Editorial - R: The R Project for Statistical Computing

1 The Newsletter of the R Project News Volume 4/1, June 2004 . Editorial by Thomas Lumley cal niches is due in large part to the wide variety of packages produced by the R community. We have R has been well accepted in the academic world for articles describing contributed packages for princi- some time, but this issue of R News begins with pal component analysis (ade4, used in creating Eric a description of the use of R in a business setting. Lecoutre's winning graphic) and Statistical process Marc Schwartz describes how his consulting com- control (qcc) and the recommended survival pack- pany, MedAnalytics, came to use R instead of com- age.

2 Jianhua Zhang and Robert Gentlement describe mercial Statistical software, and has since provided tools from the Bioconductor Project that make it eas- both code and financial support to the R Project . ier to explore the resulting variety of code and docu- The growth of the R community was also evident mentation. at the very successful useR! 2004 , the first conference The Programmers' Niche and Help Desk columns for R users. While R aims to blur the distinctions be- both come from guest contributors this time.

3 Gabor tween users and programmers, useR! was definitely Grothendieck,known as frequent poster of answers different in aims and audience from the previous on the mailing list r-help, has been invited to con- DSC conferences held in 1999, 2001, and 2003. John tribute to the R Help Desk. He presents Date and Fox provides a summary of the conference in this is- Time Classes in R . For the Programmers' Niche, I. sue for those who could not make it to Vienna. have written a simple example of classes and meth- A free registration to useR!

4 Was the prize in ods using the old and new class systems in R. This the competition for a new graphic for http://www. example arose from a discussion at an R program- You will have seen the winning ming course. graphic, from Eric Lecoutre, on the way to down- Programmers will also find useful Doug Bates' ar- loading this newsletter. The graphic is unedited ticle on least squares calculations. Prompted by dis- R output (click on it to see the code), showing cussions on the r-devel list, he describes why the the power of R for creating complex graphs that simple matrix formulae from so many textbooks are are completely reproducible.

5 I would also en- not the best approach either for speed or for accuracy. courage R users to visit the Journal of Statisti- cal Software ( ), which Thomas Lumley publishes peer-reviewed code and documentation. R Department of Biostatistics is heavily represented in recent issues of the journal. University of Washington, Seattle The success of R in penetrating so many statisti- Contents of this issue: Tools for interactively exploring R packages .. 20. The survival package .. 26. Editorial .. 1 useR! 2004 .

6 28. The Decision To Use R .. 2 R Help Desk .. 29. The ade4 package - I : One-table methods .. 5 Programmers' Niche .. 33. qcc: An R package for quality control charting Changes in R .. 36. and Statistical process control .. 11 Changes on CRAN .. 41. Least Squares Calculations in R .. 17 R Foundation News .. 46. Vol. 4/1, June 2004 2. The Decision To Use R. A Consulting Business Perspective and service companies to develop web-based elec- tronic data capture, study management, and report- by Marc Schwartz ing.

7 We have worked in many medical specialties in- cluding cardiac surgery, cardiology, ophthalmology, orthopaedics, gastroenterology and oncology. Preface Prior to founding MedAnalytics, I had 5 years of clinical experience in cardiac surgery and cardiology The use of R has grown markedly during the past and over 12 years with a medical database software few years, which is a testament to the dedication and company, where I was principally responsible for the commitment of R Core, to the contributions of the management and analysis of several large multi-site growing useR base.

8 And to the variety of disciplines national and regional sub-specialty databases that in which R is being used. The recent useR! meeting in were sponsored by professional medical societies. Vienna was another strong indicator of growth and My duties included contributing to core dataset de- was an outstanding success. sign, the generation of periodic aggregate and com- In addition to its use in academic areas, R is parative analyses, the development of multi-variable increasingly being used in non-academic environ- risk models and contributing to peer-reviewed pa- ments, such as government agencies and various pers.

9 In that position, the majority of my analyses businesses, ranging from small firms to large multi- were performed using SAS (Base, Stat and Graph), national corporations, in a variety of industries. though S-PLUS (then from StatSci) was evaluated in In a sense, this diversification in the user base the mid-90's and used for a period of time with some is a visible demonstration of the greater comfort smaller datasets. that business-based decision makers have regard- ing the use of Open-Source operating systems, such as Linux, and applications, such as R.

10 Whether these tools and associated support programs are pur- Evaluating The Tools of the Trade - chased (such as commercial Linux distributions) or A Value Based Equation are obtained through online collaborative commu- nities, businesses are increasingly recognizing the The founder of a small business must determine how value of Open-Source software. he or she is going to finance initial purchases (of In this article, I will describe the use of R (and which there are many) and the ongoing operating other Open-Source tools) in a healthcare-based con- costs of the company until such time as revenues sulting firm, and the value realized by us and, impor- equal (and, we hope, ultimately exceed) those costs.