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This manual is available as a free downloadable pdf file. Please click on the following link: User_Manual_Tutorial_v7_HQprint.pdf

Please use the following to cite this book or any of its content: Clarke KR, Gorley RN, Somerfield PJ & Warwick RM. (2014). Change in marine communities: an approach to statistical analysis and interpretation, 3rd edition. PRIMER-E: Plymouth.

We're delighted that you've chosen to use PRIMER software. If you run in to any difficulties, we're here to help! Getting in touch with us For any up-to-date news, including details of upcoming courses, please consult our website: https://www.primer-e.com/. Pl...

Here we provide instructions for the download and installation of PRIMER 7 (with PERMANOVA+). Please read this information in conjunction with our End-User Licence Agreement (EULA). These instructions are applicable to enable activation of single end-user lice...

First, head to our download page. Where it says 'Choose your Software', choose 'PRIMER 7 with PERMANOVA+, Full version - valid licence key required'. Enter your details, and click 'Download software'. On the screen that says 'Thank you!', click on the l...

Install the software Double click on the downloaded installation file ('PRIMER7Setup.exe') to start the installation process: A 'PRIMER 7 Setup' window will appear. Please read the 'End-User License Agreement for PRIMER'. If you agree to the terms and cond...

If you need to move the PRIMER software to a new machine (or re-image the machine), first uninstall your Licence Key (when connected to the internet) and then uninstall the PRIMER software, if required. Uninstall-reinstall cycles are intended to cope with the ...

The following manuals can be downloaded from within the software itself: Getting Started...: Clarke, K.R., Gorley, R.N. (2015) Getting started with PRIMER v7. PRIMER-e: Auckland, New Zealand. User/Tutorial Manual...: Clarke KR, Gorley RN (2015) PRIMER v7: U...

You must be connected to the internet to download the example datasets. The Help menu item in PRIMER has options to retrieve folders that contain a large number of example datasets. These include: Examples Trial...: available when the software is in free-tri...

Data from the Fal estuary Example datasets in PRIMER can be obtained via the Help menu item. In trial mode, click Help > Get Examples Trial..., and you can download the following four files of example data (held in a folder called 'Examples Trial') to a locati...

Step 1. Ensure your data are in a format suitable for import into PRIMER Suppose we have a dataset in Excel that is already in a suitable format for import into PRIMER. The environmental data from the Fal estuary provides an example of this. These data are fou...

Anderson (2001a) Anderson, M.J. (2001a) A new method for non-parametric multivariate analysis of variance. Austral Ecology, 26, 32-46. Anderson (2001b) Anderson, M.J. (2001b) Permutation tests for univariate or multivariate analys...

Check the orientation After import, make sure you have specified the orientation correctly by examining the labels on the columns and rows of the data frame. For example, after importing the Fal environmental data from Excel (see the previous page), you can se...

Save your data in PRIMER (*.pri) format To save a data sheet in PRIMER (*.pri) format, click on the data sheet inside the PRIMER workspace you want to save and click File > Save Data As.... Note the default file-type for saving a data file is 'PRIMER Data Fil...

Rationale Multivariate data are very complex and can be difficult to analyse and interpret. Each variable can be considered it's own dimension, with its own story to tell. Thus, when there are a lot of variables (e.g., if we have sampled occurrence, abundance,...

Perform the transformation There are a range of possible transformations one might use in a pre-treatment of biotic data. For some discussion regarding appropriate pre-treatment transformations, see Chapter 9 in 'Change in Marine Communities'. In the case of t...

For a description of the Bray-Curtis resemblane measure and the rationale for its use with biotic data, see and Chapter 2 in 'Change in Marine Communities'. With the data sheet named '4th-root' from the previous step as the active window, click on Analyse > ...

Now that we have a resemblance matrix, we can proceed with a cluster analysis of the data. The purpose of a cluster analysis is to join together samples that are similar to one another, and also to clarify separations of groups (or clusters) of samples that ma...

The cluster analysis goes some way towards helping us to understand potential patterns of similarity among the samples. It is particularly good at showing us clusters of samples that are highly similar. To better visualise patterns of relationships among all o...

The ordination plot gives us a visualisation of the rank-order relationships among the samples, based on the dissimilarity measure. Next, we may wish to test the null hypothesis that there are no differences among the five creeks. We can use a non-parametric m...