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3.3 How does PERMANOVA do it?
Following the PERMANOVA table of results, a suite of key additional details regarding the analysi...
Entering data directly
Most users will already have their data stored in rectangular form in some other software, e.g. a...
Compatibility of files
PRIMER 7 is fully forward-compatible from v6, and can input PRIMER 6, 5 and 4 data (*.pri and *.p...
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...
Example data
Help>Get Examples V7 will take you to the data sets used throughout this manual [and Help>Get Exa...
Help system & manuals
The Help main menu has the entries shown, starting with View Help, the HTML Help system: This li...
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 2: Jaccard resemblance
Calculate the Jaccard resemblance From the 'Molluscs' data sheet, click Analyse > Resemblance.......
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 3: Cluster
Now that we have a resemblance matrix, we can proceed with a cluster analysis of the data. The pu...
Download manuals
The following manuals can be downloaded from within the software itself: Getting Started...: Cl...
1.5 The pseudo-F statistic
Once the partitioning has been done we are ready to calculate a test statistic associated with th...
1.2 Univariate techniques
For diversity indices and other single-variable extractions from the data matrix, standard statis...
0.2 Acknowledgements
Any initiative spanning quite as long a period as the PRIMER software represents (the first recog...