Re: [R] ran out of iteration in coxph
Thank you very much for your reply. How is it possibe to approximate the max number of variables that should be used considering the number of samples and censored data? Experimentally, I saw that for my specific data, I have to reduce down to 120 variables. So I wondered how it could be approximate, if possible for other data sets. Best wishes carol Prof Brian Ripley [EMAIL PROTECTED] wrote: It is quite possible that you are trying to find an MPLE where none exists, in which case non-convergence is a good thing. Using only 300 cases for 188 or 215 variables is asking a lot, especially when 26% of them are only partially observed. Since you did not sign your message we have no idea of your background, but it looks like the problem here is with statistical expectations and not R usage. On Sun, 4 Feb 2007, carol white wrote: hi, I applied coxph to my matrix of 300 samples and 215 variables and got the following error Error in fitter(X, Y, strats, offset, init, control, weights = weights, : NA/NaN/Inf in foreign function call (arg 6) In addition: Warning message: Ran out of iterations and did not converge in: fitter(X, Y, strats, offset, init, control, weights = weights, 26% of time data is censored and here is the result of density of the matrix xy Min. :-6.943 Min. :-5.258e-18 1st Qu.:-4.086 1st Qu.: 2.341e-04 Median :-1.228 Median : 4.584e-03 Mean :-1.228 Mean : 8.740e-02 3rd Qu.: 1.630 3rd Qu.: 5.857e-02 Max. : 4.487 Max. : 7.099e-01 -- in another trial of the same matrix, the number of var is reduced to 188. the variables were normalized (mean = 0 and standard dev = 1 for each variable) and here is the result of density x y Min. :-8.1532 Min. :4.571e-16 1st Qu.:-4.3334 1st Qu.:1.043e-04 Median :-0.5136 Median :1.102e-03 Mean :-0.5136 Mean :6.538e-02 3rd Qu.: 3.3062 3rd Qu.:5.373e-02 Max. : 7.1260 Max. :4.337e-01 I get still the warning Warning message: Ran out of iterations and did not converge in: fitter(X, Y, strats, offset, init, control, weights = weights, but not error in fitter the number of iterations is 20 and didn't converge. saw from coefficient values and their p-value Why do I get this message? Look forward to your reply carol - [[alternative HTML version deleted]] __ R-help@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 and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 - Never miss an email again! [[alternative HTML version deleted]] __ R-help@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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] ran out of iteration in coxph
It is quite possible that you are trying to find an MPLE where none exists, in which case non-convergence is a good thing. Using only 300 cases for 188 or 215 variables is asking a lot, especially when 26% of them are only partially observed. Since you did not sign your message we have no idea of your background, but it looks like the problem here is with statistical expectations and not R usage. On Sun, 4 Feb 2007, carol white wrote: hi, I applied coxph to my matrix of 300 samples and 215 variables and got the following error Error in fitter(X, Y, strats, offset, init, control, weights = weights, : NA/NaN/Inf in foreign function call (arg 6) In addition: Warning message: Ran out of iterations and did not converge in: fitter(X, Y, strats, offset, init, control, weights = weights, 26% of time data is censored and here is the result of density of the matrix xy Min. :-6.943 Min. :-5.258e-18 1st Qu.:-4.086 1st Qu.: 2.341e-04 Median :-1.228 Median : 4.584e-03 Mean :-1.228 Mean : 8.740e-02 3rd Qu.: 1.630 3rd Qu.: 5.857e-02 Max. : 4.487 Max. : 7.099e-01 -- in another trial of the same matrix, the number of var is reduced to 188. the variables were normalized (mean = 0 and standard dev = 1 for each variable) and here is the result of density x y Min. :-8.1532 Min. :4.571e-16 1st Qu.:-4.3334 1st Qu.:1.043e-04 Median :-0.5136 Median :1.102e-03 Mean :-0.5136 Mean :6.538e-02 3rd Qu.: 3.3062 3rd Qu.:5.373e-02 Max. : 7.1260 Max. :4.337e-01 I get still the warning Warning message: Ran out of iterations and did not converge in: fitter(X, Y, strats, offset, init, control, weights = weights, but not error in fitter the number of iterations is 20 and didn't converge. saw from coefficient values and their p-value Why do I get this message? Look forward to your reply carol - [[alternative HTML version deleted]] __ R-help@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 and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@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 and provide commented, minimal, self-contained, reproducible code.
[R] ran out of iteration in coxph
hi, I applied coxph to my matrix of 300 samples and 215 variables and got the following error Error in fitter(X, Y, strats, offset, init, control, weights = weights, : NA/NaN/Inf in foreign function call (arg 6) In addition: Warning message: Ran out of iterations and did not converge in: fitter(X, Y, strats, offset, init, control, weights = weights, 26% of time data is censored and here is the result of density of the matrix xy Min. :-6.943 Min. :-5.258e-18 1st Qu.:-4.086 1st Qu.: 2.341e-04 Median :-1.228 Median : 4.584e-03 Mean :-1.228 Mean : 8.740e-02 3rd Qu.: 1.630 3rd Qu.: 5.857e-02 Max. : 4.487 Max. : 7.099e-01 -- in another trial of the same matrix, the number of var is reduced to 188. the variables were normalized (mean = 0 and standard dev = 1 for each variable) and here is the result of density x y Min. :-8.1532 Min. :4.571e-16 1st Qu.:-4.3334 1st Qu.:1.043e-04 Median :-0.5136 Median :1.102e-03 Mean :-0.5136 Mean :6.538e-02 3rd Qu.: 3.3062 3rd Qu.:5.373e-02 Max. : 7.1260 Max. :4.337e-01 I get still the warning Warning message: Ran out of iterations and did not converge in: fitter(X, Y, strats, offset, init, control, weights = weights, but not error in fitter the number of iterations is 20 and didn't converge. saw from coefficient values and their p-value Why do I get this message? Look forward to your reply carol - [[alternative HTML version deleted]] __ R-help@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 and provide commented, minimal, self-contained, reproducible code.
