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An example of a 2-way crossed layout was introduced in Section 1, for meiofaunal communities in sediment patches either disturbed or undisturbed by soldier crabs (treatment factor Trt, levels D/U, factor A), over four areas of Tasmanian sandflat (block factor ...

For an example of a 2-way crossed ANOSIM test in a very different context, save and close the above workspace and return to the particle size distributions from Danish sediments introduced at the very end of Section 4 – the workspace Denmark ws in C:\Examples ...

In the unordered 1-way design, replication is essential for any sort of test (otherwise how can you tell whether single samples from groups A, B, C, … are from the same or different communities? – there are no within-group rank dissimilarities to compare with ...

The test for an ordered factor (A) in the 2-way crossed design parallels the construction seen earlier for the 2-way (unordered) crossed case, in that the 1-way R$^\text{O}$ statistic is calculated separately for each level of the other factor (B) and those R...

The 2-way crossed ANOSIM for an unordered factor, and with each combination of the two factors only having a single replicate, is covered in CiMC, Figs. 6.9 to 6.12, firstly for a treatment  block design and then for the example considered here of sites cross...

Subtidal rocky reefs, at c10m depth, at the Calafuria station in the Ligurian Sea, N Italy, were the subject of a clearance and recovery experiment by Airoldi L 2000 Mar Ecol Prog Ser 195: 81-92 (see also Clarke KR, Somerfield PJ, Airoldi L, Warwick RM 2006, J...

A dietary study of W Australian fish concerns composition by the volume of taxa (21 broad dietary categories: gastropods, bivalves, annelids, etc) in the foregut of King Wrasse from one of 4 length-classes, caught in 3 locations in 2 periods of the year and 2 ...

The 3-way fully nested design has factor C at the lowest level, nested in B at the mid level, which itself is nested in A at the top level, denoted C(B(A)). Factors can again be ordered or not, and the routine is essentially a repeated application of the 2-way...

The two other possible 3-way designs can be written C(A$\times$B) and B$\times$C(A). The first is straight-forward: an example might be of locations (A) each containing the same set of habitat types (B), and within each combination of habitat and location a nu...

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...