Short course: An introduction to R

Manchester Metropolitan University

Faculty of Science and Engineering
School of Science & the Environment


Thurs. and Fri. 20-21 September 2012
(1-5pm Thurs., 10am-5pm Fri.)

Ed Harris

http://www.operorgenetic.com/introToR/
http://www.sste.mmu.ac.uk/short_courses/introduction_to_r/default.htm

00 Schedule and workshop description
00 Schedule and introduction

00.00 Schedule

Day 1
Thursday 20 September 2012
1 pm to 5 pm
Room C1.02

-introduction and content description
-Workbook 1
-Workbook 2

Coffee at 2:30


Day 2
Friday 21 September 2012
10 am to 5 pm
Room C1.03

-Workbook 3
-Workbook 4
-Workbook 5
-Workbook 6 (optionally)

Lunch break 12 pm to 1pm

Coffee at 2:30
00.01 Files

Pdf
00 Schedule, intro and learning outcomes
01 Workbook 1 - R help, basic math, and data I/O, personal reference card
02 Workbook 2 - Functions, scripts and data objects
03 Workbook 3 - Workflow, workspaces, and using GUIs
04 Workbook 4 - Basic descriptive statistics and graphs i
05 Workbook 5 - Basic descriptive statistics and graphs ii
06 Workbook 6 - Comparing means (and other stuff)


Slides
01 R is InteRactive: an intro to R and workbook 1
02 Workbook 2 Functions, scripts and data objects, Oh My!
03 Workbook 3 R Commander and R Studio
04 Workbook 4 Basic stats and graphs i
05 Workbook 5 Basic stats and graphs ii
06 Workbook 6 Comparing means

Data
We'll use various data files described in the workbooks will be available for downloading

00.02 Introductory information and learning outcomes

Short course: an introduction to R

The open source statistical computing software R has become increasingly popular over the past 10 years. Once
restricted to specialized research applications, R is now widely used in quantitative data analysis in a number of
fields (e.g., ecology and conservation, genetics and bioinformatics, social sciences) and has begun to replace
commercial software such as SPSS to perform statistical analyses in research and teaching. While R has several
significant advantages over comparable commercial statistical software (very small installation size, cutting edge
implementation of the latest analysis techniques, free of cost), it has a steep learning curve for typical users.

The aim of this short course is to introduce new users to the possibilities and basic mechanics of R. The short course
is aimed at lectures and graduate students who already have some statistical training and who wish to begin using R
in teaching or research. Much of the short course will be practical and will emphasize a "hands on" approach to
learn to apply R to statistical problems and communicate results.

Learning outcomes

After attending this short course, you should be able to
-discuss the merits of R
-perform data entry in R
-use R to manipulate data
-use the R help system to discover solutions
-use best practice to collaborate or teach using R scripts
-use the R Commander graphical user interface
-perform exploratory data analysis in R
-construct graphs in R
-perform basic inferential statistics in R


Recommended websites

http://www.statmethods.net/ Quick R - tutorials and "how-to" information, very user friendly
http://cran.r-project.org/ CRAN, Comprehensive R Archive Network - Download R, official manuals
http://www.r-tutor.com/ R Tutorial - another good, user friendly "how-to" site


Recommended books

beginner:
Crawley, M.J., 2005. Statistics: An Introduction Using R, Wiley-Blackwell.
Dalgaard, P., 2008. Introductory Statistics with R 2nd ed., Springer.
Verzani, J., 2004. Using R for Introductory Statistics 1st ed., Chapman and Hall/CRC.
Zuur, A.F., 2009. (A Beginners Guide to R) By Zuur, Alain F. (Author) Paperback on, Springer.

intermediate:
Bolker, B.M., 2008. Ecological Models and Data in R, Princeton University Press.
Zuur, A.F., Ieno, E.N. & Smith, G.M., 2007. Analysing Ecological Data 1st ed., Springer.

advanced:
Bivand, R.S., Pebesma, E.J. & Gmez-Rubio, V., 2008. Applied Spatial Data Analysis with R 1st ed., Springer.
Cryer, J.D. & Chan, K.-S., 2009. Time Series Analysis: With Applications in R 2nd ed. 2008. Corr. 3rd printing., Springer.
Lumley, T., 2010. Complex Surveys: A Guide to Analysis Using R, Wiley-Blackwell.
Wood, S.N., 2006. Generalized Additive Models: An Introduction with R, Chapman and Hall/CRC.
Zuur, A.F. et al., 2009. Mixed Effects Models and Extensions in Ecology with R 1st ed., Springer.
00.03 Practical approach and conventions

Workbooks

Most of this course will be using a hands-on, practical approach to begin using R. There are a series of self-guided
"workbooks" to work through, followed by some problems to solve on your own, with a partner, or to discuss as a
group. Working on your own is fine, but in my experience collaboration, discussion and debate is the fastest way to
get up and running with R for new users.

The very spirit in which R was constructed was to use it as a collaborative tool, to share scripts of data summaries
and visualizations with colleagues and naturally to debate the best representation of your interpretation of results.
This is an ideal approach to use in research, but also works extremely well for teaching and learning using R.


Some conventions:

-Regular instructions will be typed in Times New Roman font like this sentence is

-R code will be typed in the Courier New font like this sentence is

-Keep the handbook document open on your screen, or print it if you prefer

-I assume here you are using the Windows operating system. Linux or Mac OSes will work too, but might be
slightly different.

-Important points and key terms will sometimes be in bold font

-There should be some problems at the end of each workbook, some easy, some medium and some more difficult to
solve

-type everything rather than copying and pasting - you'll learn the R language faster!

-use R help, Google, CRAN, yell for help or any method that works to solve the problems - be creative!