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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...

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...

A summary of the essential commands associated with performing this PERMANOVA analysis of the holdfast data according to the 3-factor hierarchical experimental design is given in the table below: Step To implement in PRIMER: 1. Select variable subset Fr...

Anderson, M.J. (2026). "What's New in PRIMER 8." PRIMER-e Learning Hub. PRIMER-e, Auckland, New Zealand. https://learninghub.primer-e.com/books/whats-new-in-primer-8.

PRIMER 8 with PERMANOVA+ is a substantial upgrade on its predecessor, offering a host of marvelous new tools and statistical methods. These range from simple utilities to make your life easier (such as a tool to easily rename the levels of a factor), through t...

Most of the methods in the list below are unique to PRIMER 8 and are not available in any other software package. Some of the methods are not new (such as the non-parametric univariate Mann-Whitney U test), but are implemented in a novel way in P8. Expanded ...

New default colour palette - The new colour palette for PRIMER graphics ensures distinctive colours by default that carefully accommodate several different forms of colour-blindness. New selection options - Select subsets of variables and/or samples by nam...

Adegoke (2019) Adegoke, N. (2019) Contributions to improve power, efficiency and scope of control-chart methods . PhD thesis, School of Natural and Computational Sciences (SNCS), Massey University, New Zealand, 284 pp. link to source A...

Summary statistics provide essential information to help you get to know your variables, their fundamental statistical properties and numerical characteristics. In P8, if you click on Tools > Summary Stats... you will see (Fig. 1.1) that we have greatly expand...

Given a set of values $\{ y_1, y_2, ..., y_n \}$ for any individual variable $Y$, the following summary statistics can be calculated by clicking on Tools > Summary Stats... in PRIMER 8: Average: $\hspace{1mm}$ $\bar{y} = \sum_{i=1}^n{y_i} / n $, the average ...

To show the utility of this tool, we will calculate some summary statistics from a study examining changes in macrofaunal communities inhabiting sediments near an oil platform (Ekofisk) in the North Sea, provided by . These data consist of counts of the abunda...

To run summary statistics on your variables separately for multiple groups of data, just choose a factor by which you would like to split the data in the dialog. For example, for the Ekofisk dataset, suppose we wished to obtain summary statistics (means and st...

For environmental data, we might choose to calculate different sorts of summary statistics than the kinds of things we would want to know about biotic data consisting of counts. For count data, quantities like the numbers of zeros, singletons, doubletons and f...

Overview The Wilcoxon signed-rank test was described by . It is designed for the situation where there are two groups of values, and any individual value in one group is paired with a specific value in the other group. For example, you might have a treatment a...