Intro to R for Biologists

EEOB, OSU, Spring Quarter 2012

                         Jennings Hall 0160

                         Tuesdays 3-5pm

                          Office hours:
                            Monday 9 April 3-5pm, Rm 322, Aronoff
                         All subsequent Mondays 9-11am, Rm 322, Aronoff

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Objectives

1. Learn to use R for the management, description, analysis and visualisation of ecological data.
2. Learn best principles of data exploration, analysis and visualisation.

Recommended Course Book (to be published soon!)

Getting Started with R: website

R cheat sheet

Course Schedule

26 March 2012 - Why R? Introduction and overview of R

First, read this New York Times article.
Then, watch these online videos: here, and Parts 1, 2, 3 and 4.

Next...
    Install R on to your laptop! (go to www.r-project.org, and follow links through to your OS)

    And get ready for some gRRRReat fun!

3 & 10 April 2012 - Guided introduction to R and basic ideas

Class 1. Introduction to R                                              (ppt | R code)

Class 2. Tour of R                                                         (ppt)

Class 3. First R session, guided                                      (ppt | R code)

Class 4. Subsets and Data Management                         (R code | squid )


Exercises:

  Exercises 1 | data: ISIT  .txt    deer                                                                                            answers1

  Exercises 2 | data: Birdflu.txt   Birdflu.xls   Birdflu_Corrected.txt                                                    answers2

17 & 24 April 2012 - Exploring and Visualising Data

Class 5. Useful Functions (apply etc).                                   data: vegetation2, deer

  Exercises 5 | data: temp.xls   temp.txt                                                                                         answers5


Class 6. Basic Graphics                                                       data: vegetation2

  Exercises 6 | data: amphib road kill                                                                                             answers6


  The Visual Display of Quantitative Information             pdf


Class 7. Advanced Graphics                                                 data: birdflucases birdfludeaths RIK2 owls deer
                                                                                                   teethnitrogen
  Exercises 7 | data: birdfludeaths vegetation2 codparasite owls                                                        answers7

  More graphics resources: palettes colour1 colour2 colour3 plot.math plot.math2

Mid-term test

Mid-term test | questions & data  | Answers

1 & 8 May 2012 - Statistical Analysis of Data

  A Protocol for Data Exploration to Avoid Common Mistakes     (pdf | article)

Class 8. Classical Tests                                                     data: twosample, skewdata                    answers8

Class 9. Linear Regression                                                                                                          answers9

Class 10. ANOVA                                                              data: growth

Class 11. Generalized Linear Models                                   data: clusters, sexratio, isolation, species, germination

                                                                                                                                                 answers             

18 May 2012 - Advanced Statistics & Programming in R

Class 12. Writing Functions

  Exercises 12 | data: species.counts  |  answers

Class 13. If, For, While, Repeat                                          data: indices

  Exercises 13 | answers

Class 14. Random Sampling & Numbers

  Exercises 14 | answers

22 & 29 May 2012 - Specialised Topics in R

Class 15. Mixed Effects Models                                           data: seedling, fruit | Bolker article

Class 16. Phylogenetic Comparative Methods                        data: geospiza, tree

Class 17. Community Ordination                                         data: veg, site | John2007

Class 18. Spatial Point Pattern Analysis                                Spatstat handbook
 

Final Exam

Exam  | Answers

Resources

Programming

Code Academy - " Learn to code. Codecademy is the easiest way to learn how to code. It's interactive, fun, and you can do it with your friends"
Software Carpentry "Our mission is to help scientists be more productive by teaching them basic computing skills"

text editors

a list of text editors for Windows, Mac and Linux

books

Ben Bolker Ecological Models and Data in R
Mick Crawley The R Book
Venables & Ripley Modern Applied Statistics in S-Plus
Andrew Gelman & Jennifer Hill Hierarchical Models
Alain Zuur et al A Beginner's Guide to R

graphics

Edward Tufte: The Visual Display of Quantitative Information, Envisioning Information, Beautiful Evidence
Murrell R Graphics
Bill Cleveland The Elements of Graphing Data, Visualizing Data
R Graph Gallery
Gallery of Data Visualisation
dot plots
simple graphs
ggplot2

websites

R project
R help
R wiki
R Introduccion (en linea, ingles)

Ecology and Epidemiology in R

Burns stats     StatsRus

spreadsheets

spreadsheet addiction
why does Excel suck so much?

blogs

Andrew Gelman
Methods in Ecology and evolution Journal
badscience

programming

online programming R resources

Braun W.J., Murdoch D.J. A First Course in Statistical Programming with R
Phil Spector Data Manipulation with R

Peter Hurd

scientific notation