Displaying 20 results from an estimated 1000 matches similar to: "simple save question"
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
2011 Oct 20
3
Survival analysis
Hello,
I need some results from the survival analysis of my data
that I do not know whether exist in Survival Package or how to obtain if
they do:
1. The Mean survival time
2. The standard error of the mean
3. Point and 95% Lower & Upper Confidence Intervals estimates
Any help will be greatly appreciated.
Cem
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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
2013 Apr 29
1
R help - bootstrap with survival analysis
Hi,
I'm not sure if this is the proper way to ask questions, sorry if not. But
here's my problem:
I'm trying to do a bootstrap estimate of the mean for some survival data.
Is there a way to specifically call upon the rmean value, in order to store
it in an object? I've used print(...,print.rmean=T) to print the summary of
survfit, but I'm not sure how to access only rmean
2012 Oct 11
2
Question on survival
Hi,
I'm going crazy trying to plot a quite simple graph.
i need to plot estimated hazard rate from a cox model.
supposing the model i like this:
coxPhMod=coxph(Surv(TIME, EV) ~ AGE+A+B+strata(C) data=data)
with 4 level for C.
how can i obtain a graph with 4 estimated (better smoothed) hazard curve
(base-line hazard + 3 proportional) to highlight the effect of C.
thanks!!
laudan
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2012 May 16
1
survival survfit with newdata
Dear all,
I am confused with the behaviour of survfit with newdata option.
I am using the latest version R-2-15-0. In the simple example below I am building a coxph model on 90 patients and trying to predict 10 patients. Unfortunately the survival curve at the end is for 90 patients. Could somebody please from the survival package confirm that this behaviour is as expected or not - because I
2005 Feb 04
2
no. at risk in survfit()
Hi,
when I generated a survfit() object, I can get number
of patients at risk at various time points by using
summary():
fit<-survfit(Surv(time,status)~class,data=mtdata)
summary(fit)
class=1
time n.risk n.event survival std.err lower 95% CI
upper 95% CI
9.9 78 1 0.987 0.0127 0.963 1
41.5 77 1 0.974 0.0179 0.940 1
54.0 76
2009 Dec 22
1
Slow survfit -- is there a faster alternative?
Using R 2.10 on Windows:
I have a filtered database of 650k event observations in a data frame
with 20+ variables.
I'd like to be able to quickly generate estimate and plot survival
curves. However the survfit and cph() functions are extremely slow.
As an example: I tried
results.cox<-coxph(Surv(duration, success) ~ start_time + factor1+
factor2+ variable3, data=filteredData) #(took a
2009 Mar 05
1
RV: help
Dear Sirs,
I want to estimate the survival mean of a few specific teams. I'm trying to
calculate it through a Kaplan Meier estimator. For doing so, I load the
"survival" package and run the following instructions:
"options(survfit.print.mean=TRUE)" allows showing the mean and mean
standard error
"KM=survfit(Surv(Dias,Censura))"
2004 Oct 05
1
save print survfit object to data frame
Hello, I have estimated a survival model with six strata:
>model.b <-
survfit(Surv(time=start.tijd,time2=eind.tijd2,event=va)~strata(product.code)
,
data=wu.wide)
I would like to save the output of
>print(model.b,print.n="records",show.rmean=FALSE)
in a dataframe so that I can export it later. How do I do this? Note that
summary(model.b) gives an error:
Error in
2010 Oct 27
2
coxph linear.predictors
I would like to be able to construct hazard rates (or unconditional death prob) for many subjects from a given survfit.
This will involve adjusting the ( n.event/n.risk)
with (coxph object )$linear.predictors
I must be having another silly day as I cannot reproduce the linear predictor:
fit <- coxph(Surv(futime, fustat) ~ age, data = ovarian)
fit$linear.predictors[1]
[1] 2.612756
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
2005 Feb 04
5
How to access results of survival analysis
Hello,
it seems that the main results of survival analysis with package survival
are shown only as side effects of the print method.
If I compute e.g. a Kaplan-Meier estimate by
> km.survdur<-survfit(s.survdur)
then I can simply print the results by
> km.survdur
Call: survfit(formula = s.survdur)
n events median 0.95LCL 0.95UCL
100.0 58.0 46.8 41.0 79.3
Is
2011 Mar 18
1
median survival time from survfit
Hello,
I am trying to compute the mdeian of the survival time from the function
survfit:
> fit <- survfit(Surv(time, status) ~ 1)
> fit
Call: survfit(formula = Surv(time, status) ~ 1)
records n.max n.start events median 0.95LCL 0.95UCL
111 111 111 20 NA NA NA
The results is NA? the fit$surv gives values between 1 and 0.749! Am I doing
this correct?
2004 Apr 25
2
nonparametric multiple sample comparison
Hello all,
Here goes one of my first functions.
I want to make a nonparametric multiple sample comparison with unequal sample
sizes (see Zar?s Biostatistical Analysis, 3rd. Ed., pg. 201 Example 10.11, pg.
288 Example 11.10). In the real world, I want to compare samples of fish
length captured with different fishing gears.
After using the Kruskal-Wallis test I want to check the differences
2009 Mar 30
1
Possible bug in summary.survfit - 'scale' argument ignored?
Hi all,
Using:
R version 2.8.1 Patched (2009-03-07 r48068)
on OSX (10.5.6) with survival version:
Version: 2.35-3
Date: 2009-02-10
I get the following using the first example in ?summary.survfit:
> summary( survfit( Surv(futime, fustat)~1, data=ovarian))
Call: survfit(formula = Surv(futime, fustat) ~ 1, data = ovarian)
time n.risk n.event survival
2011 Oct 17
3
Extracting results from a function output
Hello,
I am having hard time obtaining a value from a function. "fit" is a survival
function that produces some results, such as "median", "confidence
intervals" etc. But str() function does not list these values. How can I
extract these to be able use them? For example, I need "median" value for
the group DrugA which is 48. "Print" function does
2013 Apr 15
2
Convert results from print(survfit(formula, ...)) into a matrix or data frame
Hello All,
Below is some sample survival analysis code. I'd like to able to get the results from print(gehan.surv) into a matrix or data frame, so I can manipulate them and then create a table using odfWeave. Trouble is, I'm not quite sure how make such a conversion using the results from a print method.
Is there some simple way of doing this?
Thanks,
Paul
require(survival)
2009 Jan 25
1
[LLVMdev] gfortran benchmarks
Since the fact that gfortran performance has improved
over the major releases, I decided to benchmark the current
releases on a MacPro with the Polyhedron 2005 benchmarks
using -ffast-math -funroll-loops -msse3 -O3. The results
are...
gcc release
gcc 4.2.4 gcc 4.3.3 gcc 4.4-pre gcc 4.3.3/ gcc 4.4-pre/
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