Displaying 20 results from an estimated 4000 matches similar to: "Accelerated failure time interpretation of coefficients"
2006 Apr 07
2
Why is transform="km" the default for cox.zph?
To enhance my understanding, and that of my students, I have a question
about cox.zph in the survival package.
If I have correctly gleaned the high-level point from the 1994
Biometrika paper of Grambsch and Therneau, it looks to me like
cox.zph provides a mechanism to test for a simple trend in plots
of a function of time, g(t) versus the scaled schoenfeld
residuals and it also provides some
2010 Jan 28
1
AFT-model with time-varying covariates and left-truncation
Dear Prof. Brostr?m,
Dear R-mailinglist,
first of all thanks a lot for your great effort to incorporate
time-varying covariates into aftreg. It works like a charm so far
and I'll update you with detailled benchmarks as soon as I have them.
I have one more questions regarding Accelerated Failure Time models
(with aftreg):
You mention that left truncation in combination with time-varying
2009 Sep 23
2
scaled Schoenfeld residuals
hi
sorry if this has been discussed before, but I'm wondering why the scaled
Schoenfeld residuals do not follow the defining formula for obtaining them
from the ordinary Schoenfeld residuals, but are instead offset by the
estimated parameter values.
e.g.
library(survival)
attach(ovarian)
sv<-Surv(futime,fustat)
f1<-coxph(sv~age+ecog.ps)
f1
2007 Sep 27
1
plot(cox.zph())
Hello,
I got error message when applying the plot function to the cox.zph
object to create the Schoenfeld residual plots.
> plot(zph.revasFit[1])
Error in plot.window(xlim, ylim, log, asp, ...) :
need finite 'ylim' values
In addition: Warning messages:
1: NaNs produced in: sqrt(x$var[i, i] * seval)
2: no non-missing arguments to min; returning Inf in: min(x)
3: no
2010 Feb 05
3
AFTREG with ID argument
Dear all,
I have some trouble using the "id"-argument with aftreg (accelerated
failure time regression analysis from the eha library).
As far as I understand it, the id argument is used to group
individuals together if there are time-varying covariates and the
data is arranged in counting process style.
Unfortunately, i cannot figure out how to use the "id"-argument. The
2006 Mar 31
1
andersen plot vs score process or scaled Schoenfeld residuals to test for proporti0nal hazards
Dear all,
I use the Andersen plot to check for proportional hazards assumption for a
factor (say x) in the Cox regression model and obtained a straight line that
pass through the origin. However, the formal test done by the R-function
cox.zph, which is based on the plot of Schonefeld residuals against time,
indicates that proportional hazards assumption is violated. Further, a plot
of the score
2009 Apr 03
2
Schoenfeld Residuals
Dear All,
Sorry to bother you again.
I have a model:
coxfita=coxph(Surv(rem.Remtime/365,rem.Rcens)~all.sex,data=nearma)
and I'm trying to do a plot of Schoenfeld residuals using the code:
plot(cox.zph(coxfita))
abline(h=0,lty=3)
The error message I get is:
Error in plot.window(...) : need finite 'ylim' values
In addition: Warning messages:
1: In sqrt(x$var[i, i] * seval) : NaNs
2009 Jun 15
2
Schoenfeld Residuals with tied data
Dear all,
I am struggling with calculation of Schoenfeld residuals of my Cox Ph
models.
Based on the formula as attached, I calculated the Schoenfeld residuals for
both non tied and tied data, respectively.
And then I validated my results with R using the same data sets. However, I
found that my results for non-tied data was ok but the results for tied data
were different from R's.
How
2009 May 12
1
AFT-model with time-dependent covariates
Dear R-community,
Dear Prof. Therneau,
I would like to fit an AFT-model with time-dependent covariates and right-censored data.
Searching the mailing list for information on the subject, I found some old posts which said it didn't work back then.
My questions:
(1) Has this kind of fitting already been implemented in the survival library in R?
(2) If not: Are there any alternatives/
2010 Feb 18
2
Extract p-value from aftreg object
Dear all,
does anyone know how I can extract specific p-values for covariates
from an aftreg object? After fitting a model with aftreg I can find
all different variables by using str(), but there's no place where
p-values are kept. The odd thing is that print() displays them
correctly.
EXAMPLE:
> testdata
start stop censor groupvar var1 var2
1 0 1 0
2010 Jul 28
1
Time-dependent covariates in survreg function
Dear all,
I'm asking this question again as I didn't get a reply last time:
I'm doing a survival analysis with time-dependent covariates. Until now,
I have used a simple Cox model for this, specifically the coxph function
from the survival library. Now, I would like to try out an accelerated
failure time model with a parametric specification as implemented for
example in the survreg
2010 Feb 19
1
eha aftreg performance
G?ran, thanks for the update, I'm just about to install it!
Just wanted to drop you a short line about performance (as you once
requested):
aftreg takes ages on my windows machine to calculate a small set of
7 observations which are not even grouped together by "id". To be a
bit more precise, it takes 2:40 mins on my Intel T9300 Core2 Duo @
2.5 GHz. Bigger samples with about 700
2008 Nov 10
1
coxph diagnostics plot for shape of hazard function?
Hi,
I've been banging my head against the following problem for a while
and thought the fine people on r-help might be able to help. I'm
using the survival package.
I'm studying the survival rate of a population with a preexisting
linear-like event rate (there are theoretical reasons to believe
it's linear, but of course it's subject to the usual sampling noise)
Some of the
2009 Dec 10
1
PH Model assumption
Hi all,
I was trying to test the assumption of proportional hazards
assumption, I used the cox.zph function
>cox.zph(coxfit6)
Results are:
rho chisq p
x1 -0.0396 1.397 2.37e-01
x2 0.1107 9.715 1.83e-03
x3 -0.0885 7.743 5.39e-03
x4 0.0366 1.092 2.96e-01
x5 0.0242 0.455 5.00e-01
GLOBAL
2005 Aug 27
1
survival parametric question
Hi to all,
I am working on design package using survival function.
First using PSM and adopting a weibull specification for the baseline hazard , I have got the following results(since weibull has both PH and AFT propreties ,in addition I have used the PPHSm command):
Value Std. Error z p
(Intercept) 1.768 1.0007 1.77 7.73e-02
SIZE -0.707 0.0895 -7.90 2.80e-15
2010 Feb 11
4
Access variables by string
Dear all,
I have two probably very easy questions:
(1) Is there a way to access certain variables by their string-based
name representation?
Example:
numbers <- c("one", "two", "three")
varname <- "numbers"
print(varname[2])
(2) I need this functionality for a customized na.exclude() function
that I am building, which should only exclude rows
2010 Jul 01
1
Modelling survival with time-dependent covariates
Hi all,
I am looking at the tutorial/appendix from John Fox on ?Cox Proportional-Hazards Regression for Survival Data? available here:
http://cran.r-project.org/doc/contrib/Fox-Companion/appendix-cox-regression.pdf
I am particularly interested in modelling survival with time-dependent covariates (Section 4).
The data look like this:
> Rossi.2[1:50,]
start
stop arrest.time week arrest fin
2009 May 05
3
Cox Proportional Hazard with missing covariate data
Dear friends,
I have used R for some time now and have a tricky question about the coxph-function: To sum it up, I am not sure whether I can use coxph in conjunction with missing covariate data in a model with time-variant covariates. The point is: I know how "old" every piece that I oberserve is, but do not have fully historical information about the corresponding covariates. Maybe you
2010 Nov 16
1
Re : interpretation of coefficients in survreg AND obtaining the hazard function for an individual given a set of predictors
Thanks for sharing the questions and responses!
Is it possible to appreciate how much the coefficients matter in one
or the other model?
Say, using Biau's example, using coxph, as.factor(grade2 ==
"high")TRUE gives hazard ratio 1.27 (rounded).
As clinician I can grasp this HR as 27% relative increase. I can
relate with other published results.
With survreg the Weibull model gives a
2004 Apr 14
2
zph / squid syntaxis ?
Hi,
I''ve used old ZPH patch under squid 2.4 Stable4
and it works great !
Now I want to patch squid 2.4 stable 5,
with new patch, on http://www.it-academy.bg/zph/
I''ve patched and installed squid 2.5 stable 5
succefully, but I can''t get ZPH works.
I''m trying with
...
$TC class add dev $LANDEV parent 1: classid 1:7 htb rate 1Mbit
$TC filter add dev $LANDEV