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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...

A useful analysis pathway (including the Example Analysis Pathway done above, with its five steps), can be accomplished in one fell swoop using the Basic multivariate analysis wizard. This will perform a suite of multivariate analyses commonly performed for ei...

The Matrix display wizard produces a shade plot of a multivariate data matrix, with a useful ordering of its rows and columns that can help to clarify inter-sample and inter-species relationships, as well as gradients in turnover based on a resemblance matrix ...

A summary of the essential routines in PRIMER that were used to produce the 5-step analysis pathway described above for the nematode (biotic) data from the Fal estuary is given in the table below: Step To implement in PRIMER: 1. Fourth-root transformati...

If you have purchased the PERMANOVA+ add-on, then you will have an additional menu item that allows you to perform a broad range of additional analyses using a suite of routines that are not available in the base PRIMER 7 package, including PERMANOVA, PERMDISP...

We will run PERMANOVA on an example dataset consisting of assemblages of molluscs collected from holdfasts of the kelp Ecklonia radiata in a 3-factor hierarchical experimental design. There were n = 5 holdfasts collected from each of 2 areas (tens of meters ap...

The two essential steps required to run a PERMANOVA analysis in PRIMER are always: first, specify the design; and then, run the PERMANOVA analysis, given the design, on a chosen resemblance matrix (arising from the data of interest). Generally, we first ne...

Open up the example data file Launch PRIMER, then click File > Open... from the main menu, navigate to the folder named 'NZ holdfast fauna' in the 'Examples v7' directory, and select 'NZ holdfast fauna abundance.pri'. Click Open to display the species matrix. ...

Calculate the Jaccard resemblance From the 'Molluscs' data sheet, click Analyse > Resemblance.... In the 'Resemblance' dialog, choose ($\bullet$Other) and then click on the drop-down menu to find 'S7 Jaccard', then click OK. (Note: 'S7' refers to the nomencla...

PERMANOVA requires a design file to run. You can see the Factors associated with the holdfast data matrix (or its resemblance matrix) by clicking on Edit > Factors.... These factors will be 'visible' to the PERMANOVA dialog that we will use to create our desig...

Once the design file is created, we are ready to go ahead with the PERMANOVA analysis. Click on the 'Jaccard' resemblance matrix in the Explorer tree so that it is the active item in the workspace, then click PERMANOVA+ > PERMANOVA... Check to see that th...

Having seen the results of a PERMANOVA analysis, it is natural to wish to see a visualisation of the patterns among centroids belonging to different groups or combinations of levels of different factors in the study design. In many cases, particularly if there...

Following the PERMANOVA table of results, a suite of key additional details regarding the analysis can be seen in the PERMANOVA output file. (Note: It is not necessary to fully unpack all of these details to continue on with the analysis and interpretation of ...

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...