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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...
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...
Matrix display
The Matrix display wizard produces a shade plot of a multivariate data matrix, with a useful orde...
1. General information
We're delighted that you've chosen to use PRIMER software. If you run in to any difficulties, we'...
Editing labels
Take File>Open>(Filename: Tasmania copepods v4.pm1)>Type•Species-sample to input this (archival) ...
Text-format input files
The Tasmania meiofauna directory also contains three different text format versions of the copepo...
Opening the same file twice
PRIMER 7 will allow the same file to be opened into the workspace more than once, since the respo...
Overview
If you have purchased the PERMANOVA+ add-on, then you will have an additional menu item that allo...
Summary of the PERMANOVA analysis
A summary of the essential commands associated with performing this PERMANOVA analysis of the hol...
Summary of the pathway
A summary of the essential routines in PRIMER that were used to produce the 5-step analysis pathw...
Step 4 (continued): Key additional details about PERMANOVA in PRIMER
Following the PERMANOVA table of results, a suite of key additional details regarding the analysi...
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...
(Ekofisk oil-field fauna)
The abundance file Ekofisk macrofauna counts.pri is displayed within the PRIMER desktop. It shows...
3.5 What about $R^2$ values?
Another clear difference between the output given by adonis2 by comparison with the output given ...