Search Results

The three Wizards menu items carry out sequences of routines, all of which can be run separately but which it is either convenient or instructional to have bundled up in this way, at least until you are confident about the steps involved and can dispense with ...

The benthic faunal study in the Fal estuary, Cornwall UK, was seen in Section 4. Sediment samples were taken at a total of 27 sites across 5 creeks running into the Fal estuary, with differing levels of heavy metal contamination from historic tin and copper mi...

In the Fal estuary study, where there are environmental data matching each of the 27 sites, it is not unreasonable to consider a different form of analysis, in which creek designations are considered secondary to the biotic relationships among sites in relatio...

Finally, try running Analyse>Basic multivariate analysis on this environmental data matrix, Fal environment, to look at the pattern in the abiotic variables collectively, rather than singly (a match of this multivariate environmental structure to the multivari...

Another significant addition to the descriptive tools now available in PRIMER 7 is that of Plots>Shade Plot. This is particularly helpful in two ways. Firstly, we have already seen it used in simple form in Section 4 in relation to choice of transformation. A ...

A data set not met elsewhere in this manual but which is used a great deal in CiMC, e.g. to start the description of 1-way ANOSIM permutation tests (Chapter 6), is from sub-tidal sampling by Day grabs for benthic macrofauna at 6 sites (labelled A-E, G) in Frie...

Of the 110 species, many occur only in one or two replicates, often as singleton individuals, so that whilst display of the whole matrix is perfectly possible, it will be cumbersome and less effective than viewing species which account for a non-negligible per...

The next dialog box on Matrix display is (Transformation:       ), with default of Square root. This in effect runs the routine Pre-treatment>Transformation(overall) and thus offers the choices of None, Square root, Fourth root, log(X+1) and Presence/absen...

The first branch takes the square root of the full matrix Frierfjord macrofauna counts, giving Data1, on which sample Bray-Curtis is calculated, Resem1. This was only used to seriate the x axis on the original shade plot but, as seen above, Special>Reorder>Sam...

The Graph options taken automatically by Matrix Display to produce the final shade plot output are as follows. Firstly, Graph>Sample Labels & Symbols>(Symbols✓Plot)>(✓By factor: Site). Next Special>Reorder>Samples>(Order•Seriate>Sample resemblance Resem1) & (C...

Slightly more detail on how the seriate options are constructed, on both samples and species axes, can be found in Chapter 7 of CiMC but will be described here also, since the concept of a seriation model matrix has not yet been met (see Section 14). There are...

A good example of how ordering of species in a shade plot can aid interpretation is seen for macrobenthic communities at different distances from the Ekofisk oilfield, last saved in Section 9 but which we have seen several times since it was introduced as the ...

A Western Australian study of the dietary assemblages of a single fish species (King Wrasse) were analysed as a 3-way crossed ANOSIM design, followed by an nMDS means plot, in Section 9. The three factors were samples taken at 3 locations (j1, j2, p2), at 2 pe...

With OK to get back to the first dialog screen under Special, we now look at the options available there. (Dendrogram size 100) will increase the size of the variables dendrogram (and a samples dendrogram at the same time, if one has been selected) so that its...

A further option on the initial Special menu for a shade plot (✓3D>Opacity (0-100): 75) turns the 2-d matrix into a 3-d bar plot, also carrying across any dendrograms and sample or variable labels and symbols on the axes. The (transformed) quantities in the ce...

A final choice on the Special dialog for shade plots can be useful when planning to compare plots. Save sample order and Save variable order allow the current order (top to bottom for species and left to right for samples) to be saved to a factor or indicator ...

The time-averaged Exe nematode community data were used extensively in Section 8 to illustrate nMDS ordination, and the workspace Exe ws in C:\Examples v7\Exe nematodes should contain the data sheet Exe nematode abundance of the 19 sites, averaged over the 6 b...

The core task faced by the Special>Reorder operation is to reduce what is inevitably a high-d similarity structure, on either axis, to a 1-d representation of those samples (or species). The default for Matrix display, when no group structure is provided for t...

The final option that Reorder offers, attempting to find a useful ordering on a 1-d axis of a non-serial structure, is (Order•Nearest Neighbour) which implements a simplified travelling salesman algorithm. This is available for both samples and species axes, a...

For the final example of the options in shade plot, save and close Exe ws and return to the Bristol Channel ws used extensively in Section 6 to illustrate different clustering methods (and seen again in Section 7 – and 8, for MDS bubble plots). If not availabl...