Quantum Forest

After a series of post on environmental issues, it is good to come back to software and statistics. I am a user of many different statistical packages: Splus and Genstat for general statistics, PASS for power calculations and ASReml for generalised linear mixed models (GLMM, particularly for quantitative genetics analyses).

While I consider that PASS and ASReml are pretty good value for money — especially the latter — I sometimes question my choice of generic software. Until 1996 I used to be a ‘heavy duty’ SAS user (at least of base, stat, iml and graph). Some of the many drawbacks of SAS were its low quality graphics, low speed for large analyses and its price (near AU$10,000 a year for the modules I used for work). SAS is also quite monolithic and usually is much slower on the adoption of new analytical techniques. On the other hand, SAS database facilities are quite good and it can cope with large analyses relatively well, albeit very slowly.

In 1996 I discovered ASReml (~AUD$1,500) and, given that most of my work was of the GLMM kind, I switched and never looked back. ASReml is lightning fast (orders of magnitude more than SAS) and it allows to implement very large analyses, enough for running a national genetic evaluation for forest trees.

Genstat is a good generic package, but the graphics have lower quality than Splus’s, the language is too Fortranian for my taste and the community of users is quite small. The small community makes discussion and implementation of new routines slower than in Splus, and gives the feeling of a ‘dead end’ from a language evolution point of view.

Splus is a terrific piece of software. However, buying it is around AU$4,500 and AU$1,000 per year of maintenance. This is still quite a bit of money, particularly for small businesses. This takes me to R, an open source implementation of S, without the fancy GUI but with the same analytical capabilities of Splus. If you are a ‘power user’ of Splus there are very good incentives to move to R; firstly, it is free and, secondly, you are already quite proficient on R, because the syntax is very similar. If you ask me, Splus is slowly pricing itself outside the small business market and many ‘power users’ of Splus, which rarely use its GUI, will not see any benefits on keeping paying for software licenses, because this time there is ‘almost a free lunch’. At work we are evaluating R for use by the biometricians and, maybe, by the more sophisticated researchers. Other researchers will still probably stay with Genstat, at least until R develops a decent GUI. But that time — if ever happens — we may decide to switch everybody to R.