Guide to Ecological Community Analysis

Methods covered:

• Principle Component Analysis (PCA)
• Multidimensional Scaling
  • parametric (MDS)
  • non-parametric (NMDS)

Dataset

The dataset protein.csv is the protein consumption of various European countries.

After reading in the dataset you will process it at least two ways:

1. Tidy
2. Standardise

Tidying the data means ensuring the dataset will run smoothly through the functions. Here I pipe (|>) together the tidying and standardising functions. Firstly, I set the Country column to the rownames. This removes the column from the analysis and indicates the values that will be mapped in the ordination plots. Secondly, I select the variables that I want in the plot. Note, I indicate that the select function is from the dplyr package as the MASS package also has a select function. This can be omitted if

Unsupervised

PCA

To Do

MDS

To Do

• NMDS Plots in R by Jackie Zorz

Cluster

To Do

Supervised

ANOSIM

To Do

To Do

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