Displaying 20 results from an estimated 3000 matches similar to: "Changelog for the survival package"
2009 May 20
1
Where to find a changelog for the survival package
Dear All,
since some days I try to use the versions 2.35-4 of the survival
package instead of versions 2.31, I had installed until now. Several
changes in print.survfit, plot.survfit and seemingly in the structure
of ratetabels effect some of my syntax files.
Is there somewhere a documentation of these changes, besides the code itself?
Thanks in advance,
Heinz
2011 Apr 20
2
survexp with weights
Hello,
I probably have a syntax error in trying to generate an expected
survival curve from a weighted cox model, but I can't see it. I used
the help sample code to generate a weighted model, with the addition
of a "weights=albumin" argument (I only chose albumin because it had
no missing values, not because of any real relevance). Below are my
code with the resulting error
2010 Nov 11
3
Evaluation puzzle
The survexp function can fail when called from another function. The "why" of
this has me baffled, however.
Here is a simple test case, using a very stripped down version of survexp:
survexp.test <- function(formula, data,
weights, subset, na.action, rmap,
times, cohort=TRUE, conditional=FALSE,
ratetable=survexp.us, scale=1, npoints, se.fit,
2000 Apr 05
1
problem with survexp in survival5
survexp in survival5 doesn't seem to work for me. see below:
> library(survival5)
Attaching Package "package:survival5":
The following object(s) are masked from package:base :
sort.list
> library(chron)
> data(ratetables)
> survexp(~ratetable(year=julian(6,1,1991),
+ sex=1,age=35*365.24),times=(0:30)/6*365.24)
Error in as.character(as.date(c(min(R[, 3]),
2005 Dec 15
2
survexp ratetables for european contries?
Dear All,
Does someone have, or know of survexp ratetables for european contries,
especially Austria and Germany?
I know only about slopop in the package relsurv.
Thanks in advance
Heinz T??chler
2010 Dec 31
3
survexp - example produces error
Dear All,
reposting, because I did not find a solution, maybe someone could
check the example below.
It's taken from the help page of survdiff. Executing it, gives the error
"Error in floor(temp) : Non-numeric argument to mathematical function"
best regards,
Heinz
library(survival)
## Example from help page of survdiff
## Expected survival for heart transplant patients based
2011 May 26
5
Survival: pyears and ratetable: expected events
Dear all,
I am having a (really) hard time getting pyears to work together with a
ratetable to give me the number of expected events (deaths).
I have the following data:
dos, date of surgery, as.Date
dof, date of last follow-up, as.Date
dos, date of surgery, as.Date
sex, gender, as.factor (female,male)
ev, event(death), 0= censored at time point dof, 1=death at time point dof
Could someone
2009 Jan 19
1
further notes on model.frame issue
This is a follow-up on my note of Saturday. Let me start with two important
clarifications
- I think this would be a nice addition, but I've had exactly one use for it
in the 15+ years of developing the survival package.
- I have a work around for the current case.
Prioritize accordingly.
The ideal would be to change survexp as follows:
fit <- survexp( ~ gender,
2001 Nov 12
2
check() warnings for survival-2.6
I am not sure if this is the right place for that kind of questions, but
I wondered
that the recommended package survival did not pass R's check procedure
without
warnings:
1) unbalanced braces:
* Rd files with unbalanced braces:
* man/Surv.Rd
* man/cluster.Rd
* man/cox.zph.Rd
* man/coxph.Rd
* man/coxph.detail.Rd
* man/date.ddmmmyy.Rd
* man/lines.survfit.Rd
*
2009 May 22
1
survfit, summary, and survmean (was Changelog for survival package)
> Further I appreciate your new function survmean(). At the moment it
> seems to be intended as internal, and not documented in the help.
The computations done by print.survfit are now a part of the results returned by
summary.survfit. See 'table' in the output list of ?summary.survfit. Both
call an internal survmean() function to ensure that any future updates stay in
2012 Oct 06
2
Expected number of events, Andersen-Gill model fit via coxph in package survival
Hello,
I am interested in producing the expected number of events, in a
recurring events setting. I am using the Andersen-Gill model, as fit
by the function "coxph" in the package "survival."
I need to produce expected numbers of events for a cohort,
cumulatively, at several fixed times. My ultimate goal is: To fit an
AG model to a reference sample, then use that fitted model
2012 Apr 30
0
need help with avg.surv (Direct Adjusted Survival Curve), Message-ID:
Well, I would suggest using the code already in place in the survival
package. Here is my code for your problem.
I'm using a copy of the larynx data as found from the web resources for
the Klein and Moeschberger book.
larynx <- read.table("larynx.dat", skip=12,
col.names=c("stage", "time", "age", "year",
2012 Apr 29
0
need help with avg.surv (Direct Adjusted Survival Curve)
Hello R users,
I am trying to obtain a direct adjusted survival curve. I am sending my whole code (see below). It's basically the larynx cancer data with Stage 1-4. I am using the cox model using coxph option, see the fit3 coxph. When I use the avg.surv option on fit3, I get the following error: "fits<-avg.surv(fit3, var.name="stage.fac", var.values=c(1,2,3,4), data=larynx)
2014 Jul 05
1
Predictions from "coxph" or "cph" objects
Dear R users,
My apologies for the simple question, as I'm starting to learn the concepts
behind the Cox PH model. I was just experimenting with the survival and rms
packages for this.
I'm simply trying to obtain the expected survival time (as opposed to the
probability of survival at a given time t). I can't seem to find an option
from the "type" argument in the predict
1998 Nov 26
1
heap memory exhausted
Hi
I always have following error message when I try to read
a big ascii-file:
> inzp<-read.data()
> Error: heap memory (1953 Kb) exhausted [needed 0 Kb more]
read.data() is a small function that reads the ascii-file.
When I cut the ascii-file to a small one I don't have this
problem.
Can I extend this 'heap memory' for reading big data files? How?
I'm working with R on a
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
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!
2004 Sep 28
2
Validating a Cox model on an external set
Good morning,
Sorry to trouble the list.
I have a problem I hope to seek your advice on.
Essentially, I am trying to 'validate' a multivariate Cox proportional
hazards model built in a training set, by testing it on an external
test set. I have performed a survfit using the Cox model to predict
survival for the test set, and obtained individual predictions for
survival time, with
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)
2005 Sep 19
2
Problem with tick marks in lines.survfit (package survival)
I have attempted to follow posting guidelines but I have failed to find out
what I am doing wrong here.
I am trying to use lines.survfit to plot a second curve onto a survival
curve produced by plot.survfit. In my case this is to be a progression free
survival curve superimposed upon an overall survival curve, but I will
illustrate my problem using the example given in the help for