Welcome to a Little Book of R for Multivariate Analysis!

By Avril Coghlan, University College Cork, Cork, Ireland. Email: a.coghlan@ucc.ie

This is a simple introduction to multivariate analysis using the R statistics software.

There is a pdf version of this booklet available at: https://github.com/avrilcoghlan/LittleBookofRMultivariateAnalysis/raw/master/_build/latex/MultivariateAnalysis.pdf.

If you like this booklet, you may also like to check out my booklet on using R for biomedical statistics, http://a-little-book-of-r-for-biomedical-statistics.readthedocs.org/, and my booklet on using R for time series analysis, http://a-little-book-of-r-for-time-series.readthedocs.org/.

Contents:

• How to install R
  • Introduction to R
  • Installing R
    • How to check if R is installed on a Windows PC
    • Finding out what is the latest version of R
    • Installing R on a Windows PC
    • How to install R on non-Windows computers (eg. Macintosh or Linux computers)
  • Installing R packages
    • How to install an R package
    • How to install a Bioconductor R package
  • Running R
  • A brief introduction to R
  • Links and Further Reading
  • Acknowledgements
  • Contact
  • License
• Using R for Multivariate Analysis
  • Multivariate Analysis
  • Reading Multivariate Analysis Data into R
  • Plotting Multivariate Data
    • A Matrix Scatterplot
    • A Scatterplot with the Data Points Labelled by their Group
    • A Profile Plot
  • Calculating Summary Statistics for Multivariate Data
    • Means and Variances Per Group
    • Between-groups Variance and Within-groups Variance for a Variable
    • Between-groups Covariance and Within-groups Covariance for Two Variables
  • Calculating Correlations for Multivariate Data
  • Standardising Variables
  • Principal Component Analysis
    • Deciding How Many Principal Components to Retain
    • Loadings for the Principal Components
    • Scatterplots of the Principal Components
  • Linear Discriminant Analysis
    • Loadings for the Discriminant Functions
    • Separation Achieved by the Discriminant Functions
    • A Stacked Histogram of the LDA Values
    • Scatterplots of the Discriminant Functions
    • Allocation Rules and Misclassification Rate
  • Links and Further Reading
  • Acknowledgements
  • Contact
  • License

Acknowledgements

Thank you to Noel O’Boyle for helping in using Sphinx, http://sphinx.pocoo.org, to create this document, and github, https://github.com/, to store different versions of the document as I was writing it, and readthedocs, http://readthedocs.org/, to build and distribute this document.

Contact

I will be very grateful if you will send me (Avril Coghlan) corrections or suggestions for improvements to my email address a.coghlan@ucc.ie

License

The content in this book is licensed under a Creative Commons Attribution 3.0 License.