Nothing
tpPAJ <- function(object,
s,
conf = FALSE,
conf.level = 0.95)
{
if (missing(object))
stop("Argument 'object' is missing, with no default")
# if (!inherits(object, "survIDM")) stop("'object' must be of class 'survIDM'")
if (missing(s))
s <- 0
data <- object[[1]]
TPobj <- with(data, TPmsm::survTP(time1, event1, Stime, event))
res <-
TPmsm::transPAJ(
object = TPobj,
s = s,
t = Inf,
conf = conf,
conf.level = conf.level
)
#res <- list()
probs <- matrix(0, 3, 3)
colnames(probs) <- c("1", "2", "3")
rownames(probs) <- c("1", "2", "3")
probs[1, ] <- res$est[length(res$time), 1:3]
probs[2, ] <- c(0, res$est[length(res$time), 4:5])
probs[3, ] <- c(0, 0, 1)
cn <- colnames(res$est)
c3 <- "probs"
rn <- as.character(res$time)
m <- length(rn)
ptrans <- c("1 1", "1 2", "1 3", "2 2", "2 3")
if (conf == TRUE) {
c3 <- c("probs", "LCI", "UCI", "Var")
all.probs <- array(NA, dim = c(m, 4, 5), dimnames = list(rn, c3, cn))
all.probs[, 1, 1:5] <- res$est
all.probs[, 2, 1:5] <- res$inf
all.probs[, 3, 1:5] <- res$sup
# results:
res <- list(
# states information:
s = s,
t = max(res$time),
states = c("1", "2", "3"),
ns = 3,
tr.states = c("1", "2"),
conf.type = "bootstrap",
# event times:
times = res$time,
probs = probs,
all.probs = all.probs,
# posible transitions:
p.trans = ptrans,
conf = conf
)
#est
suppressWarnings(aux <- matrix(
res$all.probs[, 1, ],
ncol = 5,
nrow = length(res$times)
))
aux <- data.frame(t = res$times, aux)
names(aux) <- c("t", "p00", "p01", "p02", "p11", "p12")
#ci
auxci <- res$all.probs[, 2:3, ]
suppressWarnings(auxci <- data.frame(matrix(
auxci, ncol = 10,
nrow = length(res$times)
)))
names(auxci) <-
c(
"p00.li.ci",
"p00.ls.ci",
"p01.li.ci",
"p01.ls.ci",
"p02.li.ci",
"p02.ls.ci",
"p11.li.ci",
"p11.ls.ci",
"p12.li.ci",
"p12.ls.ci"
)
res <- list(
est = aux,
CI = auxci,
conf.level = conf.level,
s = res$s,
t = res$times,
conf = conf,
conf.type = res$conf.type
)
} #end if
else{
all.probs <- array(NA, dim = c(m, 1, 5), dimnames = list(rn, c3, cn))
all.probs[, 1, 1:5] <- res$est
# results:
res <- list(
# states information:
s = s,
t = max(res$time),
states = c("1", "2", "3"),
ns = 3,
tr.states = c("1", "2"),
conf.type = "",
# event times:
times = res$time,
# occupation or transition probabilities:
probs = probs,
all.probs = all.probs,
#posible transitions:
p.trans = ptrans,
conf = conf
)
suppressWarnings(aux <- matrix(
res$all.probs,
ncol = 5,
nrow = length(res$times)
))
aux <- data.frame(t = res$times, aux)
names(aux) <- c("t", "p00", "p01", "p02", "p11", "p12")
res <- list(
est = aux,
s = res$s,
t = res$times,
conf = conf,
conf.type = res$conf.type
)
}
return(res)
}
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