Displaying 20 results from an estimated 3000 matches similar to: "How to compute hazard function using coxph.object"
2012 May 02
1
coxph reference hazard rate
Hi,
In the following results I interpret exp(coef) as the factor that multiplies
the base hazard rate if the corresponding variable is TRUE. For example,
when the bucket is ks008 and fidelity <= 3, then the rate, compared to the
base rate h_0(t), is h(t) = 0.200 h_0(t). My question is then, to what case
does the base hazard rate correspond to? I would expect the reference to be
the first
2011 Oct 06
1
non-cumulative hazard in Cox model with time-dependent covariates
Dear all,
Is there a way to calculate the non-cumulative hazard (instantaneous
hazard), which is the product of baseline hazard and exp{beta*covariate} ?
I knew in survfit, we can get the estimator of cumulative baseline hazard,
but how can we get the non-cumulative one?
Thank you very much!
Koshihaku
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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),
2004 Sep 22
1
Cox proportional hazards model
Good afternoon,
I am currently trying to do some work on survival analysis.
- I hope to seek your advice re: 2 questions (1 general and 1 specific)
(1) I'm trying to do a stratified Cox analysis and subsequently
plot(survfit(object)). It seems to work for some strata, but not for
others.
I have tumor grade, which is a range of 1 - 4.
When I divide this range of 1:4 into 2 groups, it
2010 May 25
2
Relative Risk/Hazard Ratio plots for continuous variables
Dear all,
I am using Windows and R 2.9.2 for my analyses. I have a large dataset and
I am particularly interested in looking at time to an event for a continuous
variable. I would like to produce a plot of log(relative risk) or relative
risk (also known as hazard ratio) against the continuous variable.
I have spent a long time looking for advice on how to do this but my search
has proved
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
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 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
2006 Oct 25
1
Incorrect 'n' returned by survfit()
I've a data set with 60000 rows of data representing 6000+ distinct loans. I did a coxph() regression on it (see call below), but a subsequent survfit() call on the coxph object is almost certainly wrong. It gives n=6 when it should be
more like 6000+ (I think)
> survfit(resultag)
Call: survfit.coxph(object = resultag)
n events median 0.95LCL 0.95UCL
6 489 Inf
2011 Oct 01
4
Is the output of survfit.coxph survival or baseline survival?
Dear all,
I am confused with the output of survfit.coxph.
Someone said that the survival given by summary(survfit.coxph) is the
baseline survival S_0, but some said that is the survival S=S_0^exp{beta*x}.
Which one is correct?
By the way, if I use "newdata=" in the survfit, does that mean the survival
is estimated by the value of covariates in the new data frame?
Thank you very much!
2012 Nov 17
4
survfit & number of variables != number of variable names
This works ok:
> cox = coxph(surv ~ bucket*(today + accor + both) + activity, data = data)
> fit = survfit(cox, newdata=data[1:100,])
but using strata leads to problems:
> cox.s = coxph(surv ~ bucket*(today + accor + both) + strata(activity),
> data = data)
> fit.s = survfit(cox.s, newdata=data[1:100,])
Error in model.frame.default(data = data[1:100, ], formula = ~bucket + :
2009 Feb 25
3
survival::survfit,plot.survfit
I am confused when trying the function survfit.
my question is: what does the survival curve given by plot.survfit mean?
is it the survival curve with different covariates at different points?
or just the baseline survival curve?
for example, I run the following code and get the survival curve
####
library(survival)
fit<-coxph(Surv(futime,fustat)~resid.ds+rx+ecog.ps,data=ovarian)
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
2013 Mar 04
2
survfit plot question
Hello,
I create a plot from a coxph object called fit.ads4:
plot(survfit(fit.ads4))
plot is located at:
https://www.dropbox.com/s/9jswrzid7mp1u62/survfit%20plot.png
I also create the following survfit statistics:
> print(survfit(fit.ads4),print.rmean=T)
Call: survfit(formula = fit.ads4)
records n.max n.start events *rmean *se(rmean)
median 0.95LCL 0.95UCL
203.0
2012 Nov 26
1
Plotting an adjusted survival curve
First a statistical issue: The survfit routine will produce predicted survival curves for
any requested combination of the covariates in the original model. This is not the same
thing as an "adjusted" survival curve. Confusion on this is prevalent, however. True
adjustment requires a population average over the confounding factors and is closely
related to the standardized
2013 Jan 31
1
obtainl survival curves for single strata
Dear useRs,
What is the syntax to obtain survival curves for single strata on many subjects?
I have a model based on Surv(time,response) object, so there is a single row per subject and no start,stop and no switching of strata.
The newdata has many subjects and each subject has a strata and the survival based on the subject risk and the subject strata is needed.
If I do
newpred <-
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
2010 Aug 31
1
Speeding up prediction of survival estimates when using `survifit'
Hi,
I fit a Cox PH model to estimate the cause-specific hazards (in a competing risks setting). Then , I compute the survival estimates for all the individuals in my data set using the `survfit' function. I am currently playing with a data set that has about 6000 observations and 12 covariates. I am finding that the survfit function is very slow.
Here is a simple simulation example
2012 Nov 27
4
Fitting and plotting a coxph with survfit, package(surv)
Hi Dear R-users
I have a database with 18000 observations and 20 variables. I am running
cox regression on five variables and trying to use survfit to plot the
survival based on a specific variable without success.
Lets say I have the following coxph:
>library(survival)
>fit <- coxph(Surv(futime, fustat) ~ age + rx, data = ovarian)
>fit
what I am trying to do is plot a survival
2012 Nov 26
1
Plotting an adjusted kaplan-meier curve
Dear R-users
I am trying to make an adjusted Kaplan-Meier curve (using the Survival package) but I am having difficulty with
plotting it so that the plot only shows the curves for the adjusted results.
My data come from a randomised controlled trial, and I would like the adjusted Kaplan-Meier
curve to only show two curves for the adjusted survival: one for those on treatment (Treatment==1)