Displaying 20 results from an estimated 6000 matches similar to: "Help on coxph"
2009 Mar 05
1
new r user
When adding a trend line to a scatterplot (e.g. abline (90,4,col="red"), I
believe the "90" is the intercept and "4" is the slope. How do I determine
the intercept and slope for the abline command?
Kristopher R. Deininger
Management Strategy & Entrepreneurship
PhD Student 2012
Robert H. Smith School of Business
University of Maryland
3330L Van Munching Hall
2008 Jan 13
2
ERROR during HTTP install from a Centos mirror
Hi!
I'm trying to install centos 5.1 as a http installation from a centos
mirror.
i've done it before with Fedora, figured I could do it with Centos, too,
but every time I try it, it goes all the way thru Anaconda to the point
of entering the root password, then I get an error about not being
able to find the repodata.
I note that the section in the "upstream" manuals about
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 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 0.939 0.161
2006 Dec 29
2
Survfit with a coxph object
I am fitting a coxph model on a large dataset (approx 100,000 patients), and
then trying to estimate the survival curves for several new patients based
on the coxph object using survfit. When I run coxph I get the coxph object
back fairly quickly however when I try to run survfit it does not come
back. I am wondering if their is a more efficient way to get predicted
survival curves from a coxph
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
2006 Jan 17
2
help with parsing multiple coxph() results
Dear All:
I have a question on using coxph for multiple genes:
I have written code to loop through all 22283 genes in the Hgu-133A and
apply coxph on survival data.
However, I don't know how to work with the result for each gene:
survtest<-coxph(Surv(pcc.primary.stg.3.cox[,'fup_interval'],pcc.primary.stg.
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
2011 Mar 13
1
using pre-calculated coefficients and LP in coxph()?
I need to force a coxph() function in R to use a pre-calculated set of beta
coefficients of a gene signature consisting of xx genes and the gene
expression is also provided of those xx genes.
If I try to use "coxph()" function in R using just the gene expression data
alone, the beta coefficients and coxph$linear.predictors will change and I
need to use the pre-calcuated linear predictor
2004 Aug 06
2
multiple shout streams
I'm running multiple instances of ices. Also, I found what the problem
was with the constant stream. I was getting a default stream because I
was using my local ip address to run the server, and when I tried to
access the different streams from my outside ip address something got
confused. I'm running it from my outside ip address and everything works
fine. Does anyone know a what to run
2007 Nov 08
2
mapply, coxph, and model formula
Hello -
I am wanting to create some Cox PH models with coxph (in package
survival) using different datasets.
The code below illustrates my current approach and problem with
completing this.
### BEGIN R SAMPLE CODE ##############################
library(survival)
#Define a function to make test data
makeTestDF <- function(n) {
times <- sample(1:200, n, replace = TRUE)
event
2004 Mar 05
1
Application of step to coxph using method="exact" (PR#6646)
Full_Name: John E. Kolassa
Version: Version 1.8.1
OS: Solaris
Submission from: (NULL) (128.6.76.36)
Stepwise model selection for coxph appears to fail with method="exact".
The code
step(coxph(Surv(1:100,rep(1,100))~factor(rep(1:4,25)),method="exact"))
produces the error message
Start: AIC= 733.07
Surv(1:100, rep(1, 100)) ~ factor(rep(1:4, 25))
Error in
2008 Jun 16
1
回复: cch() and coxph() for case-cohort
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 lower
and upper CI and P-value are a little different. Can we
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(formula =
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-loop is completed but have no idea which model
2004 May 16
2
Error in using coxph()
Hi,
I am getting errors of the following kind. I can't
seem to point the source of the error. I would greatly
appreciate any advice.
Many thanks and good day,
-Melinda
Error message :
----------------
"Ran out of iterations and did not converge in:
fitter(X, Y, strats, offset, init, control, weights =
weights,..."
Details :
---------
E is a vector of survival times (or censored
2012 Jul 26
2
coxph weirdness
Hi all,
I cant' wrap my head around an error from the coxph function (package
survival). Here's an example:
library(survival)
n = 100;
set.seed(1);
time = rexp(n);
event = sample(c(0,1), n, replace = TRUE)
covar = data.frame(z = rnorm(n));
model = coxph(Surv(time, event)~ . , data = covar)
R gives the following error:
> model = coxph(Surv(time, event)~ . , data = covar)
Error in
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 with this? is there
anyway to get the
2012 Feb 08
2
need help with understanding coxph encoding
Hi, in coxph,
coxph(Surv(time, status)~x,data=alm).
How to encode x? For example, if x has two groups, the treatment group and
control group. if I encode them as 1 and 2. Is the HR results
treatment/control? What if I encode them as 0 and 1. I am confused with how
survival package works for HR. What should I do to get a treatment/control
HR?
Thank you.
--
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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, status) ~ rx +