Summary of the pathway
A summary of the essential routines in PRIMER 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 | To implement in PRIMER: |
|---|---|
| 1. Fourth-root transformation | From the original data sheet: click Pre-treatment > Transform(overall) > (Transformation: Fourth root), 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: One-Way - A) & Factors > A: Creek) & (Max permutations: 9999) & ($\checkmark$Plot histogram), click OK. |