[R] independent censoring

Dear All, Independent censoring is one of the fundamental assumptions in the survival analysis. However, I cannot find any test for it or any paper which discusses how real that assumption is. I would be grateful if anybody could point me to some useful references. I have found the following

[R] removing dropouts from survival analysis

Dear All. Apologies for posting a question regarding survival analysis, and not R, to the R-help list. In the past I received the best advices from the R community. The random censorship model (the censoring times independent of the failure times and vice versa) is one of the fundamental assu

[R] coxph (survival) paper from '82

ls of Statistics 10, 1100-1120 I would be really grateful if someone could help me with the electronic copy of the paper. Writing to the R-help emailing list was my last resort. Thanks in advance. With kind regards DK Damjan Krstajic Director Research Centre for Cheminform

[R] R survival package error message - bug?!

Dear all, I have encountered a weird behaviour in R survival package which seems to me to be a bug. The weird behaviour happens when I am using 100 variables in the ridge function when calling coxph with following formula Surv(time = futime, event = fustat, type = "right") ~ ridge(X1, X2, X

[R] survival - ratio likelihood for ridge coxph()

It seems to me that R returns the unpenalized log-likelihood for the ratio likelihood test when ridge regression Cox proportional model is implemented. Is this as expected? In the example below, if I am not mistaken, fit$loglik[2] is unpenalized log-likelihood for the final estimates of coeffi

[R] scientific (statistical) foundation for Y-RANDOMIZATION in regression analysis

vance. DK ------ Damjan Krstajic Director Research Centre for Cheminformatics Belgrade, Serbia -- _ Tell us your greatest

[R] confidence intervals for non-linear regression

kind of black box. Any references to the literature or R packages would be very welcome. Thanks in advance. DK -- Damjan Krstajic Director Research Centre for Cheminformatics Belgrade, Serbia

[R] statistics and R package for election results

Dear all, Is there any R package which would help in analysing election results between two elections? Does anybody know any good papers which are related to this field? I am a statistician and my main research area so far has been regression and classification modelling. The analysis of two e

[R] Introducing R to statisticians

Dear all, I will present R language and R software environment to the Statistical Society of Serbia. As I will doing it to professional statisticians it seems unneccesary to me to present them how R language works in details. I am more interested to present them with the latest facts regarding

[R] survival - summary and score test for ridge coxph()

It seems to me that summary for ridge coxph() prints summary but returns NULL. It is not a big issue because one can calculate statistics directly from a coxph.object. However, for some reason the score test is not calculated for ridge coxph(), i.e score nor rscore components are not included i

[R] survival: ridge log-likelihood workaround

Dear all, I need to calculate likelihood ratio test for ridge regression. In February I have reported a bug where coxph returns unpenalized log-likelihood for final beta estimates for ridge coxph regression. In high-dimensional settings ridge regression models usually fail for lower values of

Re: [R] survival: ridge log-likelihood workaround

r ridge coxph are based on published papers. Damjan Krstajic > Subject: Re: [R] survival: ridge log-likelihood workaround > From: thern...@mayo.edu > To: r-help@r-project.org; dkrsta...@hotmail.com > Date: Fri, 10 Dec 2010 09:07:42 -0600 > > -- begin inclusion - > D

[R] bug in glmnet 1.7.1 for multinomal when alpha=0?

Dear all, If I am not mistaken, I think that I have found a bug in glmnet 1.7.1 (latest version) for multinomial when alpha=0. Here is the code > library(glmnet) Loading required package: Matrix Loading required package: lattice Loaded glmnet 1.7.1 > x=matrix(rnorm(40*500),40,500) > g4=sample(1

[R] differences between 1.7 and 1.7.1 glmnet versions

Dear All,   I have found differences between glmnet versions 1.7 and 1.7.1 which, in my opinion, are not cosmetic and do not appear in the ChangeLog. If I am not mistaken, glmnet appears to return different number of selected input variables, i.e. nonzeroCoef(fit$beta[[1]]) differes between ve

Re: [R] differences between 1.7 and 1.7.1 glmnet versions

Thank you very much. I will use 1.7.1 version. Have you had time to look at the issue regarding a weird behaviour of multinomial glmnet when alpha=0? I posted it to r-help more than two weeks ago and maybe you missed it. Damjan Krstajic Subject: Re: differences between 1.7 and 1.7.1 glmnet

[R] estimating survival times with glmnet and coxph

Dear all, I am using glmnet (Coxnet) for building a Cox Model and to make actual prediction, i.e. to estimate the survival function S(t,Xn) for a new subject Xn. If I am not mistaken, glmnet (coxnet) returns beta, beta*X and exp(beta*X), which on its own cannot generate S(t,Xn). We miss baseline

[R] (bug?) in survfit in R-2-15-0

Dear all,   I am using glmnet + survival and due to the latest release of glmnet 1.7.4 I was forced to use the latest version of R 2.15.0. My previous version of R was 2.10.1. I changed glmnet version and R version and when I started to get weird results I was not sure where the bug was.  

[R] survival survfit with newdata

Dear all, I am confused with the behaviour of survfit with newdata option. I am using the latest version R-2-15-0. In the simple example below I am building a coxph model on 90 patients and trying to predict 10 patients. Unfortunately the survival curve at the end is for 90 patients. Could som

Re: [R] survival survfit with newdata

oject.org > From: dwinsem...@comcast.net > To: dkrsta...@hotmail.com > Subject: Re: [R] survival survfit with newdata > Date: Thu, 17 May 2012 00:52:55 -0400 > > > On May 16, 2012, at 5:08 PM, Damjan Krstajic wrote: > > > > > Dear all, > > > > I am confused wit