Introduction to R Statistical Software

Plant Breeding and Genomics October 03, 2013 Print Friendly and PDF

Author:

Heather L. Merk, The Ohio State University

This webinar introduces R statistical software with an emphasis on application to plant breeding, including ANOVA using simple linear models, ANOVA using mixed models with multi-year data, variance components calculation to estimate heritability, and simple marker trait analysis. The webinar also includes instruction to obtain R, enter basic commands, import and export data, and install and load packages.

About the Webinar

During this webinar, Dr. Heather Merk, The Ohio State University, introduces R software for statistical analysis, including

  • Downloading this free software
  • How to perform basic commands
  • Where to learn more

Dr. Merk also demonstrates how R has been used to analyze tomato phenotypic data collected for the Solanaceae Coordinated Agricultural Project (SolCAP).

This one hour webinar has been divided into seven videos, which are listed in order on this webpage. The eighth video is the full webinar. The powerpoint slides (in pdf format), sample data files, and sample script are provided at the bottom of the page.

Learning Objectives

At the end of this webinar you should be able to do the following using R:

  • Install and run R
  • Find R packages, install, and load them
  • Read in data and visualize distribution
  • Test if there are differences between varieties (ANOVA using linear regression)
  • Distinguish varieties (Means and t-test)
  • Estimate variance components
  • Use loops to simplify analysis

Videos

Watch the videos here or on a YouTube playlist

  • Part 1 - An introduction to R statistical software and rationale for using R
  • Part 2 - Basic commands using R and an introduction to text editors
  • Part 3 - Description of the sample data, commands to check data importation, and creating histograms
  • Part 4 - Analysis of simple ANOVA models
  • Part 5 - Combining data sets and export tables
  • Part 6 - Loops and where to get help
  • Part 7 - Resources for learning R and the question and answer segment of the live webinar
  • Full Video

Part 1

An introduction to R statistical software and rationale for using R.

If you experience problems viewing this video connect to our YouTube channel or see the YouTube troubleshooting guide.

Part 2

Basic commands using R and an introduction to text editors.

If you experience problems viewing this video connect to our YouTube channel or see the YouTube troubleshooting guide.

Part 3

Description of the sample data, commands to check data importation, and creating histograms.

If you experience problems viewing this video connect to our YouTube channel or see the YouTube troubleshooting guide.

Part 4

Analysis of simple ANOVA models.

If you experience problems viewing this video connect to our YouTube channel or see the YouTube troubleshooting guide.

Part 5

Combining data sets and export tables.

If you experience problems viewing this video connect to our YouTube channel or see the YouTube troubleshooting guide.

Part 6

Loops and where to get help.

If you experience problems viewing this video connect to our YouTube channel or see the YouTube troubleshooting guide.

Part 7

Resources for learning R and the question and answer segment of the live webinar.

If you experience problems viewing this video connect to our YouTube channel or see the YouTube troubleshooting guide.

Full Video

Full 58 minute webinar recording.

If you experience problems viewing this video connect to our YouTube channel or see the YouTube troubleshooting guide.

 

Register for, or watch other plant breeding and genomics "How To" webinars

About the Presenter

Dr. Merk combines her background in plant breeding and genetics with her interest in science communication in her role of content coordinator for the plant breeding and genomics community of practice at eXtension.org. As content coordinator, Dr. Merk leads development, review, and publication of online outreach materials targeted to plant breeding professionals. Dr. Merk obtained her Honors Bachelor of Science from the University of Toronto and her Ph.D. from The Pennsylvania State University.

References Cited

  • Adler, J. 2010. R in a nutshell: a desktop quick reference. O’Reilly, Sebastapol, CA.
  • Crawley, M. 2007. The R book. Wiley, Hoboken, NJ.
  • Dalgaard, P. 2008. Introductory statistics with R. Springer-Verlaugh, NY.
  • Murrell, P. 2006. R graphics. Chapman & Hall/CRC, NY.
  • Zuur, A. F., E. N. Leno, and E.H.W.G. Meesters. 2009. A beginner’s guide to R. Springer, NY.

External Links

Funding Statement

Development of this page was supported in part by the National Institute of Food and Agriculture (NIFA) Solanaceae Coordinated Agricultural Project, agreement 2009-85606-05673, administered by Michigan State University. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the United States Department of Agriculture.

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This work is supported by the USDA National Institute of Food and Agriculture, New Technologies for Ag Extension project.