Search Results

From the Graph>Special menu, remove the vector overlay by unchecking the (✓Overlay vectors) box on the Overlays tab, and on the same tab, join the points along the transect with (✓Overlay trajectory>Trajectory numeric factor: Site#) – if the factor doesn’t exi...

Of the other options on the Graph>Special menu, overlaying groups from a CLUSTER run (which to be consistent must use Euclidean distance) is no different than for MDS ordination, in Section 8, and bubble plots likewise are executed in just the same way as for ...

As with MDS, use of Graph>Special>Main>Axes, with (Plot type•2D or •3D), allows any pairs or triples of axes to be plotted: (PC1, PC2), (PC1, PC3), (PC1, PC4), (PC2, PC3), (PC2, PC4), …; or (PC1, PC2, PC3), (PC1, PC2, PC4), … etc. By default, PCA is drawn with...

Another subtle distinction from MDS is that only a single PCA graph window is produced initially, allowing a choice between displaying a 2-d or 3-d scatter plot. This is because the PC algorithm generates just one solution, with as many PCs as requested: a 2-d...

An example where a 3-d plot is marginally more necessary is given by the biomarker data last seen for a 1-way ANOSIM test in Section 9. Re-open the N Sea ws workspace, or if not available, open N Sea flounder biomarkers from C:\ Examples v7\N Sea biomarkers. ...

The main rationale for the Analyse>BEST procedure in PRIMER is to find the best match between the multivariate among-sample patterns of an assemblage and that from environmental variables associated with those samples. The extent to which these two patterns ma...

BEST amalgamated the earlier (PRIMER 5) BIOENV and BVSTEP procedures (hence BEST = Bio-Env + Stepwise) since they had an identical purpose – to search for high matrix correlations, rank-based, between a fixed sample similarity matrix (typically from a species ...

In what is one of the very few examples of ‘moving the furniture around’ between PRIMER 7 and earlier versions, the active window for a run of Analyse>BEST is no longer the data matrix of (usually abiotic) variables, from which selections are made to best matc...

After the initial choice of Method, the next area on the BEST dialog inputs the explanatory (fitted) data worksheet and, in a new option in PRIMER 7, allows the user to specify an indicator for that sheet which groups its variables into indivisible sets. For e...

After the (✓Group variables(indicator)) check box, the next option is a Select variables/groups button, which gives the usual type of selection dialog with three panes. The default is for all the variables – for which read ‘groups of variables’ if the previous...

On the right of this main dialog box for BEST is another option new to PRIMER 7, also covered in Chapter 11 of CiMC, namely the check box (✓Within levels of factor       ). Essentially, this gives a constrained (or 2-way) BEST procedure in which the matc...

On the mid-right of the main dialog for BEST, the box headed (Correlation method:) now offers three non-parametric choices and one parametric correlation: Spearman rank, Weighted Spearman rank, Kendall tau and Pearson, covered in equations (11.3), (11.4) and (...

The final area of the main BEST dialog, headed Permutations, which carries out the global BEST test for statistical significance of the best matching combination of variables, is deferred until later in this section. The Next > button, under (Method•BIOENV), g...

The Next > button now takes you to a Results dialog box, which controls two features of the BEST results window, the quantity of output and how the explanatory variables are identified. For a run of BIOENV, (Results detail: Brief or Normal) will output just tw...

A study of diatom assemblages (abundances of 193 species) at 17 sites in the lagoons of Messolongi, Aitoliko and Kleissova in Eastern Central Greece was undertaken by Danielidis DB (1991), Ph.D. thesis, Univ Athens. At each site, a suite of 11 water-column dat...

The question of statistical significance testing on the results of the Bio-Env (or BVStep) procedure naturally arises. Section 14 describes Analyse>RELATE, a (non-parametric) form of Mantel test. For any two independently-derived resemblance matrices, defining...

Another technique for linking sample patterns based on assemblage data to a suite of environmental (or other) explanatory variables was also discussed in Clarke KR et al 2008 J Exp Mar Biol Ecol 366: 56-69 (see the last topic in Chapter 11, CiMC). The well-est...

The Analyse>Cluster>LINKTREE routine has a number of features that are designed to mesh to the PRIMER approach. Firstly, as seen for unconstrained UNCTREE clustering (Section 6), each successive split of the biotic samples into two groups (of potentially unequ...

Continuing the lagoon diatom study, having first selected (highlighting then Select>Highlighted) the optimal 3-variable set (Sal, PO$_4$, In-N), from the above BEST run, in Messolongi environment, and again with the diatom resemblance matrix as the active shee...

Low values of B% correspond to samples which are rather close together on the MDS plot and the question naturally arises as to whether these samples should be split at all – is there any evidence that the biological assemblages differ among the sites 5, 7, 11,...