It's not entirely clear from the help pages, but reading Thereau and
Gramsch' "Modeling Survival Data" it appears to me that the basehaz
function in the survival package returns the estimated baseline
_cumulative_ hazard function H(t|mean covariates). Such a function
will be monotonic upward. Search on "Nelson-Aalen estimator" for more
detail on cumulative hazard functions. The literature on survival
analysis seems ambiguous in that sometimes the cumulative hazard
function is meant, and sometimes the instantaneous hazard function.
Clarify with your statistician what is needed. I found that a plot
which reversed the default plotting arrangement of the basehaz object
was more helpful.
with(basehaz.fit, plot(time, hazard, ylab = "Cumulative Hazard |
Mean covariates") )
--
David Winsemius
On Mar 14, 2009, at 4:14 AM, Bob Green wrote:
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 use R) asked
me to obtain the hazard function values. I am wanting to confirm
whether basehaz is the correct command to obtain such values, to
better understand what is occurring in the log plots.
Below is the code that I have been using. Any assistance is
appreciated,
regards
Bob
library(survival)
recidivismv <- read.csv("g://Chapsurv_v.csv",header=T)
cox.V <- coxph(Surv(intDaysUntilFVPO, Event_v) ~ intAgeAtMHCIndex +
PRE + group + MHC + strGender, data = recidivismv)
summary (cox.V)
# produces a log-log plot
mvfit <- survfit (Surv(recidivismv$intDaysUntilFVPO, recidivismv
$Event_v) ~ MHC, data = recidivismv)
neg.ll <- function(mvfit) -log(-log(mvfit))
library (Design)
survplot(mvfit, fun = neg.ll, conf = "none", logt=TRUE)
# hazard values
mhc2 <- coxph (Surv(recidivismv$intDaysUntilFVPO, recidivismv
$Event_v) ~ MHC, data = recidivismv)
basehaz(mhc2)
______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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David Winsemius, MD
Heritage Laboratories
West Hartford, CT
______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
