Nothing
free.loglikelihood <-
function(para, X, Y.col, Y.c, ziMatrix)
{
#library(base)
p <- dim(X)[2]
n <- length(Y.col)
q <- dim(ziMatrix)[2]
B.col <- para[1:p]
B.current <- matrix(B.col, p, 1)
p.current <- exp(X %*% B.current) / (1 + exp(X %*% B.current))
psi <- para[p + 1]
phi <- exp(psi) / (1 + exp(psi))
s1 <- as.vector(p.current * (1 - phi) / phi)
s2 <- as.vector((1 - phi) / phi * (1 - p.current))
eta.col <- para[(p+2):(p+q+1)]
eta.current <- matrix(eta.col, q, 1)
patzero.current <- exp(ziMatrix %*% eta.current) /
(1 + exp(ziMatrix %*% eta.current))
loglike <- rep(0, n)
zeroInd <- Y.col == 0
loglike[zeroInd] <- log(patzero.current[zeroInd] +
(1 - patzero.current[zeroInd]) *
beta(s1[zeroInd], Y.c[zeroInd] + s2[zeroInd]) /
beta(s1[zeroInd], s2[zeroInd]))
loglike[!zeroInd] <- log(1 - patzero.current[!zeroInd]) +
lchoose(Y.c[!zeroInd], Y.col[!zeroInd]) +
lbeta(Y.col[!zeroInd] + s1[!zeroInd],
Y.c[!zeroInd] - Y.col[!zeroInd] + s2[!zeroInd]) -
lbeta(s1[!zeroInd], s2[!zeroInd])
#loglike <- (1 - z) *
# (lchoose(Y.c, Y.col) + lbeta(Y.col + s1, Y.c - Y.col + s2) - lbeta(s1, s2))
return(-sum(loglike))
}
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