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Save and close Tasmania ws and, as a last example, open the recently closed N Sea ws workspace. On the Normalised biomarkers sheet, run Analyse>SIMPER>(Design•One way>Factor A: Site) & (Measure•Euclidean distance), unchecking the box which truncates the listin...

Both the Edit (see Section 1) and Tools main menus carry out ‘housekeeping’ manipulations on a dataset (or a resemblance or variable information sheet, such as an aggregation file). The operations are usually rather straightforward, and with an obvious outcome...

Tools>Average and Sum operate in the same way on data sheets. For example, when (Samples• Averages for factor: area) & (Variables•No averaging) is selected, they average (or sum) across all samples with the same level of the specified factor, separately for ea...

So far we have only seen variable information sheets, containing taxonomic (or other) hierarchies (*.agg files), used in calculating specialised forms of resemblance which exploit the relatedness of species in the samples being compared (Section 5). More signi...

Use the open aggregation file, Groundfish taxonomy, to show the smaller set of Tools items (Tree, Check, Duplicate) available when the active window is of variable information. Tools>Duplicate has been seen previously for worksheets and plots (in Sections 3 an...

The other Tools menu item for aggregation sheets is distinctive to this case, namely Tools>Tree; it simply displays the hierarchical structure of an aggregation file in the same way as the Explorer tree, in a left-hand panel. Successive clicking on the ic...

Tools>Duplicate operates in the same way whether the active window is a data array, resemblance matrix, variable information sheet or plot. In the case of a Graph window, Duplicate is the only specific option offered on the Tools menu, and there are no choices...

The nematode and copepod datasheets from 16 samples at a Tasmanian sand-flat (C:\Examples v7\ Tasmania meiofauna) were seen in both the previous two sections, in workspace Tasmania ws, but if the latter is not available open Tasmania nematodes and Tasmania cop...

Occasionally, use of strict label names does not give the this desired outcome, and the default behaviour can be changed to force PRIMER to consider an identical label, but in a different matrix, to be treated as a different name. For example, this might be ne...

The best policy to avoid confusion is to use precise, unique species and sample labels (typically, the sample label would be a conglomeration of all the different study design factors and a replicate number). However, conflicting desirable criteria can sometim...

Perhaps the greatest benefit of the strict label matching in PRIMER is the ability to Tools>Merge assemblage data when two sets of samples, taken at different times or places, are not recorded on a common data sheet, with predetermined taxonomic categories. Sp...

The subject of missing data has arisen several times already (Sections 1, 3, 5) and the point made that the terminology and sheet entry Missing! refers only to variables (usually environmental -type variables) that are not recorded for some samples. It does no...

Tools>Missing is designed to operate only on matrices for which: a) assumptions of multivariate normality can be made; b) there are many fewer variables than samples, so that there are enough data values to be able to estimate the parameters representing means...

Transformation options for the Clyde environmental matrix, Clyde environment, are discussed in more detail in the following (PCA) section, but the tool to carry out separate transforms on sets of variables, Pre-Treatment>Transform(individual), rather than tran...

The following section (on PCA) will discuss further the choice of particular transformations to avoid the sensitivity of PCA (and Euclidean distances in general) to outliers in some environmental variables, but choice of individual transformations is often a w...

Ranking is also a menu option when the active sheet is a resemblance (Tools>Rank distance), but it operates a little differently. This time, all elements of the triangular matrix are ranked together, rather than separate ranking of the rows or columns of the r...

The Clyde environment sheet has samples as rows and variables as columns. This is the opposite of the ecological matrices typically seen so far, such as Clyde macrofauna biomass, in which rows are the variables (species). The environment matrix is displayed ac...

Unlike previous versions, in PRIMER 7 the Transform(individual) routine has been moved to a more convenient – and logical – position in the Pre-treatment menu. Its routine use is therefore covered in Section 4, and its application has been seen several times a...

For an example of an Expression combining two (or more) variables, use the Clyde environmental sheet but copy it (Tools>Duplicate), which is always a good idea when experimenting! The aim is to create a new variable (column) which is the C:N ratio, so first Ed...

Similarly, expressions can combine samples, or even factors (or indicators) on those samples (or variables) – and expressions can even incorporate different worksheets. In fact some of the most useful applications of complex expressions are in combinations of ...