Hi List,
A friend of mine recently asked the same question as Heinz T?chler. Since
I've already written the code I'd like to share with the list.
# x is an object returned by "survfit";
# "smed" returns a matrix of 5 columns of
# n, events, median, 0.95LCL, 0.95UCL.
# The matrix returned has rownames as the
# group labels (eg., treatment arms) if any.
smed <- function(x) {
ox <- capture.output(print(x))
n <- length(ox)
tmp <- t(sapply(ox[4:n],
function(l) strsplit(l, split=' +')[[1]]))
nres <- strsplit(ox[3],split=' +')[[1]][2:6]
res <- matrix(as.numeric(tmp[,2:6]), ncol=5,
dimnames=list(tmp[,1], nres))
res
}
# example:
library(survival)
fit1 <- survfit(Surv(time, status) ~ 1, data=aml)
sf1 <- smed(fit1)
sf1
fit <- survfit(Surv(time, status) ~ x, data=aml)
sf <- smed(fit)
sf
--
Xiaochun Li, Ph.D.
Research Scientist
Department of Biostatistics and Computational Biology
Dana Farber Cancer Institute
Harvard School of Public Health
M1B25
(617) 632 3602
Hello Xiaochun Li! Thank you for submitting the function. At the time I had that problem I solved it in a somewhat different way. I changed a few lines in the print.survfit method. I introduced a parameter "ret.res=FALSE" set to false to preserve the normal behaviour of print. The second last line "invisible(x)" I changed to: if (ret.res) invisible(list(x,x1)) else invisible(x) So print.survfit returned the results. Of course, Your method has the advantage to work as long as the output structure of print.survfit does not change. At the end I would prefer the original function to be changed and when I find the time I will submit a worked proposal to Thomas Lumley, the maintainer of the survival package. In that way it would be available also in future versions of survival. Greetings Heinz At 10:40 05.05.2006 -0400, you wrote:>Hi List, > >A friend of mine recently asked the same question as Heinz T?chler. Since >I've already written the code I'd like to share with the list. > ># x is an object returned by "survfit"; ># "smed" returns a matrix of 5 columns of ># n, events, median, 0.95LCL, 0.95UCL. ># The matrix returned has rownames as the ># group labels (eg., treatment arms) if any. > >smed <- function(x) { > ox <- capture.output(print(x)) > n <- length(ox) > tmp <- t(sapply(ox[4:n], > function(l) strsplit(l, split=' +')[[1]])) > nres <- strsplit(ox[3],split=' +')[[1]][2:6] > res <- matrix(as.numeric(tmp[,2:6]), ncol=5, > dimnames=list(tmp[,1], nres)) > res >} > > ># example: > >library(survival) > >fit1 <- survfit(Surv(time, status) ~ 1, data=aml) >sf1 <- smed(fit1) >sf1 > > >fit <- survfit(Surv(time, status) ~ x, data=aml) >sf <- smed(fit) >sf > >-- >Xiaochun Li, Ph.D. >Research Scientist >Department of Biostatistics and Computational Biology >Dana Farber Cancer Institute >Harvard School of Public Health > >M1B25 >(617) 632 3602 > >
On Sun, 7 May 2006, Heinz Tuechler wrote:> Hello Xiaochun Li! > > Thank you for submitting the function. At the time I had that problem I > solved it in a somewhat different way. > I changed a few lines in the print.survfit method. I introduced a parameter > "ret.res=FALSE" set to false to preserve the normal behaviour of print. > The second last line "invisible(x)" I changed to: > > if (ret.res) > invisible(list(x,x1)) > else > invisible(x) > > So print.survfit returned the results. Of course, Your method has the > advantage to work as long as the output structure of print.survfit does not > change. At the end I would prefer the original function to be changed and > when I find the time I will submit a worked proposal to Thomas Lumley, the > maintainer of the survival package. In that way it would be available also > in future versions of survival.But all print() methods are required to return their first argument unchanged, so foo print(foo) do the same thing. See ?print. -- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595