Re: [R] impenetrable warning
In this case, this trick will identify the specify command in the lme code that produce the error. If that does not lead you to an answer, have you tried simplifying your lme call to identify more clearly which part (or combination) seems to generate the problem? hope this helps. spencer graves Liaw, Andy wrote: Generally you can set options(warn=2), run the code, then do traceback(). Andy From: Simon.Bond Dear R-help, Can anyone explain the meaning of the warning, Singular precision matrix in level -1, block 1 ? Or how to track down where it comes from? More precisely, using the nlme package, I'm issued with the warning itt2 <- lme(lrna~rx.nrti+lbrna, random=~1|patid, cor=corExp(form=~days|patid,nugget=T), weights=varPower( form=~lbrna),data=rna3) Warning messages: 1: Singular precision matrix in level -1, block 1 2: Singular precision matrix in level -1, block 1 the output is: Linear mixed-effects model fit by REML Data: rna3 Log-restricted-likelihood: -4990.142 Fixed: lrna ~ rx.nrti + lbrna (Intercept) rx.nrtiZDV+3TC rx.nrtiZDV+ABC lbrna 2.6597552 0.8589514 0.4259504 0.2929222 Random effects: Formula: ~1 | patid (Intercept) Residual StdDev:1.251113 0.2105329 Correlation Structure: Exponential spatial correlation Formula: ~days | patid Parameter estimate(s): range nugget 204.6422150 0.3349336 Variance function: Structure: Power of variance covariate Formula: ~lbrna Parameter estimates: power 0.9733358 Number of Observations: 2390 Number of Groups: 124 Thanks, Simon Bond. __ [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 __ [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 -- Spencer Graves, PhD, Senior Development Engineer O: (408)938-4420; mobile: (408)655-4567 __ [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
RE: [R] impenetrable warning
Generally you can set options(warn=2), run the code, then do traceback(). Andy > From: Simon.Bond > > Dear R-help, > > Can anyone explain the meaning of the warning, > > Singular precision matrix in level -1, block 1 > > ? Or how to track down where it comes from? > > More precisely, using the nlme package, I'm issued with the warning > > itt2 <- lme(lrna~rx.nrti+lbrna, random=~1|patid, > cor=corExp(form=~days|patid,nugget=T), weights=varPower( > form=~lbrna),data=rna3) > Warning messages: > 1: Singular precision matrix in level -1, block 1 > 2: Singular precision matrix in level -1, block 1 > > the output is: > > Linear mixed-effects model fit by REML > Data: rna3 > Log-restricted-likelihood: -4990.142 > Fixed: lrna ~ rx.nrti + lbrna >(Intercept) rx.nrtiZDV+3TC rx.nrtiZDV+ABC lbrna > 2.6597552 0.8589514 0.4259504 0.2929222 > > Random effects: > Formula: ~1 | patid > (Intercept) Residual > StdDev:1.251113 0.2105329 > > Correlation Structure: Exponential spatial correlation > Formula: ~days | patid > Parameter estimate(s): > range nugget > 204.6422150 0.3349336 > Variance function: > Structure: Power of variance covariate > Formula: ~lbrna > Parameter estimates: > power > 0.9733358 > Number of Observations: 2390 > Number of Groups: 124 > > > > Thanks, > > Simon Bond. > > __ > [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 > > __ [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
[R] impenetrable warning
Dear R-help, Can anyone explain the meaning of the warning, Singular precision matrix in level -1, block 1 ? Or how to track down where it comes from? More precisely, using the nlme package, I'm issued with the warning itt2 <- lme(lrna~rx.nrti+lbrna, random=~1|patid, cor=corExp(form=~days|patid,nugget=T), weights=varPower( form=~lbrna),data=rna3) Warning messages: 1: Singular precision matrix in level -1, block 1 2: Singular precision matrix in level -1, block 1 the output is: Linear mixed-effects model fit by REML Data: rna3 Log-restricted-likelihood: -4990.142 Fixed: lrna ~ rx.nrti + lbrna (Intercept) rx.nrtiZDV+3TC rx.nrtiZDV+ABC lbrna 2.6597552 0.8589514 0.4259504 0.2929222 Random effects: Formula: ~1 | patid (Intercept) Residual StdDev:1.251113 0.2105329 Correlation Structure: Exponential spatial correlation Formula: ~days | patid Parameter estimate(s): range nugget 204.6422150 0.3349336 Variance function: Structure: Power of variance covariate Formula: ~lbrna Parameter estimates: power 0.9733358 Number of Observations: 2390 Number of Groups: 124 Thanks, Simon Bond. __ [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
