Guide to Ecological Community Analysis

Methods covered:

• Principle Component Analysis (PCA)
• Multidimensional Scaling (MDS)
  • parametric (MDS)
  • non-parametric (NMDS)
• Cluster Dendrogram
• Analysis of Similarity (ANOSIM)

Dataset

The example dataset is dune from the vegan package.

Data Preparation

• Dissimilarity matrix

Unsupervised/Exploratory

PCA

Link to script.

Biplot

---

MDS

Link to script.

Multidimensional scaling is a form of dimension reduction.

Stress

This table can be used as a rule of thumb.

Stress	Meaning
0.2	poor fit
0.1–0.2	interpret cautiously
<0.1	good ordination
<0.05	excellent

---

Resources

• NMDS Plots in R by Jackie Zorz

Cluster

---

Supervised/Predictive

ANOSIM

Link to script.

The analysis of similarity (ANOSIM) is a non-parametric test that uses a rank-based approach to test whether groups of samples are different.

To Do

• Technique explanations
• Add cluster analysis
• Add ANOSIM
• Expanded figure customisation
• Add table presentation for RMarkdown
• Improve biplot in PCA script