1. Data, graphics, and programming in R 28.1, 30.1, 2-4.2 Daily:10:00-12:45 & 13:45-16:30 EXCEPT WED 4 th 9:00-11:45 & 12:45-15:30 Teacher: Anna Kuparinen

2. Course program Wed –Basics of R (AM & PM) Fri –Datasets in R (AM), graphics (PM) Mon –Statistical tests and linear models (AM), more graphics (PM) Tue –Basics of programming (AM), generalized linear models (PM) Wed –Mixed models (AM), working with own data (PM) Teaching based on short lectures, demos, and exercises

3. Course material Lectures, demo codes, exercises, and other material can be found by following the course link in www.mv.helsinki.fi/home/akuparin/R_course.htm Other R material (e.g. downloading R) http://www.r-project.org/

4. How to get most out of the course? Do notes –also comment your own solution codes for the exercises Be active –ask questions, ask clarification, ask to slow down In the evenings, re-read the materials of the day Start to use R immediately after the course

5. What is ? R is a software that provides a very handy environment and a large collection of tools for –Exploring and editing data –Computations, calculations, numerical mathematics –Statistical analyses –Producing graphics –Programming R is a freeware program R is developed by its users, i.e. anyone can write their own R extensions and share them with other users through R web –New methods are quickly implemented to R –There is a large variety of tools available

6. Getting started R work space Notepad or R script Write code first here! Then copy-paste to R.

7. How to use R? R is a text-based interface, i.e. commands are given by text lines –> one should remember at least most common text commands In practice, commands are typically written in an editor program and them copy-pasted to R –Notepad, R script, Tinn-R… –Commenting the code is highly recommended! R is based on objects and functions –Objects can be variables, lists, data frames… –Functions are made to carry out specific operations –Functions are stored in “library packages” R stores objects and commands on workspace –Workspace and command history can be saved and loaded later on –Large objects reserve a lot of memory in the workspace

8. First commands Write your command on a command line > 2+3 Then press enter [1] 5 R returns the value

9. Placing a value to a variable Write your command on a command line > a=2+3 Then press enter > R does not return the value, but it has saved it to variable a

10. Operators in R = places a value (<- would also work) == checks identity of values on the left and on the right side An command A=4/9 sets a value 4/9 to a variable called A. An command A==4/9 checks if A equals to 4/9 or not. The command returns a logical value TRUE or FALSE >= larger or of equal size <= smaller or of equal size DEMO 1

11. Vector Length of this vector is 4. 1st element 4th element

12. Vectors in R Generic way of creating a vector > a=c(2.3,6.8,1.1,4.9) Pointing to a vector element > a[1] [1] 2.3 Or several elements > a[c(1,3)] [1] 2.3 1.1 Any calculations such as + or exp() can be applied to vectors.

13. Matrix 1st column 1st row A matrix element is pointed by its row and column number: A[2,4]=-2.2 Size of this matrix is 4 X 4

14. Matrix in R Generic way of creating a matrix > a=matrix(c(2,5,6,1),nrow=2,ncol=2,byrow=T) > a [,1] [,2] [1,] 2 5 [2,] 6 1 > a[1,] [1] 2 5 > a[,2] [1] 5 1

15. Tools to create vectors and matrixes Tools to create vectors A = c(1.0,5.8,9.0) A = 1:6 A = rep(1,9) A = rep(c(1,2),4) A = rep(c(1,2),each=4) A = seq(1,10,by=0.2) A = seq(1,10,length.out=57) Creating matrixes B = matrix(1,nrow=8,ncol=9) B = matrix(0,nrow=9,ncol=4) -> DEMO 2

16. R as a calculator Basic math operators in R: +, -, /, *, ^ Matrix calculations: –transpose matrixes by t() –Matrix calculations specified with %: for example * multiplies by elements, and %*% is for multiplication of matrixes Basic mathematical functions: –log, exp, sqrt, cos, sin, tan, abs etc Rounding: round, floor, ceiling

17. Anatomy of an R function Object=function(parameters ) PARAMETER VALUES AND SETTINGS: not all have to be defined (see help files for the defaults) NAME OF THE FUNCTION OBJECT RETURNED BY THE FUNCTION

18. Help in R Many ways to find help: –In R directly: ? ”name of the function” or help.search (“keyword”) e.g. ?rep or help.search (“vector”) –From R web pages –For more advanced problems also from R discussion groups –> DEMO 3