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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.

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 ...

R is a general tool (). It is a statistical programming language (). There are a lot of people using R. There are a lot of good reasons for this. R is freely available You can download and use R for free. What's not to like about that? R can be used on any pla...

Like any software, R has some down sides. R has a steep learning curve R is a programming language. It was invented by (and is used primarily by) statisticians. To use it successfully, you really do have to be comfortable writing and executing command-line cod...

To re-cap and summarise, below is a table outlining the primary pros and cons of using R, as I see it: Pros Cons $\bullet$ A flexible programming language $\bullet$ Steep learning curve $\bullet$ Free, platform-independent $\bullet$ Packages vary in q...

Anderson, M.J. (2024) Should I use PRIMER or R? PRIMER-e Learning Hub. PRIMER-e, Auckland, New Zealand. https://learninghub.primer-e.com/books/should-i-use-primer-or-r.

PRIMER has a special focus - robust multivariate methods PRIMER is a specialised piece of software that is purposefully designed to analyse multivariate data. It is especially good at handling high-dimensional, non-normal data, which are not able to be analyse...

Like any software package, PRIMER has some down sides. PRIMER has a pretty specific niche As already mentioned, PRIMER's focus is on non-parametric and semi-parametric techniques and graphics for analysing multivariate data, particularly ecological data. It do...

To re-cap and summarise, below is a table outlining the primary pros and cons of using PRIMER, as I see it: Pros Cons $\bullet$ Easy to use $\bullet$ Not free $\bullet$ High-quality results you can trust $\bullet$ Not platform-independent (Windows onl...

Use Both! The take-home message here is: use both! Neither replaces the other. They are good at different things. R is a wonderful programming language and is very flexible and general. You can use it to do heaps of stuff, but it is difficult to use well. Dep...

PERMANOVA vs 'adonis2' It is instructive to look at a particular example. Let's compare the results we get using a routine in R and a routine in PRIMER that should (on the face of it) do the same thing. We'll compare: PERMANOVA (a routine in the PERMANOVA+ ad...

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...

When we compare the output obtained using the two different pieces of software, we can see that there are fundamental differences in the results (Fig. 1). They don't match! Fig. 1. Comparison of results for the holdfast data using PERMANOVA in PRIMER and adon...

Following the PERMANOVA table of results, a suite of key additional details regarding the analysis can be seen in the PERMANOVA output file. These details highlight what makes the implementation of PERMANOVA in PRIMER so unique, surpassing all other software t...

The adonis2 function (in the vegan package in R) will provide a partitioning of the total sum of squares according to a given ANOVA design. However, adonis2 constructs pseudo-F ratios for all of the terms in any model using the residual mean square ($MS$$Res$)...

Another clear difference between the output given by adonis2 by comparison with the output given by PERMANOVA in PRIMER is the fact that adonis2 provides an additional column, headed 'R2'. These are values of $R^2$ for a given term in the model, calculated dir...

In summary: I recommend using PERMANOVA in PRIMER. I do not recommend using adonis2 in R. Except in very limited circumstances, adonis2 does not construct: (i) correct F-ratios; or (ii) correct permutation algorithms. The implementation in adonis2 is far t...