# Summary of the PERMANOVA analysis

A summary of the essential steps associated with performing this PERMANOVA analysis of the holdfast data according to the 3-factor hierarchical experimental design is given in the table below:

| Step<div style="width:190px"></div> | To implement in PRIMER: |
| -------- | ----------- |
| 1. Select **variable subset** | *From the original data sheet:* click **Select** > **Variables...** > ($\bullet$Indicator levels > Indicator name: <ins>Phylum</ins>), click **Levels...**> (Selection > Include: <ins>Mollusca</ins>), click **OK**. |
| 2. Jaccard **resemblance** | *From the subset-selected data sheet:* click **Analyse** > **Resemblance** > (Measure $\bullet$Other > <ins>S7 Jaccard</ins>) & (Analyse between $\bullet$Samples), click **OK**. |
| 3. Specify the **design** | <ul><li>*From the resemblance matrix:* click **PERMANOVA+** > **Create PERMANOVA design...** </li><li>*Fill in the appropriate details of the design in the design file, including types of factors and any nested structures.*</li></ul> |
| 4. Run **PERMANOVA** | *From the resemblance matrix:* click **PERMANOVA+** > **PERMANOVA...** > (Design Worksheet: <ins>Design1</ins>) & (default settings for the rest), click **OK**.  |
| 5. Ordination of **centroids**  | <ul><li>*From the resemblance matrix:* click **PERMANOVA+** > **Distance Among Centroids...** > (Grouping factor: <ins>Area</ins>), click **OK**.</li> <li>*From the resulting resemblance matrix among area centroids:* click **Analyse** > **MDS** > **Non-metric MDS...**, take all the defaults and click **OK**.</li> <li>*To specify labels and symbols:* click **Graph** > **Sample Labels & Symbols...**.</li></ul> |