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R course - Michael Lachmann

News

(30/9/2010) Today's class at 17:00.

(28/9/2010) Sorry, today's class at 17:00, as is thursday's.

(27/9/2010) Remember that today's class is at 17:00!

(23/9/2010) Homework: ex1+ex2 can be submitted till monday. Please email them to me. Tomorrow at 11 homework class. 4th floor big seminar room.

(21/9/2010) Tomorrow, 22/9/2010 11:00 class for questions about the homework. You can also come and do the homework there.

(20/9/2010) Tomorrow, 21/9/2010 11:00 class to set up computers.

(20/9/2010) New R course begins!

Lecture notes and exercises
There are three types for every file: .tm for use in TeXmacs, .pdf for reading, and .R for working with in a regular editor.

Lecture 1: Basics of R, TeXmacs, Komodo edit.
notes: pdf  TeXmacs   R

Lecture 2: More about vectors, sampling, drift.

Notes: pdf  TeXmacs   R
Exercise 1: pdf  TeXmacs   R
Reading: Using R for Data Analysis and Graphics

Lecture 3: Matrices, loops, Hardy-Weinberg.

Notes: pdf  TeXmacs   R
Exercise 2: pdf  TeXmacs   R

Lecture 4: Solution to excercise 1+2, more on Hardy-Weinberg, Fisher's fundamental theorem, loops in R.

Notes: pdf  TeXmacs   R

Lecture 5: More of solution to execise 2, functions and apply, sexual reproduction, recombintion and linkage.

Notes: pdf  TeXmacs   R
Exercise 3: pdf  TeXmacs   R

Lecture 6: More loops, conditionals, distributions, effective population size and Fst.

Notes: pdf  TeXmacs   R
Exercise 4: pdf  TeXmacs   R

Lecture 7: Lists, data Frames, reading from files and coalescents

Notes: pdf  TeXmacs   R

You also need the following program:
OSX: ms, linux: ms

Lecture 8: More lists, strings and regular expressions

Notes: pdf  TeXmacs   R
Exercise 5: pdf  TeXmacs   R

Lecture 9: Solution to 3+4, R holes: debugging, objects, speed

Notes: pdf  TeXmacs   R
Exercise 3 solution: pdf  TeXmacs   R
Exercise 4 solution: pdf  TeXmacs   R

Schedule
 Mon 20/9 Tue 21/9 Wed 22/9 Thu 23/9 Fri 24/9 11:00-12:00 Computer setup m. media Homework help m. media Homework help 4th floor seminar room 16:00-17:00 Lecture Lecture Lecture 17:00-18:00 18:00-19:00

 Mon 27/9 Tue 28/9 Wed 29/9 Thu 30/9 Fri 1/10 11:00-12:00 Homework help 4th floor seminar room Homework help 4th floor seminar room Homework help 4th floor seminar room 16:00-17:00 17:00-18:00 Lecture Lecture Lecture 18:00-19:00

 Mon 4/10 Tue 5/10 Wed 6/10 Thu 7/10 Fri 8/10 11:00-12:00 Homework help 4th floor seminar room Homework help 4th floor seminar room Homework help 4th floor seminar room 16:00-17:00 17:00-18:00 Lecture Lecture Lecture 18:00-19:00

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.

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