A Quick Guide to PRIMER
A quick guide to get you up and running with PRIMER software
by Marti J. Anderson (2024)
Citation
Anderson, M.J. (2024) A quick guide to PRIMER. PRIMER-e Learning Hub. PRIMER-e, Auckland, New Ze...
1. General information
We're delighted that you've chosen to use PRIMER software. If you run in to any difficulties, we'...
2. Installing PRIMER software
Overview
Here we provide instructions for the download and installation of PRIMER 7 (with PERMANOVA+). Ple...
Download the installer
First, head to our download page. Where it says 'Choose your Software', choose 'PRIMER 7 with PE...
Install and activate PRIMER
Install the software Double click on the downloaded installation file ('PRIMER7Setup.exe') to st...
Uninstall / re-install PRIMER
If you need to move the PRIMER software to a new machine (or re-image the machine), first uninsta...
3. Download manuals and examples
(from within the PRIMER software)
4. Getting data in to PRIMER
Opening example data
Data from the Fal estuary Example datasets in PRIMER can be obtained via the Help menu item. In t...
Importing data from Excel
Step 1. Ensure your data are in a format suitable for import into PRIMER Suppose we have a datase...
Post-import data checks
Check the orientation After import, make sure you have specified the orientation correctly by exa...
Save your data & workspace
Save your data in PRIMER (*.pri) format To save a data sheet in PRIMER (*.pri) format, click on t...
5. Example analysis pathway (CLUSTER, MDS, ANOSIM)
An analysis of biotic data
Rationale Multivariate data are very complex and can be difficult to analyse and interpret. Each ...
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...
Step 4: Ordination
The cluster analysis goes some way towards helping us to understand potential patterns of similar...
Step 5: ANOSIM test
The ordination plot gives us a visualisation of the rank-order relationships among the samples, b...
Summary of the pathway
A summary of the essential routines in PRIMER that were used to produce the 5-step analysis pathw...
6. Some Wizards
7. Run a PERMANOVA
Overview
If you have purchased the PERMANOVA+ add-on, then you will have an additional menu item that allo...
A three-factor hierarchical design
We will run PERMANOVA on an example dataset consisting of assemblages of molluscs collected from ...
Steps in a PERMANOVA analysis
The two essential steps required to run a PERMANOVA analysis in PRIMER are always: first, speci...
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.......
Step 3: Specify the design
PERMANOVA requires a design file to run. You can see the Factors associated with the holdfast dat...
Step 4: Run PERMANOVA
Once the design file is created, we are ready to go ahead with the PERMANOVA analysis. Click on ...
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...
Step 5: Ordination of centroids
Having seen the results of a PERMANOVA analysis, it is natural to wish to see a visualisation of ...
Summary of the PERMANOVA analysis
A summary of the essential commands associated with performing this PERMANOVA analysis of the hol...
8. References
Anderson (2001a) Anderson, M.J. (2001a) A new method for non-parametric multivaria...