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: r-help@stat.math.ethz.ch
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
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c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
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