[R] Survival statistics--displaying multiple plots
Hello all! I am once again analyzing patient survival data with chronic liver disease. The severity of the liver disease is given by a number which is continuously variable. I have referred to this number as meld--model for end stage liver disease--which is the result of a mathematical calculation on underlying laboratory values. So, for example, I can generate a Kaplan-Meier plot of patients undergoing a TIPS procedure with the following: plot(survfit(Surv(days,status==1),subset(tips,meld10)) where tips is my data set, days is the number of days alive, and meld is the meld score. What I would like to do is display the survival graphs of patients with meld10, 10meld20, and meld20. I am unsure about how to go about this. Any suggestions would be appreciated. Greg __ 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] Survival statistics--displaying multiple plots
I should clarify. I can generate plots for each category individually but not for all three on the same chart. Greg -Original Message- From: Gregory Pierce [mailto:[EMAIL PROTECTED] Sent: Wednesday, May 02, 2007 10:21 PM To: 'r-help@stat.math.ethz.ch' Subject: Survival statistics--displaying multiple plots Hello all! I am once again analyzing patient survival data with chronic liver disease. The severity of the liver disease is given by a number which is continuously variable. I have referred to this number as meld--model for end stage liver disease--which is the result of a mathematical calculation on underlying laboratory values. So, for example, I can generate a Kaplan-Meier plot of patients undergoing a TIPS procedure with the following: plot(survfit(Surv(days,status==1),subset(tips,meld10)) where tips is my data set, days is the number of days alive, and meld is the meld score. What I would like to do is display the survival graphs of patients with meld10, 10meld20, and meld20. I am unsure about how to go about this. Any suggestions would be appreciated. Greg __ 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] Survival statistics--displaying multiple plots
? layout() ? par() E.g., layout(matrix(c(1,2,3),1,3,byrow=TRUE) #3 plots side-by-side Then use plot() three times to generate each of your graphs. At 11:14 PM 5/2/2007, Greg wrote: I should clarify. I can generate plots for each category individually but not for all three on the same chart. Greg -Original Message- From: Gregory Pierce [mailto:[EMAIL PROTECTED] Sent: Wednesday, May 02, 2007 10:21 PM To: 'r-help@stat.math.ethz.ch' Subject: Survival statistics--displaying multiple plots Hello all! I am once again analyzing patient survival data with chronic liver disease. The severity of the liver disease is given by a number which is continuously variable. I have referred to this number as meld--model for end stage liver disease--which is the result of a mathematical calculation on underlying laboratory values. So, for example, I can generate a Kaplan-Meier plot of patients undergoing a TIPS procedure with the following: plot(survfit(Surv(days,status==1),subset(tips,meld10)) where tips is my data set, days is the number of days alive, and meld is the meld score. What I would like to do is display the survival graphs of patients with meld10, 10meld20, and meld20. I am unsure about how to go about this. Any suggestions would be appreciated. Robert A. LaBudde, PhD, PAS, Dpl. ACAFS e-mail: [EMAIL PROTECTED] Least Cost Formulations, Ltd.URL: http://lcfltd.com/ 824 Timberlake Drive Tel: 757-467-0954 Virginia Beach, VA 23464-3239Fax: 757-467-2947 Vere scire est per causas scire __ 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] Survival statistics--displaying multiple plots
Have a look at ?lines ?points ?plot - the option add, add=TRUE You will have to specify proper limits on both axes, otherwise you may only see parts of the graphs. Some functions in the survival library also allow stratified analyses in which case the plots account for different strata. Petr Gregory Pierce napsal(a): I should clarify. I can generate plots for each category individually but not for all three on the same chart. Greg -Original Message- From: Gregory Pierce [mailto:[EMAIL PROTECTED] Sent: Wednesday, May 02, 2007 10:21 PM To: 'r-help@stat.math.ethz.ch' Subject: Survival statistics--displaying multiple plots Hello all! I am once again analyzing patient survival data with chronic liver disease. The severity of the liver disease is given by a number which is continuously variable. I have referred to this number as meld--model for end stage liver disease--which is the result of a mathematical calculation on underlying laboratory values. So, for example, I can generate a Kaplan-Meier plot of patients undergoing a TIPS procedure with the following: plot(survfit(Surv(days,status==1),subset(tips,meld10)) where tips is my data set, days is the number of days alive, and meld is the meld score. What I would like to do is display the survival graphs of patients with meld10, 10meld20, and meld20. I am unsure about how to go about this. Any suggestions would be appreciated. Greg __ 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. -- Petr Klasterecky Dept. of Probability and Statistics Charles University in Prague Czech Republic __ 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] Survival statistics--displaying multiple plots
Thanks for replying Robert. Forgive me, it might be the hour or my limitations, but I am a little unclear on how to implement your suggestion. In my original example, plot(survfit(Surv(days,status==1),subset(tips,meld10)) A plot of the fraction of patients surviving following the procedure against the number of days since the procedure would be generated for patients with meld scores of less than 10. Similarly, if I wanted to generate a survival curve of patients with scores of between 10 and 20, I can with the following: plot(survfit(Surv(days,status==1),subset(tips,meld10 meld 20)) And for patients with meld20, plot(survfit(Surv(days,status==1),subset(tips,meld20)) But how do I display the curves in each cadre (meld10, 10meld20, and meld20) on the same chart? -Original Message- From: Robert A LaBudde [mailto:[EMAIL PROTECTED] Sent: Wednesday, May 02, 2007 11:48 PM To: Gregory Pierce Subject: Re: [R] Survival statistics--displaying multiple plots ? layout() ? par() E.g., layout(matrix(c(1,2,3),1,3,byrow=TRUE) #3 plots side-by-side Then use plot() three times to generate each of your graphs. At 11:14 PM 5/2/2007, Greg wrote: I should clarify. I can generate plots for each category individually but not for all three on the same chart. Greg -Original Message- From: Gregory Pierce [mailto:[EMAIL PROTECTED] Sent: Wednesday, May 02, 2007 10:21 PM To: 'r-help@stat.math.ethz.ch' Subject: Survival statistics--displaying multiple plots Hello all! I am once again analyzing patient survival data with chronic liver disease. The severity of the liver disease is given by a number which is continuously variable. I have referred to this number as meld--model for end stage liver disease--which is the result of a mathematical calculation on underlying laboratory values. So, for example, I can generate a Kaplan-Meier plot of patients undergoing a TIPS procedure with the following: plot(survfit(Surv(days,status==1),subset(tips,meld10)) where tips is my data set, days is the number of days alive, and meld is the meld score. What I would like to do is display the survival graphs of patients with meld10, 10meld20, and meld20. I am unsure about how to go about this. Any suggestions would be appreciated. Robert A. LaBudde, PhD, PAS, Dpl. ACAFS e-mail: [EMAIL PROTECTED] Least Cost Formulations, Ltd.URL: http://lcfltd.com/ 824 Timberlake Drive Tel: 757-467-0954 Virginia Beach, VA 23464-3239Fax: 757-467-2947 Vere scire est per causas scire __ 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] Survival statistics--displaying multiple plots
Greg, I suspect that you want something like this: Use the 'aml' dataset and create a 'meld' column with random values from 1:25: library(survival) set.seed(1) aml$meld - sample(25, 23, replace = TRUE) aml$meld [1] 7 10 15 23 6 23 24 17 16 2 6 5 18 10 20 13 18 25 10 20 24 6 [23] 17 Now use cut() to create a 3 level factor from the values in 'meld': aml$meld.grp - cut(aml$meld, breaks = c(-Inf, 10, 20, Inf)) aml$meld.grp [1] (-Inf,10] (-Inf,10] (10,20] (20, Inf] (-Inf,10] (20, Inf] [7] (20, Inf] (10,20] (10,20] (-Inf,10] (-Inf,10] (-Inf,10] [13] (10,20] (-Inf,10] (10,20] (10,20] (10,20] (20, Inf] [19] (-Inf,10] (10,20] (20, Inf] (-Inf,10] (10,20] Levels: (-Inf,10] (10,20] (20, Inf] Now, let's do the plot, grouping by 'meld.grp': plot(survfit(Surv(time, status) ~ meld.grp, data = aml), col = 1:3, legend.text = levels(aml$meld.grp), legend.pos = 1) If this is close, see ?cut for creating a factor from a continuous vector. You can of course further tweak the plot aesthetics as you desire. HTH, Marc Schwartz On Wed, 2007-05-02 at 23:14 -0400, Gregory Pierce wrote: I should clarify. I can generate plots for each category individually but not for all three on the same chart. Greg -Original Message- From: Gregory Pierce [mailto:[EMAIL PROTECTED] Sent: Wednesday, May 02, 2007 10:21 PM To: 'r-help@stat.math.ethz.ch' Subject: Survival statistics--displaying multiple plots Hello all! I am once again analyzing patient survival data with chronic liver disease. The severity of the liver disease is given by a number which is continuously variable. I have referred to this number as meld--model for end stage liver disease--which is the result of a mathematical calculation on underlying laboratory values. So, for example, I can generate a Kaplan-Meier plot of patients undergoing a TIPS procedure with the following: plot(survfit(Surv(days,status==1),subset(tips,meld10)) where tips is my data set, days is the number of days alive, and meld is the meld score. What I would like to do is display the survival graphs of patients with meld10, 10meld20, and meld20. I am unsure about how to go about this. Any suggestions would be appreciated. Greg __ 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-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] Survival statistics--displaying multiple plots
Marc, Thank you so much! Your solution is perfect! I hadn't known about the cut function. The graph is precisely what I needed. I have the ISwR book but not anything more advanced. Need to get some more advanced books, maybe? I have been stubbornly working on this for a few hours now, and getting nowhere. I wish I were able to repay in some way. Thank you! Greg -Original Message- From: Marc Schwartz [mailto:[EMAIL PROTECTED] Sent: Thursday, May 03, 2007 12:18 AM To: Gregory Pierce Cc: r-help@stat.math.ethz.ch Subject: Re: [R] Survival statistics--displaying multiple plots Greg, I suspect that you want something like this: Use the 'aml' dataset and create a 'meld' column with random values from 1:25: library(survival) set.seed(1) aml$meld - sample(25, 23, replace = TRUE) aml$meld [1] 7 10 15 23 6 23 24 17 16 2 6 5 18 10 20 13 18 25 10 20 24 6 [23] 17 Now use cut() to create a 3 level factor from the values in 'meld': aml$meld.grp - cut(aml$meld, breaks = c(-Inf, 10, 20, Inf)) aml$meld.grp [1] (-Inf,10] (-Inf,10] (10,20] (20, Inf] (-Inf,10] (20, Inf] [7] (20, Inf] (10,20] (10,20] (-Inf,10] (-Inf,10] (-Inf,10] [13] (10,20] (-Inf,10] (10,20] (10,20] (10,20] (20, Inf] [19] (-Inf,10] (10,20] (20, Inf] (-Inf,10] (10,20] Levels: (-Inf,10] (10,20] (20, Inf] Now, let's do the plot, grouping by 'meld.grp': plot(survfit(Surv(time, status) ~ meld.grp, data = aml), col = 1:3, legend.text = levels(aml$meld.grp), legend.pos = 1) If this is close, see ?cut for creating a factor from a continuous vector. You can of course further tweak the plot aesthetics as you desire. HTH, Marc Schwartz On Wed, 2007-05-02 at 23:14 -0400, Gregory Pierce wrote: I should clarify. I can generate plots for each category individually but not for all three on the same chart. Greg -Original Message- From: Gregory Pierce [mailto:[EMAIL PROTECTED] Sent: Wednesday, May 02, 2007 10:21 PM To: 'r-help@stat.math.ethz.ch' Subject: Survival statistics--displaying multiple plots Hello all! I am once again analyzing patient survival data with chronic liver disease. The severity of the liver disease is given by a number which is continuously variable. I have referred to this number as meld--model for end stage liver disease--which is the result of a mathematical calculation on underlying laboratory values. So, for example, I can generate a Kaplan-Meier plot of patients undergoing a TIPS procedure with the following: plot(survfit(Surv(days,status==1),subset(tips,meld10)) where tips is my data set, days is the number of days alive, and meld is the meld score. What I would like to do is display the survival graphs of patients with meld10, 10meld20, and meld20. I am unsure about how to go about this. Any suggestions would be appreciated. Greg __ 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-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] Survival statistics--displaying multiple plots
The layout() function below states there are to be 3 graphs on the first row, side by side. Each time you plot, R applies the graph to the next free position on the layout. After 3 plots with your different boolean subsets, you end up with 3 graphs side by side. If this is not what you want (you asked for this in your first request), and instead you want 3 curves on the same, single graph, use plot() for the first curve(s) and then use lines() to add the additional curves. Check the survfit() object to see how to pick off individual times and survival curves by subscripting. At 12:09 AM 5/3/2007, Greg wrote: Thanks for replying Robert. Forgive me, it might be the hour or my limitations, but I am a little unclear on how to implement your suggestion. In my original example, plot(survfit(Surv(days,status==1),subset(tips,meld10)) A plot of the fraction of patients surviving following the procedure against the number of days since the procedure would be generated for patients with meld scores of less than 10. Similarly, if I wanted to generate a survival curve of patients with scores of between 10 and 20, I can with the following: plot(survfit(Surv(days,status==1),subset(tips,meld10 meld 20)) And for patients with meld20, plot(survfit(Surv(days,status==1),subset(tips,meld20)) But how do I display the curves in each cadre (meld10, 10meld20, and meld20) on the same chart? -Original Message- From: Robert A LaBudde [mailto:[EMAIL PROTECTED] Sent: Wednesday, May 02, 2007 11:48 PM To: Gregory Pierce Subject: Re: [R] Survival statistics--displaying multiple plots ? layout() ? par() E.g., layout(matrix(c(1,2,3),1,3,byrow=TRUE) #3 plots side-by-side Then use plot() three times to generate each of your graphs. At 11:14 PM 5/2/2007, Greg wrote: I should clarify. I can generate plots for each category individually but not for all three on the same chart. Greg -Original Message- From: Gregory Pierce [mailto:[EMAIL PROTECTED] Sent: Wednesday, May 02, 2007 10:21 PM To: 'r-help@stat.math.ethz.ch' Subject: Survival statistics--displaying multiple plots Hello all! I am once again analyzing patient survival data with chronic liver disease. The severity of the liver disease is given by a number which is continuously variable. I have referred to this number as meld--model for end stage liver disease--which is the result of a mathematical calculation on underlying laboratory values. So, for example, I can generate a Kaplan-Meier plot of patients undergoing a TIPS procedure with the following: plot(survfit(Surv(days,status==1),subset(tips,meld10)) where tips is my data set, days is the number of days alive, and meld is the meld score. What I would like to do is display the survival graphs of patients with meld10, 10meld20, and meld20. I am unsure about how to go about this. Any suggestions would be appreciated. Robert A. LaBudde, PhD, PAS, Dpl. ACAFS e-mail: [EMAIL PROTECTED] Least Cost Formulations, Ltd.URL: http://lcfltd.com/ 824 Timberlake Drive Tel: 757-467-0954 Virginia Beach, VA 23464-3239Fax: 757-467-2947 Vere scire est per causas scire __ 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] Survival Statistics
Hello friends and fellow R users, I have a problem to which I have been unable to find a solution: I am gathering survival data on patients undergoing treatment with a new kind of stent. I want to generate survival data and plot survival curves of these patients based (among other things) on the treating physician. My data set has been tabulated in the following manner: Date(the date the stent was implanted) Description (diameter of the stent) Patient (name) MRN (ID number) Age (age in years of the patient) Physician (last name of the implanting physician) status (0 or 1) days (days alive since the stenting procedure) Cr INR BR MELD The data set has over ten physicians. Following the examples in Introductory Statistics with R I have been able to draw cumulative survival curves and even the survival curves by physician but there are so many curves on the graph when I do, it is uninterpretable. I would just like to plot the survival curves of say the top two or three. That would be much more useful. I have been able to create a Surv object out of my own survival data and that of a colleague in the following way using indexing: Surv(days[viatorr[6]==Pierce| viatorr[6]==Ed],status[viatorr[6]==Pierce|viatorr[6]==Ed]==1) [1] 558+ 474+ 472+ 446+ 443+ 429+ 401 395+ 390 390+ 362+ 354 344+ 342 326+ [16] 300+ 284+ 280+ 246+ 237+ 233+ 233 230+ 230+ 225+ 215 199+ 191+ 191 184+ [31] 161+ 153 150 129+ 69+ 52+ 38+ I can get even further: surv.ee.gp-Surv(days[viatorr[6]==Pierce| viatorr[6]==Ed],status[viatorr[6]==Pierce|viatorr[6]==Ed]==1) survfit(surv.ee.gp) Call: survfit(formula = surv.ee.gp) n events median 0.95LCL 0.95UCL 37 9 Inf 390 Inf But now if I want to plot the data using the following command plot(survfit(surv.ee.gp)~Physician) I receive an error: Error in model.frame(formula, rownames, variables, varnames, extras, extranames, : invalid variable type I have tried indexing Physician, but that fails as well: plot(survfit(surv.ee.gp)~Physician[viatorr[6]==Pierce| viatorr[6]==Ed]==1) Error in model.frame(formula, rownames, variables, varnames, extras, extranames, : invalid variable type I apologize for this long-winded explanation but I am new to this program and even newer to Statistics and I wanted to make sure the context and problem were clear (hopefully). I would appreciate any guidance in a way forward. Thank you, Greg __ 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
