Displaying 20 results from an estimated 4000 matches similar to: "basehaz and newdata"
2007 Dec 09
2
Getting estimates from survfit.coxph
Dear all,
I'm having difficulty getting access to data generated by survfit and
print.survfit when they are using with a Cox model (survfit.coxph).
I would like to programmatically access the median survival time for
each strata together with the 95% confidence interval. I can get it on
screen, but can't get to it algorithmically. I found myself examining
the source of print.survfit to
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 + strata(sex), test1)
2007 Sep 27
2
center option of basehaz in survfit
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
2012 Aug 08
1
basehaz() in package 'Survival' and warnings() with coxph
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
2012 Aug 09
1
basehaz() in package survival and warnings with coxph
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
2009 Oct 27
2
cox regression extract strata as numeric
Hi there,
I perform a stratified cox and then I need the strata as a numeric array "straft.ln"
ft.ln <- coxph(Surv(times,deaths)~ages+chemos+chemos:f1+chemos:f2+horms+horms:f1+horms:f2+grades+grades:f1+grades:f2+positives+positives:f1+positives:f2+sizes+sizes:f1+sizes:f2+strata(stra),data=ddd)
basehazzft.ln=basehaz(ft.ln,centered=FALSE)
H0ft.ln=c(basehazzft.ln[,1])
2004 Sep 03
1
Printing output on Plot
Hi,
I'm trying to print the p-values from the output of a CPH test onto a
Kaplan Meier plot. Can this be done? I only really want the p-values
from the CPH test to appear but if this can't be done I am willing to
have the entire CPH output.
This is what I am currently trying: (it doesn't print the CPH output)
plot_KM <- function(field)
{
library(survival)
y =
2007 Feb 05
2
Two ways to deal with age in Cox model
I hope one and all will allow a stats question:
When running a cox proportional hazards model ,there are two ways to
deal with age,
including age as a covariate, or to include age as part of the
follow-up time, viz,
Age as a covariate:
tetest1 <- list(time= c(4, 3,1,1,2,2,3),
status=c(1,NA,1,0,1,1,0),
age= c(0, 2,1,1,1,0,0),
2011 Mar 09
2
Anomaly with unique and match
I stumbled onto this working on an update to coxph. The last 6 lines
below are the question, the rest create a test data set.
tmt585% R
R version 2.12.2 (2011-02-25)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
# Lines of code from survival/tests/singtest.R
> library(survival)
Loading required package: splines
2004 Nov 19
2
function 'vcov' for coxph in R 2.0.0
Hi there,
After I fitted a cox model, I used vcov to obtain the
variance of the parameter estimate. It worked correctly in
R 1.9.1. But it failed in R 2.0.0 and the error message is
Error in vcov(cox.1) : no applicable method for "vcov"
I don't know if it is a bug or there is some update on
this function. Thanks!
Lei Liu
Assistant Professor
Division of Biostatistics and
2006 Mar 07
1
breslow estimator for cumulative hazard function
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
2007 Jan 19
1
Error in basehaz function ?
Hello R-users.
I believe that the way basehaz (in the survival package) compute the
baseline hazard function is false.
I come to question this function when it gives me hazard probabilities
greater than 1.
Looking at the code I think I've localised the error :
hazard probability is computed as :
H <- -log(surv)
but it seems to me that hazard probabilities is rather an instantaneous
2009 Mar 14
1
obtaining the values for the hazard function in a cox regression
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
2012 Jan 25
4
formula error inside function
I want use survfit() and basehaz() inside a function, but it doesn't work.
Could you take a look at this problem. Thanks for your help. Following is my
codes:
library(survival)
n <- 50 # total sample size
nclust <- 5 # number of clusters
clusters <- rep(1:nclust,each=n/nclust)
beta0 <- c(1,2)
set.seed(13)
#generate phmm data set
Z <- cbind(Z1=sample(0:1,n,replace=TRUE),
2008 Oct 14
1
Extended summary
Is there a function providing more descriptive statistics than
"summary()"? I'm working with a coxph analyses and would like to have
more info on certain numbers.
If my call is something like:
Call:
coxph(formula = Surv(followup, CasesCancer) ~ age + BMI + parity + HRT)
I'd like to know:
* How many CasesCancer was excluded (not only the total number of
excluded due to
2009 Feb 23
1
predicting cumulative hazard for coxph using predict
Hi
I am estimating the following coxph function with stratification and frailty?where each person had multiple events.
m<-coxph(Surv(dtime1,status1)~gender+cage+uplf+strata(enum)+frailty(id),xmodel)
?
> head(xmodel)
id enum dtime status gender cage uplf
1 1008666 1 2259.1412037 1 MA 0.000 0
2 1008666 2 36.7495023 1 MA 2259.141 0
3 1008666
2009 Dec 16
1
Baseline survival estimate
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
2009 Jan 06
2
Strange error message
I'm testing out some changes to survreg and got the following output, the
likes of which I've never seen before:
----------------------------------------------------------------------
R version 2.7.1 (2008-06-23)
Copyright (C) 2008 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it
2005 Jun 10
1
Estimate of baseline hazard in survival
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),
2009 May 04
1
Nelson-Aalen estimator of cumulative hazard
Hi,
I am computing the Nelson-Aalen (NA) estimate of baseline cumulative hazard in two different ways using the "survival" package. I am expecting that they should be identical. However, they are not. Their difference is a monotonically increasing with time. This difference is probably not large to make any impact in the application, but is annoyingly non-trivial for me to just