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. 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=-1.43) , 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]]
"Singh, Jatinder" <SinghJatinder at PRAIntl.com> 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=-1.43) > , > 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]] > > ______________________________________________ > R-help at stat.math.ethz.ch 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 ??ster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
At 20:40 7/10/2005, Singh, Jatinder wrote:>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=-1.43) >, >data=(kidney), >method="ML", >na.action=na.include >)Hi! Try change "na.action=na.include" for "na.action=na.omit" The singularity occurs because the fixed effects matrix is not of full rank due to the unused factor levels. Bernardo Rangel Tura, MD, MSc National Institute of Cardiology Laranjeiras Rio de Janeiro Brazil --
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: singhjatinder at praintl.com -----Original Message----- From: pd at pubhealth.ku.dk [mailto:pd at pubhealth.ku.dk] On Behalf Of Peter Dalgaard Sent: Saturday, October 08, 2005 1:29 AM To: Singh, Jatinder Cc: r-help at stat.math.ethz.ch Subject: Re: [R] Converting PROC NLMIXED code to NLME "Singh, Jatinder" <SinghJatinder at PRAIntl.com> 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]] > > ______________________________________________ > R-help at stat.math.ethz.ch 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 ?ster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
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