Nothing
rocJM.mvJMbayes <- function (object, newdata, Tstart, Thoriz = NULL, Dt = NULL,
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")
if (is.null(Thoriz) && is.null(Dt))
stop("either 'Thoriz' or 'Dt' must be non null.\n")
if (!is.null(Thoriz) && Thoriz <= Tstart)
stop("'Thoriz' must be larger than 'Tstart'.")
if (is.null(Thoriz))
Thoriz <- Tstart + Dt
Thoriz <- Thoriz + 1e-07
id <- newdata[[idVar]]
id <- match(id, unique(id))
TermsT <- object$model_info$coxph_components$Terms
environment(TermsT) <- parent.frame()#.GlobalEnv
mframe <- model.frame(TermsT, newdata)
if (length(na_ind <- attr(mframe, "na.action"))) {
id <- id[-na_ind]
}
SurvT <- model.response(mframe)
is_counting <- attr(SurvT, "type") == "counting"
is_interval <- attr(SurvT, "type") == "interval"
Time <- if (is_counting) {
ave(SurvT[, 2], id, FUN = function (x) tail(x, 1))
} else if (is_interval) {
Time1 <- SurvT[, "time1"]
Time2 <- SurvT[, "time2"]
Time <- Time1
Time[Time2 != 1] <- Time2[Time2 != 1]
Time
} else {
SurvT[, 1]
}
timeVar <- object$model_info$timeVar
newdata2 <- newdata[Time > Tstart, ]
newdata2 <- newdata2[newdata2[[timeVar]] <= Tstart, ]
pi.u.t <- if (is_counting) {
survfitJM(object, newdata = newdata2, idVar = idVar, survTimes = Thoriz,
M = M, LeftTrunc_var = all.vars(TermsT)[1L])
} else {
survfitJM(object, newdata = newdata2, idVar = idVar, survTimes = Thoriz,
M = M)
}
pi.u.t <- sapply(pi.u.t$summaries, "[", 1, 2)
# extract event process information
id <- newdata2[[idVar]]
SurvT <- model.response(model.frame(TermsT, newdata2))
if (is_counting) {
f <- factor(id, levels = unique(id))
Time <- tapply(SurvT[, 2], f, tail, 1)
event <- tapply(SurvT[, 3], f, tail, 1)
} else if (is_interval) {
Time1 <- SurvT[, "time1"]
Time2 <- SurvT[, "time2"]
Time <- Time1
Time[Time2 != 1] <- Time2[Time2 != 1]
Time <- Time[!duplicated(id)]
event <- SurvT[!duplicated(id), "status"]
} else {
Time <- SurvT[!duplicated(id), 1]
event <- SurvT[!duplicated(id), 2]
}
names(Time) <- names(event) <- as.character(unique(id))
# subjects who died before Thoriz
ind1 <- Time < Thoriz & (event == 1 | event == 3)
# subjects who were censored in the interval (Tstart, Thoriz)
ind2 <- Time < Thoriz & (event == 0 | event == 2)
ind <- ind1 | ind2
if (any(ind2)) {
nams <- unique(names(ind2[ind2]))
pi2 <- if (is_counting) {
survfitJM(object, newdata = newdata2[id %in% nams, ], idVar = idVar,
last.time = Time[nams], survTimes = Thoriz,
M = M, LeftTrunc_var = all.vars(TermsT)[1L])
} else {
survfitJM(object, newdata = newdata2[id %in% nams, ], idVar = idVar,
last.time = Time[nams], survTimes = Thoriz, M = M)
}
pi2 <- 1 - sapply(pi2$summaries, "[", 1, 2)
nams2 <- names(ind2[ind2])
ind[ind2] <- ind[ind2] * pi2[nams2]
}
# calculate sensitivity and specificity
thrs <- seq(0, 1, length = 101)
nTP <- colSums(outer(pi.u.t, thrs, "<") * c(ind))
nFN <- sum(ind) - nTP
TP <- nTP / sum(ind)
nFP <- colSums(outer(pi.u.t, thrs, "<") * c(1 - ind))
nTN <- sum(1 - ind) - nFP
FP <- nFP / sum(1 - ind)
Q <- colMeans(outer(pi.u.t, thrs, "<"))
Q. <- 1 - Q
k.1.0 <- (TP - Q) / Q.
k.0.0 <- (1 - FP - Q.) / Q
P <- mean(ind)
P. <- 1 - P
k.05.0 <- (P * Q. * k.1.0 + P. * Q * k.0.0) / (P * Q. + P. * Q)
f1score <- 2 * nTP / (2 * nTP + nFN + nFP)
F1score <- median(thrs[f1score == max(f1score)])
youden <- TP - FP
Youden <- median(thrs[youden == max(youden)])
out <- list(TP = TP, FP = FP, nTP = nTP, nFN = nFN, nFP = nFP, nTN = nTN,
qSN = k.1.0, qSP = k.0.0, qOverall = k.05.0,
thrs = thrs,
F1score = F1score, Youden = Youden,
Tstart = Tstart, Thoriz = Thoriz, nr = length(unique(id)),
classObject = class(object), nameObject = deparse(substitute(object)))
class(out) <- "rocJM"
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.