Re: [R] nesting in CoxPH with survival package
In a Cox model, the baseline hazard takes the place of an intercept. Try the following: dummy - rnorm(nrow(goodexp)) testfit - lm(dummy ~ ExpTemp + Stability + Period, data=goodexp, x=T) Now look at testfit$x, which is the design matrix for the linear model with an intercept. Examination of it will first of all clarify for you exactly what dummy variable coding was used for the model. If this X matrix is singular, the coxph fit will be singular in exactly the same way and at the same place. If you regress the last column of testfit$x on the others you should get a perfect fit, given the output below. Other than the intercept the X matrix within coxph is the same as that for lm; the intercept is still there in the form of a baseline hazard, it just cannot be summarized as a single coefficient. (All R modeling functions use the same internal routine to generate the design matrix.) My guess is that the row sums of testfit$x are constant, but that's just a guess. Terry Therneau PS -- use the spacebar more when showing an example. It makes it a lot easier for the rest of us to read. On 01/24/2013 05:00 AM, r-help-requ...@r-project.org wrote: Thank you for the suggestions. Just to clarify, my first question was more on what actual coding I should be using to indicate a nested variable when using the coxph() function. I asked this after consulting several times with a local statistician, but unfortunately neither of us are very familiar with R. After further consultation, I have changed the design to a 2*2 design (2 levels of ExpTemp and Stability each) with blocking (Period). I am still getting the x matrix deemed to be singular error. LOEmod3alt=coxph(LOE.fit~ExpTemp+Stability+Period,data=goodexp) Warning message: In coxph(LOE.fit ~ ExpTemp + Stability + Period, data = goodexp) : X matrix deemed to be singular; variable 5 summary(LOEmod3alt) Call: coxph(formula = LOE.fit ~ ExpTemp + Stability + Period, data = goodexp) n= 184, number of events= 105 coef exp(coef) se(coef) z Pr(|z|) ExpTemp -3.17825 0.04166 0.53105 -5.985 2.17e-09 *** StabilityStatic -0.84129 0.43115 0.20470 -4.110 3.96e-05 *** PeriodB 1.06794 2.90937 0.22859 4.672 2.98e-06 *** PeriodC 1.23853 3.45054 0.58457 2.119 0.0341 * PeriodD NANA 0.0 NA NA --- Signif. codes: 0 ?***? 0.001 ?**? 0.01 ?*? 0.05 ?.? 0.1 ? ? 1 exp(coef) exp(-coef) lower .95 upper .95 ExpTemp 0.0416624.0047 0.01471 0.118 StabilityStatic 0.43115 2.3194 0.28866 0.644 PeriodB 2.90937 0.3437 1.85877 4.554 PeriodC 3.45054 0.2898 1.0972310.851 PeriodDNA NANANA Concordance= 0.833 (se = 0.03 ) Rsquare= 0.591 (max possible= 0.995 ) Likelihood ratio test= 164.4 on 4 df, p=0 Wald test= 111.1 on 4 df, p=0 Score (logrank) test = 179.9 on 4 df, p=0 with(redo, table(LOEStatusfull, Period,ExpTemp)) , , ExpTemp = FIVE Period LOEStatusfull A B C D 0 42 0 35 0 1 4 0 11 0 , , ExpTemp = FOUR Period LOEStatusfull A B C D 0 0 0 0 2 1 0 46 0 44 As best as I can tell, none of my variables are collinear. Are there any other suggestions of how to deal with this error, or any more information I can provide to help understand why I would be getting this? Thank you for your time and your help, Katie O [[alternative HTML version deleted]] __ R-help@r-project.org 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] nesting in CoxPH with survival package
Thank you for the suggestions. Just to clarify, my first question was more on what actual coding I should be using to indicate a nested variable when using the coxph() function. I asked this after consulting several times with a local statistician, but unfortunately neither of us are very familiar with R. After further consultation, I have changed the design to a 2*2 design (2 levels of ExpTemp and Stability each) with blocking (Period). I am still getting the x matrix deemed to be singular error. LOEmod3alt=coxph(LOE.fit~ExpTemp+Stability+Period,data=goodexp) Warning message: In coxph(LOE.fit ~ ExpTemp + Stability + Period, data = goodexp) : X matrix deemed to be singular; variable 5 summary(LOEmod3alt) Call: coxph(formula = LOE.fit ~ ExpTemp + Stability + Period, data = goodexp) n= 184, number of events= 105 coef exp(coef) se(coef) z Pr(|z|) ExpTemp -3.17825 0.04166 0.53105 -5.985 2.17e-09 *** StabilityStatic -0.84129 0.43115 0.20470 -4.110 3.96e-05 *** PeriodB 1.06794 2.90937 0.22859 4.672 2.98e-06 *** PeriodC 1.23853 3.45054 0.58457 2.119 0.0341 * PeriodD NANA 0.0 NA NA --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 exp(coef) exp(-coef) lower .95 upper .95 ExpTemp 0.0416624.0047 0.01471 0.118 StabilityStatic 0.43115 2.3194 0.28866 0.644 PeriodB 2.90937 0.3437 1.85877 4.554 PeriodC 3.45054 0.2898 1.0972310.851 PeriodDNA NANANA Concordance= 0.833 (se = 0.03 ) Rsquare= 0.591 (max possible= 0.995 ) Likelihood ratio test= 164.4 on 4 df, p=0 Wald test= 111.1 on 4 df, p=0 Score (logrank) test = 179.9 on 4 df, p=0 with(redo, table(LOEStatusfull, Period,ExpTemp)) , , ExpTemp = FIVE Period LOEStatusfull A B C D 0 42 0 35 0 1 4 0 11 0 , , ExpTemp = FOUR Period LOEStatusfull A B C D 0 0 0 0 2 1 0 46 0 44 As best as I can tell, none of my variables are collinear. Are there any other suggestions of how to deal with this error, or any more information I can provide to help understand why I would be getting this? Thank you for your time and your help, Katie On Sat, Jan 12, 2013 at 4:54 PM, Bert Gunter gunter.ber...@gene.com wrote: Katie: You need to get local statistical help. What you are doing makes no sense. See inline below. -- Bert On Sat, Jan 12, 2013 at 1:03 PM, David Winsemius dwinsem...@comcast.net wrote: On Jan 11, 2013, at 5:35 PM, Katie Anweiler wrote: Hello all, I am trying to understand how to specify nested factors when using coxph(), and if it is appropriate to nest these factors in my situation. In the simplest form, I am testing two different temperatures, with each temperature being performed twice in different experimental periods (e.g. Temp5 performed in Period A and C, Temp4 performed in Period B and D) Period is confounded with temperature. That is the source of the singularity. in the message received below. You can estimate the C-A and the D-B differences. As I said, get statistical help. These are not R questions. -- Bert I am trying to see if survival time is affected by the treatment temperature. To do this I am using temperature and experimental period nested within temperature as factors. LOEtempmod.5days=coxph(LOE.stable.5days~Temp+Temp/Period,data=goodstable) Warning message: In coxph(LOE.stable.5days ~ Temp + Temp/Period, : X matrix deemed to be singular; variable 2 5 6 7 1. Is this an appropriate way of nesting? Have you looked at the coxme package? http://cran.r-project.org/web/packages/coxme/index.html 2. Can this error message be ignored? Sometimes R packages correctly drop variables that are exactly collinear: other times the correct solution is not clear. I would think the answer in this case would be no, but do not have a lot to go on at this point. -- David Winsemius, MD Alameda, CA, USA __ R-help@r-project.org 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. -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm __ R-help@r-project.org 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] nesting in CoxPH with survival package
Hello all, I am trying to understand how to specify nested factors when using coxph(), and if it is appropriate to nest these factors in my situation. In the simplest form, I am testing two different temperatures, with each temperature being performed twice in different experimental periods (e.g. Temp5 performed in Period A and C, Temp4 performed in Period B and D) I am trying to see if survival time is affected by the treatment temperature. To do this I am using temperature and experimental period nested within temperature as factors. LOEtempmod.5days=coxph(LOE.stable.5days~Temp+Temp/Period,data=goodstable) Warning message: In coxph(LOE.stable.5days ~ Temp + Temp/Period, : X matrix deemed to be singular; variable 2 5 6 7 1. Is this an appropriate way of nesting? 2. Can this error message be ignored? Any help would be much appreciated, thank you in advance. Katie __ R-help@r-project.org 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] nesting in CoxPH with survival package
On Jan 11, 2013, at 5:35 PM, Katie Anweiler wrote: Hello all, I am trying to understand how to specify nested factors when using coxph(), and if it is appropriate to nest these factors in my situation. In the simplest form, I am testing two different temperatures, with each temperature being performed twice in different experimental periods (e.g. Temp5 performed in Period A and C, Temp4 performed in Period B and D) I am trying to see if survival time is affected by the treatment temperature. To do this I am using temperature and experimental period nested within temperature as factors. LOEtempmod.5days=coxph(LOE.stable.5days~Temp+Temp/ Period,data=goodstable) Warning message: In coxph(LOE.stable.5days ~ Temp + Temp/Period, : X matrix deemed to be singular; variable 2 5 6 7 1. Is this an appropriate way of nesting? Have you looked at the coxme package? http://cran.r-project.org/web/packages/coxme/index.html 2. Can this error message be ignored? Sometimes R packages correctly drop variables that are exactly collinear: other times the correct solution is not clear. I would think the answer in this case would be no, but do not have a lot to go on at this point. -- David Winsemius, MD Alameda, CA, USA __ R-help@r-project.org 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] nesting in CoxPH with survival package
Katie: You need to get local statistical help. What you are doing makes no sense. See inline below. -- Bert On Sat, Jan 12, 2013 at 1:03 PM, David Winsemius dwinsem...@comcast.net wrote: On Jan 11, 2013, at 5:35 PM, Katie Anweiler wrote: Hello all, I am trying to understand how to specify nested factors when using coxph(), and if it is appropriate to nest these factors in my situation. In the simplest form, I am testing two different temperatures, with each temperature being performed twice in different experimental periods (e.g. Temp5 performed in Period A and C, Temp4 performed in Period B and D) Period is confounded with temperature. That is the source of the singularity. in the message received below. You can estimate the C-A and the D-B differences. As I said, get statistical help. These are not R questions. -- Bert I am trying to see if survival time is affected by the treatment temperature. To do this I am using temperature and experimental period nested within temperature as factors. LOEtempmod.5days=coxph(LOE.stable.5days~Temp+Temp/Period,data=goodstable) Warning message: In coxph(LOE.stable.5days ~ Temp + Temp/Period, : X matrix deemed to be singular; variable 2 5 6 7 1. Is this an appropriate way of nesting? Have you looked at the coxme package? http://cran.r-project.org/web/packages/coxme/index.html 2. Can this error message be ignored? Sometimes R packages correctly drop variables that are exactly collinear: other times the correct solution is not clear. I would think the answer in this case would be no, but do not have a lot to go on at this point. -- David Winsemius, MD Alameda, CA, USA __ R-help@r-project.org 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. -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm __ R-help@r-project.org 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.
