prederrJM.jointModel <-
function (object, newdata, Tstart, Thoriz, lossFun = c("absolute", "square"),
interval = FALSE, idVar = "id", simulate = FALSE, M = 100, ...) {
if (!inherits(object, "jointModel"))
stop("Use only with 'jointModel' objects.\n")
if (!is.data.frame(newdata) || nrow(newdata) == 0)
stop("'newdata' must be a data.frame with more than one rows.\n")
if (is.null(newdata[[idVar]]))
stop("'idVar' not in 'newdata.\n'")
lossFun <- if (is.function(lossFun)) {
lf <- lossFun
match.fun(lossFun)
} else {
lf <- match.arg(lossFun)
if (lf == "absolute") function (x) abs(x) else function (x) x*x
}
id <- newdata[[idVar]]
id <- match(id, unique(id))
TermsT <- object$termsT
SurvT <- model.response(model.frame(TermsT, newdata))
Time <- SurvT[, 1]
timeVar <- object$timeVar
newdata2 <- newdata[Time > Tstart, ]
SurvT <- model.response(model.frame(TermsT, newdata2))
Time <- SurvT[, 1]
delta <- SurvT[, 2]
aliveThoriz <- newdata2[Time > Thoriz & newdata2[[timeVar]] <= Tstart, ]
deadThoriz <- newdata2[Time <= Thoriz & delta == 1 & newdata2[[timeVar]] <= Tstart, ]
indCens <- Time < Thoriz & delta == 0 & newdata2[[timeVar]] <= Tstart
censThoriz <- newdata2[indCens, ]
nr <- length(unique(newdata2[[idVar]]))
idalive <- unique(aliveThoriz[[idVar]])
iddead <- unique(deadThoriz[[idVar]])
idcens <- unique(censThoriz[[idVar]])
Surv.aliveThoriz <- survfitJM(object, newdata = aliveThoriz, idVar = idVar, simulate = simulate, M = M,
survTimes = Thoriz, last.time = rep(Tstart, length(idalive)))
Surv.deadThoriz <- survfitJM(object, newdata = deadThoriz, idVar = idVar, simulate = simulate,
survTimes = Thoriz, last.time = rep(Tstart, length(iddead)))
Surv.aliveThoriz <- sapply(Surv.aliveThoriz$summaries, "[", 2)
Surv.deadThoriz <- sapply(Surv.deadThoriz$summaries, "[", 2)
if (nrow(censThoriz)) {
Surv.censThoriz <- survfitJM(object, newdata = censThoriz, idVar = idVar, simulate = simulate, M = M,
survTimes = Thoriz, last.time = rep(Tstart, length(idcens)))
tt <- Time[indCens]
weights <- survfitJM(object, newdata = censThoriz, idVar = idVar, simulate = simulate, M = M,
survTimes = Thoriz, last.time = tt[!duplicated(censThoriz[[idVar]])])
Surv.censThoriz <- sapply(Surv.censThoriz$summaries, "[", 2)
weights <- sapply(weights$summaries, "[", 2)
} else {
Surv.censThoriz <- weights <- NA
}
prederr <- if (!interval) {
(1/nr) * sum(lossFun(1 - Surv.aliveThoriz), lossFun(0 - Surv.deadThoriz),
weights * lossFun(1 - Surv.censThoriz) + (1 - weights) * lossFun(0 - Surv.censThoriz))
} else {
TimeCens <- exp(object$y$logT)
deltaCens <- 1 - object$y$event
KMcens <- survfit(Surv(TimeCens, deltaCens) ~ 1)
times <- TimeCens[TimeCens > Tstart & TimeCens < Thoriz & !deltaCens]
times <- sort(unique(times))
k <- as.numeric(table(times))
w <- summary(KMcens, times = Tstart)$surv / summary(KMcens, times = times)$surv
prederr.times <- sapply(times,
function (t) prederrJM(object, newdata, Tstart, t,
interval = FALSE, idVar = idVar, simulate = simulate)$prederr)
num <- sum(prederr.times * w * k, na.rm = TRUE)
den <- sum(w * k, na.rm = TRUE)
num / den
}
out <- list(prederr = prederr, nr = nr, Tstart = Tstart, Thoriz = Thoriz, interval = interval,
classObject = class(object), nameObject = deparse(substitute(object)), lossFun = lf)
class(out) <- "prederrJM"
out
}
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