Nothing
log.posterior.b <- function (b, y, Mats, ii) {
id.i <- id %in% ii
idT.i <- idT %in% ii
ids.i <- ids %in% ii
X.i <- X[id.i, , drop = FALSE]
Z.i <- Z[id.i, , drop = FALSE]
mu.y <- as.vector(X.i %*% betas.new + Z.i %*% b)
logY <- densLong(y[id.i], mu.y, sigma.new, log = TRUE, data = newdata[id.i, ])
log.p.yb <- sum(logY)
log.p.b <- densRE(b, mu = rep(0, ncol(Z.i)), D = D.new, log = TRUE, prop = FALSE)
MM <- Mats[[ii]]
st <- MM$st
st2 <- MM$st2
wk <- MM$wk
wk2 <- MM$wk2
P <- MM$P
P2 <- MM$P2
W2s <- MM$W2s
Xs <- MM$Xs
Zs <- MM$Zs
Xs.extra <- MM$Xs.extra
Zs.extra <- MM$Zs.extra
Xu <- MM$Xu
Zu <- MM$Zu
ind <- MM$ind
idT <- MM$idT
id.GK2 <- MM$id.GK2
if (param %in% c("td-value", "td-both"))
Ys <- transFun.value(c(Xs %*% betas.new + Zs %*% b), data.s[ids.i, ])
if (param %in% c("td-extra", "td-both"))
Ys.extra <- transFun.extra(c(Xs.extra %*% betas.new[indFixed] +
Zs.extra %*% b[indRandom]), data.s[ids.i, ])
if (estimateWeightFun) {
wFun <- wk2 * weightFun(st2, shapes.new, max.time)
Yu <- transFun.value(P2 * fastSumID(wFun * c(Xu %*% betas.new + Zu %*% b), id.GK2),
data.s[ids.i, ])
}
tt <- if (!estimateWeightFun) {
c(switch(param,
"td-value" = as.matrix(Ys) %*% alphas.new,
"td-extra" = as.matrix(Ys.extra) %*% Dalphas.new,
"td-both" = as.matrix(Ys) %*% alphas.new +
as.matrix(Ys.extra) %*% Dalphas.new,
"shared-betasRE" = rep(sum((betas[indBetas] + b) * alphas.new), length(st)),
"shared-RE" = rep(sum(b * alphas.new), length(st))))
} else {
c(as.matrix(Yu) %*% alphas.new)
}
eta.tw <- if (!is.null(W)) {
as.vector(W[ii, , drop = FALSE] %*% gammas.new)
} else 0
Vi <- exp(c(W2s %*% Bs.gammas.new) + tt)
log.survival <- - sum(exp(eta.tw) * P * fastSumID(wk * Vi, idT))
if (all(st == 0))
log.survival <- 1
log.p.yb + log.survival + log.p.b
}
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