#' Fluctuation for the Method of Cause-Specific Hazards
#'
#' @description This function performs a fluctuation of an initial estimate of
#' the cause-specific hazard functions via a call to \code{\link[stats]{glm}}
#' (i.e., a logistic submodel) or a call to \code{\link[stats]{optim}} (to
#' ensure fluctuations stay within model space). The structure of the function
#' is specific to how it is called within \code{\link{hazard_tmle}}. In
#' particular, \code{dataList} must have a very specific structure for this
#' function to run properly. The list should consist of \code{data.frame}
#' objects. The first will have the number of rows for each observation equal
#' to the \code{ftime} corresponding to that observation. Subsequent entries
#' will have \code{t0} rows for each observation and will set \code{trt}
#' column equal to each value of \code{trtOfInterest} in turn. The function
#' will fit a logistic regression with (a scaled version of) \code{Nj} as
#' outcome, the logit of the current (pseudo-) hazard estimate as offset and
#' the targeted minimum loss-based estimation "clever covariates". The
#' function then obtains predictions based on this fit on each of the
#' \code{data.frame} objects in \code{dataList}.
#'
#' @param dataList A list of \code{data.frame} objects.
#' @param allJ Numeric vector indicating the labels of all causes of failure.
#' @param ofInterestJ Numeric vector indicating \code{ftypeOfInterest} that was
#' passed to \code{\link{hazard_tmle}}.
#' @param nJ The number of unique failure types.
#' @param uniqtrt The values of \code{trtOfInterest} passed to
#' \code{\link{mean_tmle}}.
#' @param ntrt The number of \code{trt} values of interest.
#' @param t0 The timepoint at which \code{survtmle} was called to evaluate.
#' @param verbose A \code{logical} indicating whether the function should print
#' messages to indicate progress.
#' @param att A \code{boolean} indicating whether to compute the ATT estimate,
#' instead of treatment specific survival curves. This option only works with
#' two levels of \code{trt} that are labeled with 0 and 1.
#' @param ... Other arguments. Not currently used.
#'
#' @return The function returns a list that is exactly the same as the input
#' \code{dataList}, but with updated columns corresponding with estimated
#' cumulative incidence at each time and estimated "clever covariates" at each
#' time.
#'
#' @importFrom Matrix Diagonal
#' @importFrom stats optim
fluctuateHazards <- function(dataList, allJ, ofInterestJ, nJ, uniqtrt, ntrt,
t0, verbose, att, ...) {
eps <- NULL
for (z in uniqtrt) {
for (j in allJ) {
# clever covariates
cleverCovariatesNotSelf <- NULL
if (length(ofInterestJ[ofInterestJ != j]) > 0) {
cleverCovariatesNotSelf <- c(
cleverCovariatesNotSelf,
paste0(
"H", ofInterestJ[ofInterestJ != j],
".jNotSelf.z", z
)
)
}
if (j %in% ofInterestJ) {
cleverCovariatesSelf <- paste0("H", j, ".jSelf.z", z)
} else {
cleverCovariatesSelf <- NULL
}
# calculate offset term and outcome
dataList <- lapply(dataList, function(x, j, allJ) {
x$thisScale <- pmin(x[[paste0("u", j)]], 1 - x[[paste0("hazNot", j)]])
-x[[paste0("l", j)]]
x$thisOffset <- stats::qlogis(pmin(
(x[[paste0("Q", j, "Haz")]] - x[[paste0("l", j)]]) / x$thisScale,
1 - .Machine$double.neg.eps
))
x$thisOutcome <- (x[[paste0("N", j)]] - x[[paste0("l", j)]]) /
x$thisScale
x
}, j = j, allJ = allJ)
fluc.mod <- stats::optim(
par = rep(0, length(c(
cleverCovariatesNotSelf,
cleverCovariatesSelf
))),
fn = LogLikelihood_offset,
Y = dataList[[1]]$thisOutcome,
H = suppressWarnings(
as.matrix(Matrix::Diagonal(x = dataList[[1]]$thisScale) %*%
as.matrix(dataList[[1]][, c(
cleverCovariatesNotSelf,
cleverCovariatesSelf
)]))
),
offset = dataList[[1]]$thisOffset,
method = "BFGS", gr = grad_offset,
control = list(reltol = 1e-7, maxit = 50000)
)
if (fluc.mod$convergence != 0) {
warning("Fluctuation convergence failure. Using with initial estimates.
Proceed with caution")
beta <- rep(0, length(fluc.mod$par))
} else {
beta <- fluc.mod$par
}
eps <- c(eps, beta)
dataList <- lapply(dataList, function(x, j) {
x[[paste0("Q", j, "PseudoHaz")]][x$trt == z] <-
plogis(x$thisOffset[x$trt == z] +
suppressWarnings(
as.matrix(
Matrix::Diagonal(x = x$thisScale[x$trt == z]) %*%
as.matrix(x[x$trt == z, c(
cleverCovariatesNotSelf,
cleverCovariatesSelf
)])
) %*% as.matrix(beta)
))
x[[paste0("Q", j, "Haz")]][x$trt == z] <-
x[[paste0("Q", j, "PseudoHaz")]][x$trt == z] *
x$thisScale[x$trt == z] + x[[paste0("l", j)]][x$trt == z]
x
}, j = j)
# update variables based on new haz
dataList <- updateVariables(
dataList = dataList, allJ = allJ,
ofInterestJ = ofInterestJ,
nJ = nJ, uniqtrt = uniqtrt, ntrt = ntrt,
verbose = verbose, t0 = t0, att = att
)
}
}
attr(dataList, "fluc") <- eps
dataList
}
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