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, HardyWeinberg.
Notes: pdf TeXmacs R
Exercise 2: pdf TeXmacs
R
Lecture 4: Solution
to excercise 1+2, more on HardyWeinberg, 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

11:0012:00


Computer
setup
m.
media

Homework
help
m.
media 

Homework
help
4th
floor
seminar
room 






16:0017:00

Lecture

Lecture 

Lecture 

17:0018:00



18:0019:00







Mon 27/9

Tue 28/9

Wed 29/9

Thu 30/9

Fri 1/10

11:0012:00


Homework
help
4th
floor
seminar
room

Homework
help
4th
floor
seminar
room 

Homework
help
4th
floor
seminar
room 






16:0017:00






17:0018:00

Lecture

Lecture


Lecture


18:0019:00




Mon 4/10

Tue 5/10

Wed 6/10

Thu 7/10

Fri 8/10

11:0012:00


Homework
help
4th
floor
seminar
room

Homework
help
4th
floor
seminar
room 

Homework
help
4th
floor
seminar
room 






16:0017:00






17:0018:00

Lecture 
Lecture 

Lecture 

18:0019:00



R Documentation:
"simpleR

Using
R
for
Introductory
Statistics" by John Verzani
This is a very nice introduction to R. Pages 118 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
