & 2-d MDS in a 3-d plot
Rather than creating a small number of (arbitrary) slices through a dendrogram, superimposed on a...
Minimum spanning tree (MST)
The minimum spanning tree (MST, see CiMC for the Gower and Ross, 1969 reference) is used in the s...
Features that carry over to 3-d ordination
It is worth saying, as we start to explore the wide range of tools which can be applied to an MDS...
Diagnostics for MDS: join pairs
There are a number of new diagnostic tools available in PRIMER 7 for assessing how well a low-d o...
Shepard diagrams
That the stress is low here is also evident from the Shepard diagrams for the 2-d and 3-d solutio...
MDS results window
As with all results windows, the MDS1 window first lists the resemblance sheet on which analysis ...
Combined MDS & ‘Fix Collapse’
A further new feature of nMDS in PRIMER 7 is the ability to minimise a combination of two stress ...
Explorer tree
It will have been obvious from performing the worked examples of the previous sections that the s...
UNCTREE options
Using the Bristol Channel zooplankton workspace which should still be open, and with active sheet...
SIMPROF on a subset of samples
From the Bristol Channel zooplankton transformed data matrix Data1, select (say) the samples of t...
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 ...
Timing bar, Stop Tasks & multi-tasking
As discussed at the start of this section, if you have set SIMPROF running, with the (✓SIMPROF te...
Editing plot titles & scales
Still in the Graph Options dialog box, take the Titles tab and edit the main and sub-title conten...
SIMPROF on large matrices
The dendrogram itself is rapidly calculated, at least for the agglomerative methods, since no sea...
SIMPROF tests
All of the clustering methods are able to exploit ‘similarity profile’ (SIMPROF) permutation test...
Taxonomic dissimilarity measures
This concept of taxonomic distinctness can be carried over from a diversity index to a dissimilar...