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Shade plots showing coherent sets & variable boundaries
In order to display a shade plot carrying precisely the same information as the coherent species ...
3-d shade plot
A further option on the initial Special menu for a shade plot (✓3D>Opacity (0-100): 75) turns the...
Pairwise comparisons
The table ending the results window gives the pairwise comparisons. For each pair of groups (fish...
Bubble plots in 3-d MDS; (W Australia fish diets)
Another new feature in PRIMER 7 is the ability to construct bubble plots in 3-d ordinations, wher...
Segmented bubble plots
Given the inadequacies of vector plots for displaying species contributions to ordinations, but t...
Vector plots for species
One tempting alternative, commonly found in the literature, is to plot (species) variables as vec...
Bubble colours
A new feature in PRIMER 7 is that these bubbles will be plotted in different colours – or in mono...
Bubble plots of single variables
The above MDS draws on all 174 species (with more abundant species given greater weight) but only...
(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...