Re: [Rd] Defining a method in two packages

2010-03-06 Thread Prof Brian Ripley
On Sat, 6 Mar 2010, Uwe Ligges wrote: Terry, this happens since the ranef in coxme is a S3 generic and the one in lme4 is a S4 generic. But the packages could be more cooperative. There is also a S3 generic for ranef in package nlme. Ideally the S4 generic in lme4 would have a default me

Re: [Rd] Defining a method in two packages

2010-03-06 Thread Uwe Ligges
Terry, this happens since the ranef in coxme is a S3 generic and the one in lme4 is a S4 generic. Of course, after loading lme4, you can still use the ranef from coxme: coxme::ranef(fit) and get the desired result. If you write your own code, you might want to use that call explicitly (i.e

[Rd] thin grid lines, again (FAQ 7.36), a proposal

2010-03-06 Thread Ken Knoblauch
Hi, I'm raising the issue, again, of those pesky thin lines that show up with a pdf graphics device, otherwise known as FAQ 7.36. I have read the FAQ and understand that I can eliminate them by adjusting the anti-aliasing option for viewing them on the screen, but this doesn't necessarily elim

Re: [Rd] Improved Nelder-Mead algorithm - a potential replacement for optim's Nelder-Mead

2010-03-06 Thread Ravi Varadhan
Dear Barry, Thanks for your response. The code is written in R language. I had obtained permission from the author C.T. Kelley and the Publisher (SIAM) for releasing the R code under GPL-2 license. I don't understand what else you'd need to study. I can send you the actual email transacti

Re: [Rd] CRAN nearly down?

2010-03-06 Thread Barry Rowlingson
On Fri, Mar 5, 2010 at 5:40 PM, Paul Gilbert wrote: > Is CRAN having trouble or is it just me?  (The web interface is very > slow and install.packages() is timing out and giving me "service not > available"). Have you ever tried: http://downforeveryoneorjustme.com/cran.r-project.org - I though

Re: [Rd] Improved Nelder-Mead algorithm - a potential replacement for optim's Nelder-Mead

2010-03-06 Thread Barry Rowlingson
On Fri, Mar 5, 2010 at 8:26 PM, Ravi Varadhan wrote: > Hi, > > I have written an R translation of C.T. Kelley's Matlab version of the > Nelder-Mead algorithm.  This algorithm is discussed in detail in his book > "Iterative methods for optimization" (SIAM 1999, Chapter 8).  I have tested > this