R freeware statistics package Tara Jenson NCAR RAL JNT Tom Hopson

What is R? A statistical programming language In part, developed from the S Programming Language from Bell Labs (John Chambers) Created to allow rapid development of methods for use in different types of data. Create new graphics. Many default parameters are chosen, but users retain complete control.

Why R? R has become the dominant language in the statistical research community. R is Open Source and free. Runs on all operatingsystems Nearly 2,400 packages contributed. Packagesand applications in nearly every field of science, business and economics. See R Notes, R Journal and Journal of Statistical Software More than 100 books with accompanying code Very large, active user base.

Why not R? NCL, IDL, Matlab, SAS, … are all viable alternatives to R. If you are a part of an active community of researchers using another language, do likewise. If we were biostatisticians we would be using SAS. Book Title: “Analyzing Receiver Operating Characteristic Curves with SAS” Consider building verification functions and utilities as part of code development. Verification need not be an external process to forecasting.

The R Community Developers – R Core Group (17 members), only 2 have left since 1997 – Major update in April/October (freeze dates, beta versions, bug tracking,...) Mailing lists – Help list ~ 150 messages/day, archived, searchable. 5 International Conferences, 2 US, 1 China

Source code Binary compilations (Windows, Mac OS, Linux Documentation ( Main documents, plus numerous contributed. Some in foreign languages.) Newsletter (replaced by R Journal.) Mailing list (Several search engines) Packages on every topic imaginable Wiki with examples Reference list of books using R. ( more than 100) Task Manager Everything about R is at

Use R with scripts In Linux - Emacs Speaks Statistics – Provides syntax-based – Object name completion – Key strokeshort cuts – Commandhistory – Alt-x R to invoke R with Xemacs. In Windows, use editor – Added GUI features – R sends a line or highlighted section into R. – Install package with GUIs – Save graphics by point and click. Mac OS – Similarto Windows with advantages of system calls.

Packages in R Contributed by people world wide. Allow scientists or statisticians to push their ideas. Apply and extend R capabilities to meet the needs of specific communities. Accompany many statistical textbooks

A sample of useful packages verification fields (spatial stats) radiosondes extRemes BMA(BayesianModel Averaging) BMAensemble circular Rsqlite Rgis, spatstat (GIS) ncdf ( support for netcdf files ) Rcolorbrewer randomForests

Packages Packages must be installed to call. Packages must be called to use. Base packages are installed by default.

10 most useful function in R aggregate - applies a function to groups of data subset by categories. apply - incredibly efficient in avoiding loops. Applies functions across dimensions of arrays. layout - creatively divide a print region. xyplot (in the lattice package) slightly advance graphic techniques %in% returns logical showing which elements in A are in B. (e.g A%in%B)

More top 10 table – create contingency tabel counts. boot – apply bootstrap function correctly read.fwf – read fixed width format data par – control everything in a graph system( ) – allows you to call system command from R pairs – the most under utilized plot – plots a matrix of 4 columns in a 4x4 plot layout

Login, start your windowing system. $ R Start R as appropriate for your platform. The R program begins, with a banner. (Within R, the prompt on the left hand side will not be shown to avoid confusion.) help.start() Start the HTML interface to on-line help (using a web browser available at your machine). You should briefly explore the features of this facility with the mouse. In particular, work through 1.5, 2.1 – 2.3, and appendix A (just the first one or two sections)

R Exercises Choose groups of 3-4 – find a computer Log onto machines Bring up at least 2 xterms >cd /home/user/Desktop/longlead >vi intro2R.2013.R And work through the commands given …