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Anderson, M.J. (2026). "Get Started with PRIMER 8." PRIMER-e Learning Hub. PRIMER-e, Auckland, New Zealand. https://learninghub.primer-e.com/books/get-started-with-primer-8.

Data from the Fal estuary Example datasets can be obtained via the Help menu item. Click Help > Get Examples..., and you can download the folder of examples called 'Examples_P8' to a location of your choice. Inside this folder, there are individual folders tha...

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...

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 in the Explorer tree inside the PRIMER workspace you want to save and click File > Save Data As.... Note the default file-type for saving a data fil...

Rationale Multivariate data are very complex and can be difficult to analyse and interpret. Each variable can be considered its 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 resemblance 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...

A summary of the essential routines in PRIMER 8 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 transforma...

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 ...

If you have purchased a subscription to PRIMER 8 with PERMANOVA+, then you will have access to the PERMANOVA+ main menu item that allows you to perform a broad range of additional analyses using a suite of routines that are not available in the basic PRIMER 8 ...

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 second, run the PERMANOVA analysis, given the design, on a chosen resemblance matrix (arising from the data of interest). Generally, we first ...

Open up the example data file Launch PRIMER, then click File > Open... from the main menu, navigate to the folder named 'NE_NZ_holdfasts' in the 'Examples_P8' directory, and select 'NE_NZ_holdfast_fauna.pri'. Click Open to display the species matrix. Click on...

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...