Displaying 20 results from an estimated 10000 matches similar to: "How to calculate the Deviance for test data based on Cox model"
2008 May 09
2
how to check linearity in Cox regression
Hi, I am just wondering if there is a test available for testing if a linear fit of an independent variable in a Cox regression is enough? Thanks for any suggestions.
John Zhang
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[[elided Yahoo spam]]
2011 Mar 10
1
ANOVA for stratified cox regression
This is a follow-up to a query that was posted regarding some problems that
emerge when running anova analyses for cox models, posted by Mathias Gondan:
Matthias Gondan wrote:
>* Dear List,*>**>* I have tried a stratified Cox Regression, it is working fine, except for*>* the "Anova"-Tests:*>**>* Here the commands (should work out of the box):*>**>*
2013 Apr 24
1
Trouble Computing Type III SS in a Cox Regression using drop1 and Anova
Hello All,
Am having some trouble computing Type III SS in a Cox Regression using either drop1 or Anova from the car package. Am hoping that people will take a look to see if they can tell what's going on.
Here is my R code:
cox3grp <- subset(survData,
Treatment %in% c("DC", "DA", "DO"),
c("PTNO", "Treatment", "PFS_CENSORED",
2008 Jan 15
1
Anova for stratified Cox regression
Dear List,
I have tried a stratified Cox Regression, it is working fine, except for
the "Anova"-Tests:
Here the commands (should work out of the box):
library(survival)
d = colon[colon$etype==2, ]
m = coxph(Surv(time, status) ~ strata(sex) + rx, data=d)
summary(m)
# Printout ok
anova(m, test='Chisq')
This is the output of the anova command:
> Analysis of Deviance Table
2012 Mar 29
1
how to calculate predicted probability of Cox model
Dear List,
Because Cox proportional hazards model didn't give the baseline hazard function, how to calculate the predictive probability for each test sample at a special time point,such as 5-year or 10-year ?
In survival package, predict.coxph() function gives three different type of predicted value, for the type of "expected", Does it mean the expected number of events for a
2011 Apr 15
3
GLM output for deviance and loglikelihood
It has always been my understanding that deviance for GLMs is defined
by;
D = -2(loglikelihood(model) - loglikelihood(saturated model))
and this can be calculated by (or at least usually is);
D = -2(loglikelihood(model))
As is done so in the code for 'polr' by Brian Ripley (in the package
'MASS') where the -loglikehood is minimised using optim;
res <-
2013 Apr 24
2
Trouble Computing Type III SS in a Cox Regression
I should hope that there is trouble, since "type III" is an undefined concept for a Cox
model. Since SAS Inc fostered the cult of type III they have recently added it as an
option for phreg, but I am not able to find any hints in the phreg documentation of what
exactly they are doing when you invoke it. If you can unearth this information, then I
will be happy to tell you whether
2004 Jul 26
5
covariate selection in cox model (counting process)
Hello everyone,
I am searching for a covariate selection procedure in a cox model formulated
as a counting process.
I use intervals, my formula looks like coxph(Surv(start,stop,status)~
x1+x2+...+cluster(id),robust=T) where id is a country code (I study
occurence of civil wars from 1962 to 1997).
I'd like something not based on p-values, since they have several flaws for
this purpose.
I turned
2007 Sep 18
3
Cox regression and p-values
Hello,
I might be barking up the wrong tree here, but I want to make sure I
have a full understanding of this. What I would like to know is what
tests are performed to give the p-values for each variable in the table
that is the result of coxph regression when the variables are
categorical only.
More specifically, when expected counts are less than 5 is the Fisher's
exact test used instead
2004 Jul 04
2
smooth non cumulative baseline hazard in Cox model
Hi everyone.
There's been several threads on baseline hazard in Cox model but I think
they were all on cumulative baseline hazard,
for instance
http://tolstoy.newcastle.edu.au/R/help/01a/0464.html
http://tolstoy.newcastle.edu.au/R/help/01a/0436.html
"basehaz" in package survival seems to do a cumulative hazard.
extract from the basehaz function:
sfit <- survfit(fit)
H
2017 Nov 01
3
Cox Regression : Spline Coefficient Interpretation?
Hi,
I'm using a Cox-Regression to estimate hazard rates on prepayments.
I'm using the "pspline" function to face non-linearity, but I have no clue
how to interpret the result.
Unfortunately I did not find enough information on the "pspline" function
wether in the survival package nor using google..
I got following output:
* library(survival)*
>
>
>
>
2008 Nov 21
1
Discrepancy in the regression coefficients for Cox regression - PBC data set
Hi,
When I run the following Cox proportional hazards model on the Mayo clinic's
PBC data set (given in the "survival" package), the regression coefficients
do not agree with the results presented in Table 4.6.3 (p. 195) of Fleming &
Harrington's book.
library(survival)
data(pbc)
ans.cox <- coxph(Surv(time, status) ~ log(bili) + log(alb) + age +
log(protime) +
2001 Mar 11
2
Doing a Cox-Regression in R and SPSS
A.S.: I am sorry for sending my first mail to <r-help at R-
project.org>.
---------------------------------------------------------
Hallo,
computing a Cox proportional hazards model in SPSS 9.0 and
R 1.2.2 produces different results for beta-coefficient.
I use the follwing data set (source: example in
help(coxph), somewhat modified)
Time Status Covariate (x)
2009 Nov 03
2
about the cox result
Hi all:
I finished cox analysis like this:
fit_cox<-coxph(Surv(dat$Time, dat$death) ~ dat$CD4 + strata(dat$gender),data=dat);
> fit_cox
Call:
coxph(formula = Surv(data_ori$Time, data_ori$death) ~ data_ori$drug +
strata(data_ori$gender), data = data_ori)
coef exp(coef) se(coef) z p
data_ori$drugddI 0.216 1.24 0.146 1.47 0.14
Likelihood ratio test=2.17 on
2011 Nov 20
1
Cox proportional hazards confidence intervals
I am calculating cox propotional hazards models with the coxph
function from the survival package. My data relates to failure of
various types of endovascular interventions. I can successfully
obtain the LR, Wald, and Score test p-values from the coxph.object, as
well as the hazard ratio as follows:
formula.obj = Surv(days, status) ~ type
coxph.model = coxph(formula.obj, df)
fit =
2011 Jul 22
3
Cox model approximaions (was "comparing SAS and R survival....)
For time scale that are truly discrete Cox proposed the "exact partial
likelihood". I call that the "exact" method and SAS calls it the
"discrete" method. What we compute is precisely the same, however they
use a clever algorithm which is faster. To make things even more
confusing, Prentice introduced an "exact marginal likelihood" which is
not
2010 Mar 09
1
Question on passing in parameter to Cox hazard
Hi,
I wanted to do the cox model using a matrix. The following lines illustrate what I want to do:
--------------------------------
dat <- matrix(rnorm(30), ncol=3,dimnames = list(1:10,letters[1:3]))
Survival <- rexp(10)
Status <- ifelse(runif(10) < .7, 1, 0)
mat <- as.data.frame(cbind(dat,Survival,Status))
cmod <- coxph(Surv(Survival, Status) ~ a+b+c, mat)
2001 Feb 22
3
[newbie] Cox Baseline Hazard
Hello everybody.
First of all, I would like to present myself.
I'm a french student in public health and I like statistics though I'm
not that good in mathematics (but I try to catch up). I've discovered R
recently while trying to find a statistical program in order to avoid
rebooting my computer under windows when I need to do some statistical
work.
And here is my first question.
2005 Nov 06
2
cox models
Hello,
i'm a french student of medical oncology and i'm working on breast
cancer. I have a variable with the histologic type of tumor wich is
between 1 and 5. I use as.factor function to make some variable with
level between 1 and 5. When i put it in the cox model i have only the
level between 2 and 5. The level 1 doesn't appear. I think i have to
change the number of level but i
2011 Dec 19
1
Calculating the probability of an event at time "t" from a Cox model fit
Dear R-users,
I would like to determine the probability of event at specific time using
cox model fit. On the development sample data I am able to get the
probability of a event at time point(t).
I need probability score of a event at specific time, using scoring scoring
dataset which will have only covariates and not the response variables.
Here is the sample code:
n = 1000
beta1 = 2; beta2 =