# Running an nMDS (Exe nematodes)

From the directory C:\Examples v7\Exe nematodes, **File>Open** the workspace <ins>Exe ws</ins>, last seen in Section [6](https://learninghub.primer-e.com/books/primer-v7-user-manual-tutorial/chapter/6-clustering-methods-cluster-simprof-unctree-krcluster), of the sediment nematode communities at 19 inter-tidal sites in the Exe estuary. If this does not exist, open the data file <ins>Exe nematode abundance</ins>(.pri) in a clear workspace, and re-run the UPGMA clustering, with **Pre-treatment>Transform (overall)**>Transformation: <ins>Fourth root</ins> and **Analyse>Resemblance**>(Measure•Bray-Curtis similarity)&(Analyse between•Samples), then **Analyse>Cluster>CLUSTER**>(Cluster mode•Group average), and on the resulting dendrogram, **Graph>Special**>(Slicing✓Show slice)>(Resemblance: <ins>30</ins>)>**Create factor**>(Add factor named: <ins>30% slice</ins>). The Bray-Curtis similarity matrix is in <ins>Resem1</ins> and the dendrogram <ins>Graph1</ins>. 

With <ins>Resem1</ins> as the active window, take **Analyse>MDS>Non-metric MDS (nMDS)** and options of (Min. Dimension: <ins>2</ins>)&(Max. Dimension: <ins>3</ins>)&(Number of restarts: <ins>100</ins>)&(Minimum stress: <ins>0.01</ins>) &(Kruskal fit scheme•1)&(✓Configuration plot)&(✓Shepard diagrams)&(✓Ordinations to work sheet) leaving the other boxes unticked for now. The outcome is a results window, <ins>nMDS1</ins>, and a multi-plot <ins>MultiPlot1</ins> which, if unrolled in the Explorer tree (either by clicking the  <img src="//learninghub.primer-e.com/uploads/images/gallery/2024-05/scaled-1680-/plus.jpg" width="17">     in the tree or by clicking on any of the plot components in the multi-plot), shows four plot windows, probably named <ins>Graph3</ins> to <ins>Graph6</ins>. For the first one, remove the spread of symbols with **Graph>Sample labels & symbols**, unchecking (Symbols>By factor), to leave just the labelled default symbols. 

[![ScreenshotPage115a.png](https://learninghub.primer-e.com/uploads/images/gallery/2024-06/scaled-1680-/screenshotpage115a.png)](https://learninghub.primer-e.com/uploads/images/gallery/2024-06/screenshotpage115a.png)