Hi Peter, Apologies - I ran the script using S-Plus 6.2. I am happy to run it in R, but my feeling is that there may be something wrong with the code itself. I have included the dataset and script, in case you can help.
Jindi Singh. Jatinder Singh Senior Manager, Analysis and Reporting PRA International 300-730 View Street Victoria, B.C. V8W 3Y7 Tel: 250-483-4416 Fax: 250 483 4588 http://www.prainternational.com e-mail: [EMAIL PROTECTED] -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Peter Dalgaard Sent: Saturday, October 08, 2005 1:29 AM To: Singh, Jatinder Cc: [email protected] Subject: Re: [R] Converting PROC NLMIXED code to NLME "Singh, Jatinder" <[EMAIL PROTECTED]> writes: > Hi, > > I am trying to convert the following NLMIXED code to NLME, but am > running into problems concerning 'Singularity in backsolve'. As I am > new to R/S-Plus, I thought I may be missing something in the NLME code. Which version of R and NLME? R 2.2.0 ships with a version where the internal optimizer is changed to nlminb(). As I understand it, this was in response to reports where code that worked in S-PLUS refused to work in R. > NLMIXED > *********** > proc nlmixed data=kidney.kidney; > parms delta=0.03 gamma=1.1 b1=-0.003 b2=-1.2 b3=0.09 b4=0.35 b5=-1.43 > varu=0.5; eta=b1*age+b2*sex+b3*gn+b4*an+b5*pkn+u; > hazard=eta+log(delta)+log(gamma)+(gamma-1)*log(rtime); > survivor=(-exp(eta))*delta*(rtime**gamma); > ll=(event*hazard)+survivor; > model rtime ~ general(ll); > random u~normal(0,varu) subject=patient out=frailty; run; > > NLME > ******** > kidney.nlme<-nlme(model=rtime~ > (event* > ((b1*age+b2*sex+b3*gn+b4*an+b5*pkn+u)+log(delta)+log(gamma)+(gamma-1)* > lo > g(rtime)) > +((-exp(b1*age+b2*sex+b3*gn+b4*an+b5*pkn+u))*delta*(rtime**gamma)) > ), > fixed=list(delta~1,gamma~1,b1~1,b2~1,b3~1,b4~1,b5~1), > random=u~1|patient, > start=c(delta=0.03,gamma=1.1,b1=-0.003,b2=-1.2,b3=0.09,b4=0.35,b5=-1.4 > 3) > , > data=(kidney), > method="ML", > na.action=na.include > ) > > Error in NLME > ************* > > traceback() > 11: eval(action, sys.parent()) > 10: doErrorAction("Problem in .C(\"fit_nlme\",: Singularity in > backsolve", 1000) > 9: .C("fit_nlme", > 8: nlme(model = rtime ~ (event * ((b1 * age + b2 * sex + b3 * gn + b4 > * an + b5 * > 7: NULL > 6: nlme.formula(model = rtime ~ (event * ((b1 * age + b2 * sex + b3 * > gn > + b4 * > 5: eval(i, local) > 4: source(auto.print = auto.print, exprs = substitute(exprs.literal)) > 3: script.run(exprs.literal = { > 2: eval(expression(script.run(exprs.literal = { > 1: > Message: Problem in .C("fit_nlme",: Singularity in backsolve > > I am actually trying to fit a parametric model to the kidney catheter > data and compare NLMIXED with NLME. I am aware that COXPH and SURVREG > are also available with a frailty element added in, but wanted to fit > the likelihood model as above for a direct comparison. > > Cheers, > > Jindi > > [[alternative HTML version deleted]] > > ______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! > http://www.R-project.org/posting-guide.html > -- O__ ---- Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
