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Citation
Anderson, M.J. (2024) A quick guide to PRIMER. PRIMER-e Learning Hub. PRIMER-e, Auckland, New Zealand. https://learninghub.primer-e.com/books/should-i-use-primer-or-r.
3.1 Compare example output
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...
5. References
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...
3.2 Results don't match
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...
3.3 How does PERMANOVA do it?
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...
3.4 How does adonis2 do it?
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$)...
3.5 What about $R^2$ values?
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...
3.6 Summarising the comparison
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...
4.1 Final cautionary notes
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...
Summary of the PERMANOVA analysis
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...