Should I use PRIMER or R?
Use both! They are good at different things.
by Marti J. Anderson (2024)
Citation
Anderson, M.J. (2024) Should I use PRIMER or R? PRIMER-e Learning Hub. PRIMER-e, Auckland, New Z...
1. Let's consider using PRIMER
1.1 PRIMER has a lot going for it
PRIMER has a special focus - robust multivariate methods PRIMER is a specialised piece of softwar...
1.2 PRIMER has some down sides
Like any software package, PRIMER has some down sides. PRIMER has a pretty specific niche As alre...
1.3 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...
2. Let's consider using R
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...
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...
2.3 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...
3. PERMANOVA vs adonis2 in R
3.1 Compare example output
PERMANOVA vs 'adonis2' It is instructive to look at a particular example. Let's compare the resul...
3.2 Results don't match
When we compare the output obtained using the two different pieces of software, we can see that t...
3.3 How does PERMANOVA do it?
Following the PERMANOVA table of results, a suite of key additional details regarding the analysi...
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 ...
3.5 What about $R^2$ values?
Another clear difference between the output given by adonis2 by comparison with the output given ...
3.6 Summarising the comparison
In summary: I recommend using PERMANOVA in PRIMER. I do not recommend using adonis2 in R. Except...
4. Take-home messages
5. References
Anderson (2001a) Anderson, M.J. (2001a) A new method for non-parametric multivaria...