similar to: How to obtain the estimate of baseline survival function?

Dear R-help, I am trying to obtain the baseline survival estimate of a fitted Cox model (S_0 (t)). I know that previous posts have said use 'basehaz' but this gives the baseline hazard function and not the baseline survival estimate. Is there a way to obtain the baseline survival estimate or do I have to use the formula which does something like S(t) = exp[- the integral from 0 to t of

Dear All, I'm having just a little terminology problem, relating the language used in the Hosmer and Lemeshow text on Applied Survival Analysis to that of the help that comes with the survival package. I am trying to back out the values for the baseline hazard, h_o(t_i), for each event time or observation time. Now survfit(fit)$surv gives me the value of the survival function, S(t_i|X_i,B),

Good evening, Yuan Excuse me, I gave up Debug build earlier due to my poor hosts. I will improve able to build Debug ;) You may build with --enable-optimized=yes (or, make ENABLE_OPTIMIZED=1) btw, DLL builder has implemented since Aug. It might be easier to port DLL stuff to 2.6 :) Do you try? ...Takumi 2010年9月2日 17:16:25 UTC+9 yuan zheng <tsinghuayuan86 at gmail.com>: > Hello,

Dear R-users, I am checking the proportional hazard assumption of a cox model for a given covariate, let say Z1, after adjusting for other relavent covariates in the model. To this end, I fitted cox model stratified on the discrete values of Z1 and try to get beslow estimator for the baseline cumulative hazard function (H(t)) in each stratum. As far as i know, if the proportionality assumption

-------- Original Message -------- Subject: Re: How to obtain nonparametric baseline hazard estimates in the gamma frailty model? Date: Mon, 04 Nov 2013 17:27:04 -0600 From: Terry Therneau <therneau.terry at mayo.edu> To: Y <yuhanusa at gmail.com> The cumulative hazard is just -log(sfit$surv). The hazard is essentially a density estimate, and that is much harder. You'll notice

I've never seen this, and have no idea how to reproduce it. For resloution you are going to have to give me a working example of the failure. Also, per the posting guide, what is your sessionInfo()? Terry Therneau On 08/09/2012 04:11 AM, r-help-request at r-project.org wrote: > I have a couple of questions with regards to fitting a coxph model to a data > set in R: > > I have a

Hello, I have a couple of questions with regards to fitting a coxph model to a data set in R: I have a very large dataset and wanted to get the baseline hazard using the basehaz() function in the package : 'survival'. If I use all the covariates then the output from basehaz(fit), where fit is a model fit using coxph(), gives 507 unique values for the time and the corresponding cumulative

Hello, NAKAMURA Takumi As you said, I check out the head from svn trunk. I build the source code as the following steps: $./configure --enable-shared $ make After 1 hour, the building procedure is stopped and appear the following error message: c:/strawberry/c/bin/../lib/gcc/i686-w64-mingw32/4.4.3/../../../../i686-w64-mingw 32/bin/ld.exe:

Dear list, is there a function available which provides an estimate of the hazard function based on a cox proportional hazard model? I only found the cumulative hazard and the survival function as survfit options. Thanks for your help Peter

Hello , I am hoping for some advice regarding obtaining the values for the hazard function in a cox regression that I have undertaken. I have a model in the following form, analysed with the package survival (v. 2.34-1) and a log-log plot obtained using Design (v. 2.1-2). For two variables, the lines in the survival curves crossed. The statistician I been obtaining advice from (who does not

Using R-1.8.0 (d/l and compiled on 2003-10-01) on WinXP, I seem to be unable to determine the maximum memory allocated to R. The help still says to use memory.limit(size=NA), but this returns the value NA. In addition, I have set --max-mem-size=2G but I run out of memory somewhere around 500Mb (which is why I am trying to find out how much memory is allocated). I don't have any other programs

Dear List, Is there an automated way to use the survival package to generate survival rate estimates and their standard errors? To be clear, *not *the survivorship estimates (which are cumulative), but the survival *rate * estimates... Thank you in advance for any help. Best, Brian [[alternative HTML version deleted]]

Hi everyone. There's been several threads on baseline hazard in Cox model but I think they were all on cumulative baseline hazard, for instance http://tolstoy.newcastle.edu.au/R/help/01a/0464.html http://tolstoy.newcastle.edu.au/R/help/01a/0436.html "basehaz" in package survival seems to do a cumulative hazard. extract from the basehaz function: sfit <- survfit(fit) H

I have a very general question about what the centering option in basehaz does to factors. (basehaz computes the baseline cumulative hazard for a coxph object using the Breslow estimator). Lets say I'm interested in a survival model with two (dichotomous) factors and a continuous covariate. Variable Possible Values Factor1 0 or 1 Factor2 0 or 1

Hi, I had cloned zorg from https://llvm.org/svn/llvm-project/zorg/trunk, then I try to start the buildbot master located in buildbot/osuosl/master (the absolute path is /nfs/home/hongbin.zheng/buildbot/zorg/buildbot/osuosl/master) by simply typing "buildbot start" And I get something like this from my twistd.log: --- <exception caught here> --- File

Hongbin, Did you tweak sys.path? # Extend paths to allow loading zorg and config modules. import os, sys path = os.path.join(os.environ.get('HOME'), 'zorg', 'buildbot', 'osuosl', 'master') if path not in sys.path: sys.path.append(path) path = os.path.join(os.environ.get('HOME'), 'zorg') if path not in sys.path: sys.path.append(path)

Thanks Edwin. I found DebugInfo.cpp may be useful. Could you tell me which function I should call inorder to know the source file name and the line number for a particular instruction? Cheers, Zheng 2010/5/18 Török Edwin <edwintorok at gmail.com>: > On 05/18/2010 01:26 PM, Zheng Wang wrote: >> Hello, >> >> Could I get some debug info at the byte code level? I am

Dear List, Does anybody no how to compare mean survival times for two (more) groups in R? What test statistics should I use? Thank you very much! Joe [[alternative HTML version deleted]]

Hi John, Are there any documents about how to add a pass into LTO? Cheers, Zheng On 19 April 2010 15:11, John Criswell <criswell at uiuc.edu> wrote: > Dear Zheng Wang, > > You have a few options: > > 1) You can add your pass to the set of passes that llvm-gcc runs when it > optimizes code.  This requires re-compiling llvm-gcc; it also means that > your pass must be

I get a segfault when using savePlot("foo","pdf"). FWIW, I don't have a problem using the canonical pdf("foo.pdf") plot(something) dev.off() Best, Jim > R.Version() $platform [1] "i386-pc-mingw32" $arch [1] "i386" $os [1] "mingw32" $system [1] "i386, mingw32" $status [1] "Under development (unstable)"