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question about val.surv in R
2 messages · zhu yao, Frank E Harrell Jr
Please specify the package(s) you are using. In this case it should be rms. val.surv is mainly for an out-of-sample validation, as it does not penalize for overfitting. calibrate.cph is probably what you should be using. To use val.surv in the fashion you are trying to use it, specify y=TRUE, surv=TRUE to cph and specify the time point you are validating with the u argument to val.surv (e.g., u=1 for 1 year survival probability validation). Frank
yz wrote:
Dear R users:
I tried to use val.surv to give an internal validation of survival
prediction model.
I used the sample sources.
# Generate failure times from an exponential distribution
set.seed(123) # so can reproduce results
n <- 1000
age <- 50 + 12*rnorm(n)
sex <- factor(sample(c('Male','Female'), n, rep=TRUE, prob=c(.6, .4)))
cens <- 15*runif(n)
h <- .02*exp(.04*(age-50)+.8*(sex=='Female'))
t <- -log(runif(n))/h
units(t) <- 'Year'
label(t) <- 'Time to Event'
ev <- ifelse(t <= cens, 1, 0)
t <- pmin(t, cens)
S <- Surv(t, ev)
# I use cph instead of psm in the example
f <- cph(S ~ age + sex, y=TRUE)
w <- val.surv(f)
I got an error:
Error in survreg.distributions[[fit$dist]] :
attempt to select less than one element
Could some one explain for me?
Error in survreg.distributions[[fit$dist]] :
attempt to select less than one element
Error in survreg.distributions[[fit$dist]] :
attempt to select less than one element
*Yao Zhu*
*Department of Urology
Fudan University Shanghai Cancer Center
Shanghai, China*
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----- Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/question-about-val-surv-in-R-tp3506666p3507015.html Sent from the R help mailing list archive at Nabble.com.