# Summary of the pathway

A summary of the essential routines in PRIMER 8 that were used to produce the 5-step analysis pathway described above for the nematode (biotic) data from the Fal estuary is given in the table below:


| Step<div style="width:190px"></div> | To implement in PRIMER: |
| ------ | ----------- |
| 1. Fourth-root **transformation** | *From the original data sheet:* click **Pre-treatment** > **Transform(overall)** > (Transformation: <ins>Fourth root</ins>), click **OK**. |
| 2. Bray-Curtis **resemblance** | *From the transformed data sheet:* click **Analyse** > **Resemblance** > (Measure $\bullet$Bray-Curtis similarity) & (Analyse between $\bullet$Samples), click **OK**. |
| 3. Hierarchical group-average **cluster** analysis | *From the resemblance matrix:* click **Analyse** > **Cluster** > **CLUSTER...** > (Cluster mode $\bullet$Group average) & ($\checkmark$Plot dendrogram), click **Finish**. |
| 4. Non-metric MDS **ordination**| *From the resemblance matrix:* click **Analyse** > **MDS** > **Non-metric MDS (nMDS)...** > (see if you are happy with the default settings), click **OK**.  |
| 5. Analysis of similarities (**ANOSIM**)  | *From the resemblance matrix:* click **Analyse** > **ANOSIM...** > Design > (Model: <ins>One-Way - A</ins>) & Factors > A: <ins>Creek</ins>) & (Max permutations: <ins>9999</ins>) & ($\checkmark$Plot histogram), click **OK**. |