Nothing
prederrJM.mvJMbayes <- function (object, newdata, Tstart, Thoriz, lossFun = c("square", "absolute"),
interval = FALSE, idVar = "id", M = 100, ...) {
if (!inherits(object, "mvJMbayes"))
stop("Use only with 'mvJMbayes' 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$model_info$coxph_components$Terms
environment(TermsT) <- parent.frame()#.GlobalEnv
SurvT <- model.response(model.frame(TermsT, newdata))
is_counting <- attr(SurvT, "type") == "counting"
is_interval <- attr(SurvT, "type") == "interval"
Time <- if (is_counting) {
ave(SurvT[, 2], id, FUN = function (x) tail(x, 1))
} else if (is_interval) {
Time1 <- SurvT[, "time1"]
Time2 <- SurvT[, "time2"]
Time <- Time1
Time[Time2 != 1] <- Time2[Time2 != 1]
Time
} else {
SurvT[, 1]
}
timeVar <- object$model_info$timeVar
newdata2 <- newdata[Time > Tstart, ]
id2 <- newdata2[[idVar]]
SurvT <- model.response(model.frame(TermsT, newdata2))
if (is_counting) {
f <- factor(id2, levels = unique(id2))
Time <- ave(SurvT[, 2], f, FUN = function (x) tail(x, 1))
event <- ave(SurvT[, 3], f, FUN = function (x) tail(x, 1))
} else if (is_interval) {
Time1 <- SurvT[, "time1"]
Time2 <- SurvT[, "time2"]
Time <- Time1
Time[Time2 != 1] <- Time2[Time2 != 1]
event <- SurvT[, "status"]
} else {
Time <- SurvT[, 1]
event <- SurvT[, 2]
}
timesInd <- newdata2[[timeVar]] <= Tstart
aliveThoriz <- newdata2[Time > Thoriz & timesInd, ]
deadThoriz <- newdata2[Time <= Thoriz & (event == 1 | event == 3) & timesInd, ]
indCens <- Time < Thoriz & (event == 0 | event == 2) & timesInd
censThoriz <- newdata2[indCens, ]
nr <- length(unique(newdata2[[idVar]]))
idalive <- unique(aliveThoriz[[idVar]])
iddead <- unique(deadThoriz[[idVar]])
idcens <- unique(censThoriz[[idVar]])
prederr <- if (length(unique(Time)) > 1 && nrow(aliveThoriz) > 1 &&
nrow(deadThoriz) > 1) {
Surv.aliveThoriz <- if (is_counting) {
survfitJM(object, newdata = aliveThoriz, idVar = idVar, M = M,
survTimes = Thoriz, last.time = rep(Tstart, length(idalive)),
LeftTrunc_var = all.vars(TermsT)[1L])
} else {
survfitJM(object, newdata = aliveThoriz, idVar = idVar, M = M,
survTimes = Thoriz, last.time = rep(Tstart, length(idalive)))
}
Surv.deadThoriz <- if (is_counting) {
survfitJM(object, newdata = deadThoriz, idVar = idVar,
survTimes = Thoriz, last.time = rep(Tstart, length(iddead)),
LeftTrunc_var = all.vars(TermsT)[1L])
} else {
survfitJM(object, newdata = deadThoriz, idVar = idVar,
survTimes = Thoriz, last.time = rep(Tstart, length(iddead)))
}
Surv.aliveThoriz <- sapply(Surv.aliveThoriz$summaries, "[", 2)
Surv.deadThoriz <- sapply(Surv.deadThoriz$summaries, "[", 2)
if (nrow(censThoriz)) {
Surv.censThoriz <- if (is_counting) {
survfitJM(object, newdata = censThoriz, idVar = idVar, M = M,
survTimes = Thoriz, last.time = rep(Tstart, length(idcens)),
LeftTrunc_var = all.vars(TermsT)[1L])
} else {
survfitJM(object, newdata = censThoriz, idVar = idVar, M = M,
survTimes = Thoriz, last.time = rep(Tstart, length(idcens)))
}
tt <- Time[indCens]
weights <- if (is_counting) {
survfitJM(object, newdata = censThoriz, idVar = idVar, M = M,
survTimes = Thoriz, last.time = tt[!duplicated(censThoriz[[idVar]])],
LeftTrunc_var = all.vars(TermsT)[1L])
} else {
survfitJM(object, newdata = censThoriz, idVar = idVar, M = M,
survTimes = Thoriz, last.time = tt[!duplicated(censThoriz[[idVar]])])
}
Surv.censThoriz <- sapply(Surv.censThoriz$summaries, "[", 2)
weights <- sapply(weights$summaries, "[", 2)
} else {
Surv.censThoriz <- weights <- NA
}
if (!interval) {
(1/nr) * sum(lossFun(1 - Surv.aliveThoriz), lossFun(0 - Surv.deadThoriz),
weights * lossFun(1 - Surv.censThoriz) + (1 - weights) * lossFun(0 - Surv.censThoriz),
na.rm = TRUE)
} else {
TimeCens <- object$model_info$coxph_components$Time
deltaCens <- 1 - object$model_info$coxph_components$event
KMcens <- survfit(Surv(TimeCens, deltaCens) ~ 1)
times <- TimeCens[TimeCens > Tstart & TimeCens < Thoriz & !deltaCens]
times <- sort(unique(times))
k <- as.numeric(table(times))
w <- summary(KMcens, times = Tstart)$surv / summary(KMcens, times = times)$surv
prederr.times <- sapply(times,
function (t) prederrJM(object, newdata, Tstart, t, M = M,
interval = FALSE, idVar = idVar)$prederr)
num <- sum(prederr.times * w * k, na.rm = TRUE)
den <- sum(w * k, na.rm = TRUE)
num / den
}
} else {
nr <- NA
NA
}
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
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.