opt.longPC <-
function (betas) {
eta.yx <- as.vector(X %*% betas)
if (parameterization %in% c("value", "both")) {
Y <- as.vector(Xtime %*% betas) + Ztime.b
Ys <- as.vector(Xs %*% betas) + Zsb
eta.t <- eta.tw + c(WintF.vl %*% alpha) * Y
eta.s <- c(Ws.intF.vl %*% alpha) * Ys
}
if (parameterization %in% c("slope", "both")) {
Y.deriv <- as.vector(Xtime.deriv %*% betas[indFixed]) + Ztime.b.deriv
Ys.deriv <- as.vector(Xs.deriv %*% betas[indFixed]) + Zsb.deriv
eta.t <- if (parameterization == "both")
eta.t + c(WintF.sl %*% Dalpha) * Y.deriv
else
eta.tw + c(WintF.sl %*% Dalpha) * Y.deriv
eta.s <- if (parameterization == "both")
eta.s + c(Ws.intF.sl %*% Dalpha) * Ys.deriv
else
c(Ws.intF.sl %*% Dalpha) * Ys.deriv
}
mu.y <- eta.yx + Ztb
logNorm <- dnorm(y, mu.y, sigma, TRUE)
log.p.yb <- rowsum(logNorm, id)
log.hazard <- log(xi[ind.D]) + eta.t
log.survival <- - exp(eta.tw) * rowsum(xi[ind.K] * wkP * exp(eta.s), id.GK, reorder = FALSE)
dimnames(log.survival) <- NULL
log.p.tb <- d * log.hazard + log.survival
p.bytn <- p.byt * (log.p.yb + log.p.tb)
-sum(p.bytn %*% wGH, na.rm = TRUE)
}
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