/
superposition.R
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superposition.R
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#' Compute noncompartmental superposition for repeated dosing
#'
#' @inheritParams assert_conc_time
#' @inheritParams assert_lambdaz
#' @inheritParams PKNCA.choose.option
#' @inheritParams choose_interval_method
#' @param dose.input The dose given to generate the `conc` and `time` inputs. If
#' missing, output doses will be assumed to be equal to the input dose.
#' @inheritParams assert_dosetau
#' @param dose.times The time of dosing within the dosing interval. The
#' `min(dose.times)` must be >= 0, and the `max(dose.times)` must be < `tau`.
#' There may be more than one dose times given as a vector.
#' @param dose.amount The doses given for the output. Linear proportionality
#' will be used from the input to output if they are not equal. The length of
#' dose.amount must be either 1 or matching the length of `dose.times`.
#' @param n.tau The number of tau dosing intervals to simulate or `Inf` for
#' steady-state.
#' @param clast.pred To use predicted as opposed to observed Clast, either give
#' the value for clast.pred here or set it to true (for automatic calculation
#' from the half-life).
#' @param tlast The time of last observed concentration above the limit of
#' quantification. This is calculated if not provided.
#' @param additional.times Times to include in the final outputs in addition to
#' the standard times (see details). All `min(additional.times)` must be >=
#' 0, and the `max(additional.times)` must be <= `tau`.
#' @param check.blq Must the first concentration measurement be below the limit
#' of quantification?
#' @param steady.state.tol The tolerance for assessing if steady-state has been
#' achieved (between 0 and 1, exclusive).
#' @param ... Additional arguments passed to the `half.life` function if
#' required to compute `lambda.z`.
#' @returns A data frame with columns named "conc" and "time".
#'
#' @details The returned superposition times will include all of the following
#' times: 0 (zero), `dose.times`, `time modulo tau` (shifting `time` for each
#' dose time as well), `additional.times`, and `tau`.
#'
#' @seealso [interp.extrap.conc()]
#' @export
superposition <- function(conc, ...) {
UseMethod("superposition", conc)
}
#' @rdname superposition
#' @export
superposition.PKNCAconc <- function(conc, ...) {
# Split the data by grouping and extract just the concentration and
# time columns
nested_data <- prepare_PKNCAconc(conc)
tmp_results <-
parallel::mclapply(
X=seq_len(nrow(nested_data)),
FUN=function(idx) {
superposition.numeric(
conc=nested_data$data_conc[[idx]]$conc,
time=nested_data$data_conc[[idx]]$time,
...
)
}
)
# Replace the concentration data with the new results
nested_data$data_conc <- tmp_results
tidyr::unnest(nested_data, cols="data_conc")
}
#' @rdname superposition
#' @export
superposition.numeric <- function(conc, time, dose.input = NULL,
tau, dose.times=0, dose.amount, n.tau=Inf,
options=list(),
lambda.z, clast.pred=FALSE, tlast,
additional.times=numeric(),
check.blq=TRUE,
method = NULL,
auc.type = "AUCinf",
steady.state.tol=1e-3, ...) {
# Check the inputs
# Concentration and time
assert_conc_time(conc = conc, time = time)
if (check.blq) {
if (!(conc[1] %in% 0)) {
stop("The first concentration must be 0 (and not NA). To change this set check.blq=FALSE.")
}
}
assert_number_between(dose.input, na.ok = FALSE, null.ok = TRUE, lower = 0)
assert_dosetau(tau)
assert_numeric_between(x = dose.times, lower_eq = 0, min.len = 1, upper = tau)
# dose.amount
if (!missing(dose.amount)) {
if (missing(dose.input)) {
stop("must give dose.input to give dose.amount")
}
assert_numeric_between(x = dose.amount, lower = 0, finite = TRUE)
if (!(length(dose.amount) %in% c(1, length(dose.times))))
stop("dose.amount must either be a scalar or match the length of dose.times")
}
checkmate::assert_number(n.tau, lower = 1)
if (is.finite(n.tau)) {
n.tau <- checkmate::assert_integerish(n.tau, lower = 1)
}
# lambda.z
if (!missing(lambda.z)) {
lambda.z <- assert_number_between(x = lambda.z, lower = 0)
}
# clast.pred
checkmate::assert(
checkmate::check_number(clast.pred, lower = 0, na.ok = TRUE),
checkmate::check_logical(clast.pred, any.missing = TRUE, len = 1),
.var.name = "clast.pred"
)
if (is.na(clast.pred)) {
clast.pred <- FALSE
} else if (!is.numeric(clast.pred)) {
checkmate::assert_logical(clast.pred, any.missing = FALSE, len = 1)
}
# tlast
if (!missing(tlast)) {
checkmate::assert_number(tlast)
}
# additional.times
if (length(additional.times) > 0) {
if (any(is.na(additional.times))) {
stop("No additional.times may be NA (to not include any additional.times, enter c() as the function argument)")
}
if (!is.numeric(additional.times) | is.factor(additional.times))
stop("additional.times must be a number")
if (any(additional.times < 0))
stop("All additional.times must be nonnegative")
if (any(additional.times > tau))
stop("All additional.times must be <= tau")
}
# steady.state.tol
if (length(steady.state.tol) != 1)
stop("steady.state.tol must be a scalar")
if (!is.numeric(steady.state.tol) | is.factor(steady.state.tol) | is.na(steady.state.tol))
stop("steady.state.tol must be a number")
if (steady.state.tol <= 0 |
steady.state.tol >= 1)
stop("steady.state.tol must be between 0 and 1, exclusive.")
if (steady.state.tol > 0.01)
warning("steady.state.tol is usually <= 0.01")
# We get all or none of lambda.z, clast, and tlast
has.lambda.z <- !missing(lambda.z)
has.clast.pred <- !is.logical(clast.pred)
has.tlast <- !missing(tlast)
if (any(c(has.lambda.z, has.clast.pred, has.tlast)) &
!all(c(has.lambda.z, has.clast.pred, has.tlast)))
stop("Either give all or none of the values for these arguments: lambda.z, clast.pred, and tlast")
# combine dose.input and dose.amount as applicable to scale the
# outputs.
if (!missing(dose.amount)) {
dose.scaling <- dose.amount / dose.input
if (length(dose.scaling) != length(dose.times)) {
if (length(dose.scaling) != 1)
stop("bug in dose.amount, dose.times, and dose.input handling") # nocov
# it is a scalar and there is more than one dose
dose.scaling <- rep(dose.scaling, length(dose.times))
}
} else {
dose.scaling <- rep(1, length(dose.times))
}
# Determine the output times
tmp.times <- c(0, tau, dose.times, additional.times)
# For the output, ensure that we have each of the input times
# shifted for the dosing times.
for (d in dose.times)
tmp.times <- c(tmp.times, (d + time) %% tau)
ret <- data.frame(conc=0, time=sort(unique(tmp.times)))
# Check if all the input concentrations are 0, and if so, give that
# simple answer.
if (all(conc == 0)) {
return(ret)
} else {
# Check if we will need to extrapolate
tlast <- pk.calc.tlast(conc, time, check=FALSE)
if ((tau*n.tau) > tlast) {
if (missing(lambda.z)) {
tmp <- pk.calc.half.life(conc, time, options=options,
..., check=FALSE)
lambda.z <- tmp$lambda.z
}
if (identical(clast.pred, FALSE)) {
clast <- pk.calc.clast.obs(conc, time, check=FALSE)
} else if (identical(clast.pred, TRUE)) {
clast <- tmp$clast.pred
} else {
# Use the provided clast.pred
clast <- clast.pred
}
} else {
# We don't need lambda.z for calculations, but it is simpler to
# define it.
lambda.z <- NA
}
}
# cannot continue extrapolating due to missing data (likely due to
# half-life not calculable)
if ((n.tau * tau) > tlast & is.na(lambda.z)) {
ret$conc <- NA
} else {
# Do the math! (Finally)
current.tol <- steady.state.tol + 1
tau.count <- 0
# Stop either for reaching steady-state or for reaching the requested number of doses
while (tau.count < n.tau &
!is.na(current.tol) &
current.tol >= steady.state.tol) {
prev.conc <- ret$conc
# Perform the dosing for a single dosing interval.
for (i in seq_along(dose.times)) {
tmp.time <- ret$time - dose.times[i] + (tau * tau.count)
# For the first dosing interval, make sure that we do not
# assign concentrations before the dose is given.
mask.time <- tmp.time >= 0
# Update the current concentration (previous concentration +
# new concentration scaled by the relative dose)
ret$conc[mask.time] <-
(ret$conc[mask.time] +
dose.scaling[i]*
interp.extrap.conc(
conc = conc, time = time,
time.out=tmp.time[mask.time],
lambda.z=lambda.z, clast=clast,
options=options, check=FALSE,
method = method, auc.type = auc.type
)
)
}
tau.count <- tau.count + 1
if (any(ret$conc %in% 0)) {
# prevent division by 0. Since not all concentrations are 0,
# all values will eventually be nonzero.
current.tol <- steady.state.tol + 1
} else {
current.tol <- max(1-(prev.conc/ret$conc))
}
}
}
ret
}