Recently Updated Pages
Missing data estimation (Clyde study)
Transformation options for the Clyde environmental matrix, Clyde environment, are discussed in mo...
EM algorithm assumptions
Tools>Missing is designed to operate only on matrices for which: a) assumptions of multivariate n...
Missing data estimation
The subject of missing data has arisen several times already (Sections 1, 3, 5) and the point mad...
Merging non-uniform species lists; (Phuket coral reefs); (Clyde dump-ground study)
Perhaps the greatest benefit of the strict label matching in PRIMER is the ability to Tools>Merge...
Avoiding strict label matching
The best policy to avoid confusion is to use precise, unique species and sample labels (typically...
Tree menu; Check on datasheets & resemblances; Undefined resemblances
The other Tools menu item for aggregation sheets is distinctive to this case, namely Tools>Tree; ...
Check on aggregation files
Use the open aggregation file, Groundfish taxonomy, to show the smaller set of Tools items (Tree,...
Aggregation
So far we have only seen variable information sheets, containing taxonomic (or other) hierarchies...
Average and Sum on data matrices; Average on resemblance matrices
Tools>Average and Sum operate in the same way on data sheets. For example, when (Samples• Average...
Tools vs. Edit menu
Both the Edit (see Section 1) and Tools main menus carry out ‘housekeeping’ manipulations on a da...
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...
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...
Species typifying a group
Earlier in the results window, tables are given of the contributions of each species to the Bray-...
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 ...
SIMPER (Similarity Percentages)
Shade plots are an excellently succinct way of displaying the abundance (or other quantity) of al...
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’...
‘Mondrian’ shade plots, with sample and variable boundaries
A final possibility for this Loch Linnhe data is to display both horizontal and vertical division...
Line plots vs Shade plots
For this (reduced) Loch Linnhe data matrix, e.g. with the selection of 50 species made in Data1, ...
Running Type 3 SIMPROF
Type 3 SIMPROF can be run as a single test on the species set defined by the active matrix (which...
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...