10. Wizards and species analyses (Basic MVA, Coherence plots, Matrix display, SIMPER)
Basic multivariate analysis wizard
The three Wizards menu items carry out sequences of routines, all of which can be run separately ...
Basic MVA for structured data (Fal nematodes)
The benthic faunal study in the Fal estuary, Cornwall UK, was seen in Section 4. Sediment samples...
Basic MVA for a priori unstructured biotic data
In the Fal estuary study, where there are environmental data matching each of the 27 sites, it is...
Basic MVA for environ-mental data
Finally, try running Analyse>Basic multivariate analysis on this environmental data matrix, Fal e...
Wizard for Matrix display
Another significant addition to the descriptive tools now available in PRIMER 7 is that of Plots>...
(Frierfjord macrofauna)
A data set not met elsewhere in this manual but which is used a great deal in CiMC, e.g. to start...
Reducing the species set
Of the 110 species, many occur only in one or two replicates, often as singleton individuals, so ...
Transforms in Matrix display
The next dialog box on Matrix display is (Transformation: ), with default of Square roo...
Branches created in the Explorer tree
The first branch takes the square root of the full matrix Frierfjord macrofauna counts, giving Da...
Shade Plot options in Matrix display
The Graph options taken automatically by Matrix Display to produce the final shade plot output ar...
Seriate operation; Seriate a shade plot dendrogram
Slightly more detail on how the seriate options are constructed, on both samples and species axes...
(Ekofisk oilfield macrofauna)
A good example of how ordering of species in a shade plot can aid interpretation is seen for macr...
(King Wrasse diets)
A Western Australian study of the dietary assemblages of a single fish species (King Wrasse) were...
Special menu for shade plot; Shade plot colours
With OK to get back to the first dialog screen under Special, we now look at the options availabl...
3-d shade plot
A further option on the initial Special menu for a shade plot (✓3D>Opacity (0-100): 75) turns the...
Save sample/ variable order
A final choice on the Special dialog for shade plots can be useful when planning to compare plots...
Clustering on species and samples (Exe nematodes)
The time-averaged Exe nematode community data were used extensively in Section 8 to illustrate nM...
Ordering by a worksheet variable
The core task faced by the Special>Reorder operation is to reduce what is inevitably a high-d sim...
Nearest neighbour ordering
The final option that Reorder offers, attempting to find a useful ordering on a 1-d axis of a non...
Other tree diagrams & SIMPROF (Bristol Ch. zooplankton)
For the final example of the options in shade plot, save and close Exe ws and return to the Brist...
Coherence plots wizard & Types 2/3 SIMPROF; (L. Linnhe macrofauna)
The third item on the Wizards menu is Coherence plots. This is a combination of SIMPROF runs with...
Running Type 2 SIMPROF
A Type 2 SIMPROF test is not part of a Wizards>Coherent plots run, and there is a good case for c...
Running Type 3 SIMPROF
Type 3 SIMPROF can be run as a single test on the species set defined by the active matrix (which...
Line plots vs Shade plots
For this (reduced) Loch Linnhe data matrix, e.g. with the selection of 50 species made in Data1, ...
Shade plots showing coherent sets & variable boundaries
In order to display a shade plot carrying precisely the same information as the coherent species ...
‘Mondrian’ shade plots, with sample and variable boundaries
A final possibility for this Loch Linnhe data is to display both horizontal and vertical division...
Coherent sets of abiotic variables (N Sea biomarkers)
Save the workspace as Linnhe ws, close it and re-open the data on a suite of biomarkers (‘health’...
SIMPER (Similarity Percentages)
Shade plots are an excellently succinct way of displaying the abundance (or other quantity) of al...
Species dis-criminating two groups (Bristol Ch. zooplankton)
Re-open the Bristol Channel ws workspace from C:\Examples v7\BC zooplankton, for which the shade ...
Species typifying a group
Earlier in the results window, tables are given of the contributions of each species to the Bray-...
SIMPER on 2-way crossed layout (Tasmania nematodes)
A natural extension to the 1-way SIMPER is to the 2-way crossed design, so re-open the Tasmania w...
SIMPER on (squared) Euclidean (N Sea biomarkers)
Save and close Tasmania ws and, as a last example, open the recently closed N Sea ws workspace. O...