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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...

Anderson, M.J. (2024) A quick guide to PRIMER. PRIMER-e Learning Hub. PRIMER-e, Auckland, New Zealand. https://learninghub.primer-e.com/books/a-quick-guide-to-primer.

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...

The Help main menu has the entries shown, starting with View Help, the HTML Help system: This lists and describes all menu items but in succinct fashion since (in addition to a brief Getting Started manual which comes with the trial version) there are two com...

The Help>About PRIMER menu item will tell you: which maintenance version number you are currently operating of PRIMER 7; the licence type, e.g. Trial/Full/Academic; and (if it is not a trial version) the unique serial number registered to you in the PRIMER-e d...

You will need to run Help>Install Licence at the point at which you have purchased an installation key (32 characters in blocks of 4), which is copied and pasted into the License Key box seen below. Once you have installed this key you do not need it again in...

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...

Help>Get Examples V7 will take you to the data sets used throughout this manual [and Help>Get Examples Add-on will make available the data sets used in the PERMANOVA+ manual]. You are prompted for a directory in which to store the data files, i.e. a location i...

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...

The purpose of this exposé has been to highlight some important pros and cons associated with using PRIMER and R in routine analytical work. It is clear that both R and PRIMER have great capabilities and using them both should be encouraged. A genuine question...

The installation and subsequent run of Help>Get Examples V7 will have placed a number of sub-directories (BC zooplankton, Bermuda benthos, …, Wrasse diets) into the \Examples v7 directory, placed in a location which you have chosen. Throughout this manual it i...

Whether the extensions *.pri, *.xls(x) etc display, or not, is a function of your Windows set-up; if you have suppressed them it is still easy to distinguish the different file types by their icon. There are PRIMER 7-specific icons and extensions for the fol...

PRIMER 7 is fully forward-compatible from v6, and can input PRIMER 6, 5 and 4 data (*.pri and *.pm1), similarity (*.sid and *.sim) and aggregation (*.agg and *.pm1) files, and PRIMER 6 plot (*.ppl) and workspace (*.pwk) files, directly. But it is not, in gener...

Start the program by (double)-clicking on the desktop or task bar PRIMER 7 icon , giving the window below. A second method is to double-click on a file with a recognised PRIMER extension, e.g. a worksheet file (.pri) or a workspace file (.pwk), and PRIMER 7 w...

Most users will already have their data stored in rectangular form in some other software, e.g. as an Excel spreadsheet, which can be opened directly and straightforwardly (see later). However, data arrays can be typed directly into PRIMER, if necessary. Selec...