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For any up-to-date news about PRIMER, including details of upcoming PRIMER workshops, see our web site at: http://www.primer-e.com Please report any bugs or technical problems to: tech@primer-e.com For licensing and other general enquiries, contact the PRIMER-...

PC with Intel compatible processor. Any modern Windows operating system (XP or later). Sufficient RAM memory to run the operating system satisfactorily. More memory will be required for very large data files. A PDF reader program such as Adobe Acrobat Reader ...

You need to be logged on as an administrator. You can keep version 6 or earlier versions installed. Download the latest setup file from our web site. Install by double clicking on the file. (If installing the trial version off-line then you must have a reasona...

Detailed information and examples of virtually all the analyses offered by PRIMER v7 are found in the accompanying Methods manual: Clarke KR, Gorley RN, Somerfield PJ, Warwick RM 2014, Change in Marine Communities, 3rd edn, PRIMER-E Ltd, Plymouth (henceforth r...

In examples in this manual you may see the main menu item PERMANOVA+. This is an add-on product to PRIMER, operating with PRIMER 7 exactly as it did with PRIMER 6. Its operation is covered by another (combined) Methods/User manual: Anderson MJ, Gorley RN, Clar...

Application Areas PRIMER 7 (Plymouth Routines In Multivariate Ecological Research) consists primarily of a wide range of univariate, graphical and multivariate routines for analysing arrays of species-by-samples data from community ecology. Data are typically ...

Wizards and major new analysis options Dialog boxes generally are more ‘wizard’-based, unifying and simplifying parameter input and, importantly, there is a new Wizards menu (Section 10) with three items, as follows: Basic multivariate analysis wizard which ...

Emphases & text symbols Text in bold indicates the menu items that need to be selected, > denotes cascading sub-menu items, tab choices, dialog boxes or sub-boxes, • denotes a button entry in a dialog box (so-called ‘radio buttons’ – only one can be selected),...

Opening the examples After launching the PRIMER desktop by clicking on its icon, the first step is to open a worksheet of multivariate data, e.g. species abundances over a number of samples. The user’s own data will typically be read into the program from Exce...

Reading data in from Excel As an example of reading in data from Excel, first open and examine the file Fal environment.xls, to note the simple format of a title in box A1, column headings (unique) for the samples in row 2, row headings (also unique) for the v...

Basic MVA wizard To cater for users completely unfamiliar with the basic outputs from a multivariate analysis, e.g. of the species abundance matrix opened above, PRIMER 7 now has a Wizards>Basic multivariate analysis menu item, which automatically generates ro...

Pre-treatment of the data (sometimes in more than one way) is usually desirable. For assemblage data, transformations will reduce the dominant contribution of abundant species to Bray-Curtis similarities. Though not usually needed for controlled (‘quantitative...

On active sheet Fal nematode abundance, run Wizards>Matrix display, not taking all the defaults in this case but unticking/unchecking the (Reduce species set) box so that all species are retained, and taking (Transformation: Square root) & (✓Retain sample grou...

For environmental-type data, such as the Fal environment sheet, it is often appropriate to transform individual variables selectively, rather than all in the same way, since they may be of very disparate types. Here, the main objective is to avoid strong skewn...

Resemblance calculation The next stage in both the Fal nematode and environment runs of the Basic multivariate analysis wizard was to create an appropriate triangular resemblance matrix between all pairs of samples. This is a run of Analyse>Resemblance on the ...

The wizard then runs, for both biotic and abiotic data, Analyse>ANOSIM>(Model: One-way - A) & (Factors A: Creek)>(Type Unordered) on the respective resemblance matrices as active sheets. This tests for statistically significant differences overall among the 5 ...

The Basic MVA wizards then run a cluster analysis, again on the respective resemblance matrices. This component routine is Analyse>Cluster>CLUSTER>(Cluster mode•Group average), without taking the (✓SIMPROF test) option since the latter is the appropriate test ...

The Basic MVA wizard next produces non-metric MDS (nMDS) plots in 2-d and 3-d, together with their associated Shepard diagrams, which show how well (or badly) these distances among samples in the low-d ordination plots approximate the high-d resemblances. If t...

The final step in the Basic MVA wizard is to break down the dissimilarities (or distances) between pairs of creeks into their contributions from each of the species (or abiotic variables), in the tables of SIMPER1 (or SIMPER2), see at the end of Section 10. Th...

A further bubble plot you might like to try on the Fal nMDS is to superimpose abiotic variables from the Fal environment worksheet, and we have already referred to the constrained LINKTREE clustering that tries to explain community groupings in terms of partic...