# search for: coxph

Displaying 20 results from an estimated 291 matches for "coxph".

2012 Jul 06
1
How to compute hazard function using coxph.object
My question is, how to compute hazard function(H(t)) after building the coxph model. I even aware of the terminology that differs from hazard function(H(t)) and the hazard rate(h(t)). Here onward I wish to calculate both. Here what I have done in two different methods; ########################################################################################## ############...
2011 Sep 12
1
coxreg vs coxph: time-dependent treatment
Dear List, After including cluster() option the coxreg (from eha package) produces results slightly different than that of coxph (from survival) in the following time-dependent treatment effect calculation (example is used just to make the point). Will appreciate any explaination / comment. cheers, Ehsan ############################ require(survival) require(eha) data(heart) # create weights follow <- heart\$stop...
2004 Oct 26
2
vcov method for 'coxph' objects
Dear all, The help file for the generic function vcov states "Classes with methods for this function include: 'lm', 'glm', 'nls', 'lme', 'gls', 'coxph' and 'survreg' (the last two in package 'survival')." Since, I am not able to use vcov.coxph(), I am wondering whether I am missing something (as I suspect..) regards, vito library(survival) > o<- coxph( Surv(time, status) ~ x + strata(sex), test1) #example from ?...
2010 Jul 30
1
COXPH: how to get the score test and likelihood ratio test for a specific variable in a multivariate Coxph ?
Hello, I would like to get the likelihood ratio and score tests for specific variables in a multivariate coxph model. The default is Wald, so the tests for each separate variable is based on Wald's test. I have the other tests for the full model but I don't know how to get them for each variable. Any idea? David Biau. [[alternative HTML version deleted]]
2007 Dec 17
2
Capture warning messages from coxph()
Hi, I want to fit multiple cox models using the coxph() function. To do this, I use a for-loop and save the relevant results in a separate matrix. In the example below, only two models are fitted (my actual matrix has many more columns), one gives a warning message, while the other does not. Right now, I see all the warning message(s) after the for-lo...
2011 Mar 01
1
glht() used with coxph()
Hi, I am experimenting with using glht() from multcomp package together with coxph(), and glad to find that glht() can work on coph object, for example: > (fit<-coxph(Surv(stop, status>0)~treatment,bladder1)) coxph(formula = Surv(stop, status > 0) ~ treatment, data = bladder1) coef exp(coef) se(coef) z p treatmentpyridoxine -0.063...
2007 Apr 17
3
Extracting approximate Wald test (Chisq) from coxph(..frailty)
Dear List, How do I extract the approximate Wald test for the frailty (in the following example 17.89 value)? What about the P-values, other Chisq, DF, se(coef) and se2? How can they be extracted? ######################################################> kfitm1 Call: coxph(formula = Surv(time, status) ~ age + sex + disease + frailty(id, dist = "gauss"), data = kidney) coef se(coef) age 0.00489 0.0150 sex -1.69703 0.4609 diseaseGN 0.17980 0.5447 diseaseAN...
2010 Dec 09
1
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 lambda. As the result of it, in such settings the ridge regressions have higher values of lambda (e.g. over 100) which means...
2008 Jun 16
1

I tried to compare if cch() and coxph() can generate same result for same case cohort data Use the standard data in cch(): nwtco Since in cch contains the cohort size=4028, while ccoh.data size =1154 after selection, but coxph does not contain info of cohort size=4028. The rough estimate between coxph() and cch() is same, but the lo...
2011 Jul 10
1
Package "survival" --- Difference of coxph strata with subset?
[code]>require("survival") > coxph(Surv(futime,fustat)~age + strata(rx),ovarian) Call: coxph(formula = Surv(futime, fustat) ~ age + strata(rx), data = ovarian) coef exp(coef) se(coef) z p age 0.137 1.15 0.0474 2.9 0.0038 Likelihood ratio test=12.7 on 1 df, p=0.000368 n= 26, number of events= 12 > coxph(Su...
2008 Jan 08
1
Problem in anova with coxph object
Dear R users, I noticed a problem in the anova command when applied on a single coxph object if there are missing observations in the data: This example code was run on R-2.6.1: > library(survival) > data(colon) > colondeath = colon[colon\$etype==2, ] > m = coxph(Surv(time, status) ~ rx + sex + age + perfor, data=colondeath) > m Call: coxph(formula = Surv(time,...
2011 Oct 01
4
Is the output of survfit.coxph survival or baseline survival?
Dear all, I am confused with the output of survfit.coxph. Someone said that the survival given by summary(survfit.coxph) is the baseline survival S_0, but some said that is the survival S=S_0^exp{beta*x}. Which one is correct? By the way, if I use "newdata=" in the survfit, does that mean the survival is estimated by the value of covariates i...
2010 Apr 20
3
Help: coxph() in {survival} package
Hi All, I'm runnning coxph() on 90 different datasets (in a loop). 1. I'm wondering how can I get "log-likelihood" value from coxph() output. Currently I can only see following: Likelihood ratio test = Wald test = Score (logrank) test = 2. Once I have likelihood value, I would like to extract these from R...
2011 Jun 25
2
cluster() or frailty() in coxph
Dear List, Can anyone please explain the difference between cluster() and frailty() in a coxph? I am a bit puzzled about it. Would appreciate any useful reference or direction. cheers, Ehsan > marginal.model <- coxph(Surv(time, status) ~ rx + cluster(litter), rats) > frailty.model <- coxph(Surv(time, status) ~ rx + frailty(litter), rats) > marginal.model Call: coxph(form...
2008 Apr 23
2
help on coxph.wtest
Hi, i need to use pspline. In this pspline function coxph.wtest was used. When I try to make some change to this function by pulling out the pspline function, it turns out R gave me an error msg, saying coxph.wtest cannot be found. Even if i dont change anything in pspline and just rename it and run the function, it did not work out. Can any one help me w...
2008 Jun 07
1
expected risk from coxph (survival)
Hello, When I try to to obtain the expected risk for a new dataset using coxph in the survival package I get an error. Using the example from ?coxph: > test1 <- list(time= c(4, 3,1,1,2,2,3),+ status=c(1,NA,1,0,1,1,0),+ x= c(0, 2,1,1,1,0,0),+ sex= c(0, 0,0,0,1,1,1))> cox<-coxph( Surv(time, status) ~ x + strat...
2013 Nov 14
1
issues with calling predict.coxph.penal (survival) inside a function
...ery other one of my wrestling matches with predict inside a function has -- and there is a reasonable chance that it won't make this already overdue release. In the meantime, here is a workaround that I have sometimes used in other situations. Inside your function do the following: fit a new coxph model with fixed coefficients, and do prediction on that. myfun <- function(oldfit, subset) { newX <- model.matrix(oldfit)[subset,] newY <- oldfit\$y[subset] newfit <- coxph(newY ~ newX, iter=0, init=coef(oldfit)) newfit\$var <- oldfit\$var predict(newfit) } I...
2004 May 16
2
Error in using coxph()
...ge in: fitter(X, Y, strats, offset, init, control, weights = weights,..." Details : --------- E is a vector of survival times (or censored times), 1-F is a vector of '0's, and cov is a matrix of 1 column. There are altogether 75 observations. Tried : ------ P <- try(surv.cox <- coxph(Surv(E, 1-F) ~ cov, coxph.control(iter.max=1e10, eps = 1e-03))) Output (from above command) : ----------------------------- Call: coxph(formula = Surv(E, F) ~ cov, data = coxph.control(iter.max = 1e+10, eps = 0.001)) coef exp(coef) se(coef) z p cov -0.233 0.793 0.11 -2...
2004 Oct 15
1
categorical varibles in coxph
Hello, I wonder when I do coxph in R: coxph( Surv(start, stop, event) ~ x, data=test) If x is a categorical varible (1,2,3,4,5), should I creat four dummy varibles for it? if yes, how can I get the overall p value on x other than for each dummy variable? Thanks Lisa Wang Princess Margaret Hospital Phone 416 946 4501
2010 Nov 11
2
predict.coxph and predict.survreg
Dear all, I'm struggling with predicting "expected time until death" for a coxph and survreg model. I have two datasets. Dataset 1 includes a certain number of people for which I know a vector of covariates (age, gender, etc.) and their event times (i.e., I know whether they have died and when if death occurred prior to the end of the observation period). Dataset 2 includes an...