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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...
Citation
Anderson, M.J. (2024) A quick guide to PRIMER. PRIMER-e Learning Hub. PRIMER-e, Auckland, New Ze...
8. References
Anderson (2001a) Anderson, M.J. (2001a) A new method for non-parametric multivaria...
Step 4: Run PERMANOVA
Once the design file is created, we are ready to go ahead with the PERMANOVA analysis. Click on ...
Step 5: Ordination of centroids
Having seen the results of a PERMANOVA analysis, it is natural to wish to see a visualisation of ...
Steps in a PERMANOVA analysis
The two essential steps required to run a PERMANOVA analysis in PRIMER are always: first, speci...
Step 3: Specify the design
PERMANOVA requires a design file to run. You can see the Factors associated with the holdfast dat...
Step 1: Data selection
Open up the example data file Launch PRIMER, then click File > Open... from the main menu, naviga...
Step 2: Jaccard resemblance
Calculate the Jaccard resemblance From the 'Molluscs' data sheet, click Analyse > Resemblance.......
Install and activate PRIMER
Install the software Double click on the downloaded installation file ('PRIMER7Setup.exe') to st...
Step 5: ANOSIM test
The ordination plot gives us a visualisation of the rank-order relationships among the samples, b...
Step 1: Transformation
Perform the transformation There are a range of possible transformations one might use in a pre-t...
Step 2: Resemblance
For a description of the Bray-Curtis resemblane measure and the rationale for its use with biotic...
Step 3: Cluster
Now that we have a resemblance matrix, we can proceed with a cluster analysis of the data. The pu...