Displaying 20 results from an estimated 5000 matches similar to: "cox.zph"
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
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
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
2007 Sep 27
1
ReL plot(cox.zph())
You report an error message:
> plot(zph.revasFit[1])
Error in plot.window(xlim, ylim, log, asp, ...) :
need finite 'ylim' values
I have never seen this error before, and I cannot guess what causes it. You
need to provide more information, and likely a small data set that produces
the problem. Perhaps you have an x variable that is a constant?
Terry Therneau
2006 May 17
1
question about survSplit
Dear R-users,
I use the survsplit function in the survival package to change my data into
counting-process format
and the transformed format is as follow:
(a)
start stop event DP age ....
0 5 0 1 20
5 10 0 1 20
10 25 1 1 20
looking at the above three entries that belong to the same person, if an
event happen at
2006 Nov 14
0
R-Help : Warning messages using plot(cox.zph)
Hi,
I get a warning message when I plot cox.zph objects with the transform km and
rank, but not with id and log with the same data set.
Here's the command:
example is a coxph object
rk <- cox.zph(example, transform='rank')
rk
plot(rk)
and here's the warning message:
Warning messages:
1: suppression des ex-aequos de 'x' in: approx(xx, xtime, seq(min(xx),
max(xx),
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
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
2007 Jan 25
0
cox.zph vs log-log survival plot
Hello,
Excuse me for a more methodological than technical question. I'm developing a Cox model with 10 covariates. One of them is age (named "eta"). I've checked proportionality with cox.zph with age continuous:
> cox.zph(coxph(Surv(TTP,CENSOTTP)~eta))
rho chisq p
eta -0.0154 0.0225 0.88
and categorical (eta<60):
>
2006 Sep 30
1
Gradient problem in nlm
Hello everyone!
I am having some trouble supplying the gradient function to nlm in R for
windows version 2.2.1.
What follows are the R-code I use:
fredcs39<-function(a1,b1,b2,x){return(a1+exp(b1+b2*x))}
loglikcs39<-function(theta,len){
value<-sum(mcs39[1:len]*fredcs39(theta[1],theta[2],theta[3],c(8:(7+len))) -
pcs39[1:len] * log(fredcs39(theta[1],theta[2],theta[3],c(8:(7+len)))))
2006 Dec 21
1
zph patch website broken ?
Hi,
I used to patch my squid with ZPH patch on
http://www.it-academy.bg/zph/
> The idea behind this patch is to allow classification
> of packets generated from the squid cache engine towards
> clients.
> The classification is based on whether the content is
> being served from cache (a cache HIT), or
> is being retrieved from a remote server (a cache MISS).
Very useful
2010 May 21
1
Time dependent Cox model
> ... interactions between covariables and time.
A model such as "coxph(Surv(ptime, pstat) ~ age + age*ptime, ...."
is invalid -- it is not at all what you think. If cph flags this as an
error that is a good thing: I should probably add the same message to
coxph.
> Is is somewhat sensible to use cox.zph() to investigate which
variables need time interaction...
The cox.zph
2012 Feb 20
1
Reporting Kaplan-Meier / Cox-Proportional Hazard Standard Error, km.coxph.plot, survfit.object
What is the best way to report the standard error when publishing
Kaplan-Meier plots? In my field (Vascular Surgery), practitioners
loosely refer to the "10% error" cutoff as the point at which to stop
drawing the KM curve. I am interpreting this as the *standard error
of the cumulative hazard*, although I'm having a difficult time
finding some guidelines about this (perhaps I am
2004 Jun 28
0
fairnat with squid + Squid with ZPH
Hi,
I''m trying to share internet on a LAN
I''ve a linux router with SQUID (with ZPH support) + FAIRNAT
The idea is:
- fairness sharing internet
- priorize interactive traffic
- if a web object is on squid-cache (HIT), user
can download it, with a rate = LAN rate
I''ve:
- Last Fairnat Script: www.metamorpher.de/fairnat/
- SQUID 2.5STABLE5 with ZPH patch
2005 Jan 26
0
Changing axis labels in plots of zph objects (survival analysis)
Hi,
I am using the Survival package, more precisely the cox.zph function, to plot log(Hazard rate) over time.
if I type
plot(temp.zph[2])
then I get the plot I want. However, I want to change the label of the y axis that cox.zph prints.
plot(temp.zph[2],xlab='Days', ylab='log hazard for Fast recovery cluster')
then I get
Error in plot.default(range(xx), yr, type =
2005 Nov 23
1
survdiff for Left-truncated and right-censored data
dear all,
I would like to know whether survdiff and survReg function in the
survival package work for left-truncated and right-censored data.
If not, what other functions can i use to make comparison between two
survival curves with LTRC data.
thanks for any help given
sing yee
2004 Nov 10
1
worked in R, but not in S-Plus
Hi,
I wrote a function that worked well in R, but not in
S-Plus, can anyone suggest a solution?
> f.coxph.zph<-function(x)
{
cox.fit <- coxph(Surv(time.cox, status.cox) ~ x,
na.action = na.exclude, method = "breslow")
fit.zph<-cox.zph(cox.fit,transform='log')
fit.zph$table[,3]
}
yyy is my data frame that contains survial time,
censor status and predictor
2006 Sep 26
1
warning message in nlm
Dear R-users,
I am trying to find the MLEs for a loglikelihood function (loglikcs39) and
tried using both optim and nlm.
fredcs39<-function(b1,b2,x){return(exp(b1+b2*x))}
loglikcs39<-function(theta,len){
sum(mcs39[1:len]*fredcs39(theta[1],theta[2],c(8:(7+len))) - pcs39[1:len] *
log(fredcs39(theta[1],theta[2],c(8:(7+len)))))
}
theta.start<-c(0.1,0.1)
1. The output from using optim is
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
2008 Dec 28
1
cox regression warning/error messages
Hello,
I am hoping for some advice regarding warning/error messages I
received when running a Cox regression
# message 1 - obtained while creating a plot of residuals
> plot (NV.zph, main = "groupNUSM - UNFIT", var= 'groupNUSM')
Warning messages:
1: In approx(xx, xtime, seq(min(xx), max(xx), length.out = 17)[2 * :
collapsing to unique 'x' values
2: In