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Threshold metric MDS (tmMDS)
The mMDS Shepard diagram above strongly suggests a middle course between simple metric and non-me...
(Morlaix macrofauna, Amoco-Cadiz oil spill)
Close the World cities worksheet (it will not be needed again) and re-open workspace Morlaix ws, ...
Animating the mMDS/nMDS iterations
Another feature introduced in PRIMER 7 is more of a teaching tool than an analysis method per se,...
Identifying points on the Shepard plot
Show this by running the matching nMDS to the above mMDS, this time setting (Minimum stress: 0.00...
Metric MDS; (Great-circle distances for world cities)
A significant new feature in PRIMER 7 is the construction of metric MDS ordinations (mMDS), toget...
Bubble data selection error & Refresh
It is worth repeating the point made at the start of these examples on bubble plots: if the routi...
Bubble plots on averages
For these data, a segmented bubble plot on a 2-d ordination provides a succinct summary of the re...
(Bristol Channel zooplankton)
The BC zooplankton density data sheet in C:\Examples v7\BC zooplankton was used in the last half ...
Environment bubble & vector plots
An important use for a bubble plot is in displaying the behaviour of a further measured variable,...
Duplicate graphs
Abra prismatica appears to be a species which can tolerate the contaminant or disturbance effects...
Bubble images
A further new option on this Key dialog is to replace single-coloured circles with a (rectangular...
Bubble key
The key to the left of the plot, which gives the root-transformed scale for Abra prismatica count...
Matching variable sets; (Ekofisk oil-field study)
The final two sections of the Graph>Special dialog concern overlaying vectors and ‘bubbles’ of nu...
(Tees Bay macrofauna time series)
A clearer, static, example of the benefits of split trajectories on ordination plots is provided ...
Trajectories split & then sequence animated
In fact, if the animation is repeated with trajectories running across months, separately drawn f...
Sequence animation, captured in 2- & 3-d
The time pattern above is evident from simple addition of the trajectory but there are occasions ...
Overlay trajectories
A trajectory joining points on an ordination is simply added using Graph>Special>Overlays and tak...
Higher-d & scree plots (WA fish diet)
Run nMDS at a wider range of dimensionalities than the default and ask for a scree plot: Analyse>...
(W Australia fish diets)
Re-open the workspace WA fish ws from C:\Examples v7\WA fish diets, which will provide an example...
3-d ordination plots & axes selection
As we have seen for the nMDS run on the Exe nematode data, in the first graphic of this Section, ...