Michael Lachmann
   
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R-Course 2010
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(20/4/2006) New R course begins!

R course - Michael Lachmann

R is a programming language good for statistics, similar to S-plus.

The planned timetable:

Week 1: R basics
Week 2: Statistical tests and bootstrapping using R
Week 3: Bioconductor and database access



Lecture notes and exercises

Lecture 1
: Basics of R, TeXmacs, statistics, and bootstrapping.
notes: pdf  TeXmacs
exercise 1(right click to save as) exercise 1.pdf
Solution:

Lecture 2: Matrices, data frames, and reading files.
notes: pdf  TeXmacs
Over the weekend, you should read pages 1-22, 281-291 of "Statistics. An Introduction using R" by Michael J. Crawley.
I also asked you to find in your data a file and try to read it into R.

Lecture 3: Functions and loops.
notes: [pdf]  [TeXmacs] [example file for lecture]
[exercise 2](right click to save as) [exercise 2.pdf] [additional file for exercise2]
solution to execise 2

Lecture 4: Statistical tests.
notes: [pdf]  [TeXmacs]

Lecture 5: More about statistical tests.
notes: [pdf]  [TeXmacs]
I asked you to read pages 131-167 from "Statistical Computing". The following zip file contains the data that is used. You'll need to read it into R. data.zip.

Lecture 6: Plots and distributions.
notes: [pdf]  [TeXmacs]
[exercise 3](right click to save as) [exercise 3.pdf]

Lecture 7: Analysis of variance 1.
notes: [pdf]  [TeXmacs]
data for lecture
[solution to exercise 3](right click to save as) [exercise3_solution.pdf]

Lecture 8: Analysis of variance 2 (and regression).
notes: [pdf]  [TeXmacs]
data for lecture
data for lecture
data for lecture
data for lecture

Lecture 9: Lists, Bootstrap and Jacknife.
notes: [pdf]  [TeXmacs]
data for lecture
data for lecture
[exercise 4](right click to save as) [exercise4.pdf]
data for exercise (strange.txt)
data for lecture (species.txt)

Lecture 10: Permutation tests and files.
notes: [pdf]  [TeXmacs]
[solution to exercise 4](right click to save as) [exercise4_solution.pdf]
sample program

Lecture 11: Accessing databases: Oracle, PostgreSQL, and Access/Excel.
notes: [pdf]  [TeXmacs]
Windows part of the lecture



R Documentation:

"simpleR - Using R for Introductory Statistics" by John Verzani
This is a very nice introduction to R. Pages 1-18 cover most of what we'll learn in the first class.

"R for Beginners" by Emmanuel Paradis
This is a good introduction to the internals of R, more from a programmers direction. I will go some into the internals of R, but if you want to learn more about how to multiply matrices, more about how to read files, etc., read this.

"Using R for Data Analysis and Graphics" by J. H. Maindonald
This document mainly talks about doing graphics in R. It has a nice introduction to the windows interface.

How to install xemacs and ess on windows (This document is taken from this site)

Graph gallery- a cool site that contains pictures of graphs produced by R. This can help you make just the right plot!
Function finder - a web page that groups functions in R by what they do.

R Data Import/Export - explains how to export data from R to files, and to different database formats. The DBI interface on page 14 is what ROracle also uses, so that section explains some of what we learned in class.

The ROracle Package - explains more about interfacing an oracle database from R. It is fairly technical and is a manual of the different functions rather than a tutorial.

barney is our internal server, which points to some SQL documentation.

Links:

Main R Project page
Texmacs - the interface that we'll use in the course
Bioconductor