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2.4 Species similarities
Starting with the original data matrix of abundances (or biomass, area cover etc), the similarity...
1.2 PRIMER has some down sides
Like any software package, PRIMER has some down sides. PRIMER has a pretty specific niche As alre...
1.1 PRIMER has a lot going for it
PRIMER has a special focus - robust multivariate methods PRIMER is a specialised piece of softwar...
4.2 Should I use PRIMER or R? (in short)
Use Both! The take-home message here is: use both! Neither replaces the other. They are good at d...
3.6 Summarising the comparison
In summary: I recommend using PERMANOVA in PRIMER. I do not recommend using adonis2 in R. Except...
2.2 R has some down sides
Like any software, R has some down sides. R has a steep learning curve R is a programming languag...
2.1 R has a lot going for it
R is a general tool (). It is a statistical programming language (). There are a lot of people us...
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 ...
2.3 Pros and Cons of using R
To re-cap and summarise, below is a table outlining the primary pros and cons of using R, as I se...
1.3 Pros and Cons of using PRIMER
To re-cap and summarise, below is a table outlining the primary pros and cons of using PRIMER, as...
Uninstall / re-install PRIMER
If you need to move the PRIMER software to a new machine (or re-image the machine), first uninsta...
3.1 Compare example output
PERMANOVA vs 'adonis2' It is instructive to look at a particular example. Let's compare the resul...
5. References
Anderson (2001a) Anderson, M.J. (2001a) A new method for non-parametric multivaria...
4.1 Final cautionary notes
The purpose of this exposé has been to highlight some important pros and cons associated with usi...
3.2 Results don't match
When we compare the output obtained using the two different pieces of software, we can see that t...
3.5 What about $R^2$ values?
Another clear difference between the output given by adonis2 by comparison with the output given ...
3.3 How does PERMANOVA do it?
Following the PERMANOVA table of results, a suite of key additional details regarding the analysi...
1.4 Sums of squares from a distance matrix
We can now consider the structure of a distance/dissimilarity matrix and how sums of squares for ...
Citation
Anderson, M.J. (2024) Should I use PRIMER or R? PRIMER-e Learning Hub. PRIMER-e, Auckland, New Z...
Install and activate PRIMER
Install the software Double click on the downloaded installation file ('PRIMER7Setup.exe') to st...