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# $Id: frailty.gammacon.S 11166 2008-11-24 22:10:34Z therneau $
# Correct the loglik for a gamma frailty
# Term2 is the hard one, discussed in section 3.5 of the report
# The penalty function only adds \vu \sum(w_j) to the CoxPL, so this
# does a bit more than equation 15.
#
frailty.gammacon <- function(d, nu) {
maxd <- max(d)
if (nu > 1e7*maxd) term1 <- sum(d*d)/nu #second order Taylor series
else term1 <- sum(d + nu*log(nu/(nu+d))) #easy part
tbl <- table(factor(d[d>0], levels=1:maxd))
ctbl<- rev(cumsum(rev(tbl)))
dlev<- 1:maxd
term2.numerator <- nu + rep(dlev-1, ctbl)
term2.denom <- nu + rep(dlev, tbl*dlev)
term2 <- sum(log(term2.numerator/term2.denom))
term1 + term2
}
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