R/aucint.R

In billdenney/pknca: Perform Pharmacokinetic Non-Compartmental Analysis

#' Calculate the AUC over an interval with interpolation and/or
#' extrapolation of concentrations for the beginning and end of the
#' interval.
#'
#' @details
#' When `pk.calc.aucint()` needs to extrapolate using `lambda.z` (in other
#' words, using the half-life), it will always extrapolate using the logarithmic
#' trapezoidal rule to align with using a half-life calculation for the
#' extrapolation.
#'
#'
#' @inheritParams pk.calc.auxc
#' @inheritParams assert_intervaltime_single
#' @inheritParams assert_lambdaz
#' @param clast,clast.obs,clast.pred The last concentration above the limit of
#'   quantification; this is used for AUCinf calculations.  If provided as
#'   clast.obs (observed clast value, default), AUCinf is AUCinf,obs. If
#'   provided as clast.pred, AUCinf is AUCinf,pred.
#' @param time.dose,route,duration.dose The time of doses, route of
#'   administration, and duration of dose used with interpolation and
#'   extrapolation of concentration data (see [interp.extrap.conc.dose()]).  If
#'   `NULL`, [interp.extrap.conc()] will be used instead (assuming that no doses
#'   affecting concentrations are in the interval).
#' @param ... Additional arguments passed to `pk.calc.auxc` and
#'   `interp.extrap.conc`
#' @family AUC calculations
#' @seealso [PKNCA.options()], [interp.extrap.conc.dose()]
#' @returns The AUC for an interval of time as a number
#' @export
pk.calc.aucint <- function(conc, time,
                           interval=NULL, start=NULL, end=NULL,
                           clast=pk.calc.clast.obs(conc, time),
                           lambda.z=NA,
                           time.dose=NULL,
                           route="extravascular",
                           duration.dose=0,
                           method=NULL,
                           auc.type="AUClast",
                           conc.blq=NULL,
                           conc.na=NULL,
                           check=TRUE,
                           ...,
                           options=list()) {
  # Check inputs
  method <- PKNCA.choose.option(name="auc.method", value=method, options=options)
  conc.blq <- PKNCA.choose.option(name="conc.blq", value=conc.blq, options=options)
  conc.na <- PKNCA.choose.option(name="conc.na", value=conc.na, options=options)
  if (check) {
    assert_conc_time(conc, time)
    data <-
      clean.conc.blq(
        conc, time,
        conc.blq=conc.blq,
        conc.na=conc.na,
        check=FALSE
      )
  } else {
    data <- data.frame(conc, time)
  }
  if (all(data$conc %in% 0)) {
    return(structure(0, exclude = "DO NOT EXCLUDE"))
  }
  interval <- assert_intervaltime_single(interval = interval, start = start, end = end)
  missing_times <-
    if (is.infinite(interval[2])) {
      setdiff(c(interval[1], time.dose), data$time)
    } else {
      setdiff(c(interval, time.dose), data$time)
    }
  # Handle the potential double-calculation (before/after tlast) with AUCinf
  conc_clast <- NULL
  time_clast <- NULL
  if (auc.type %in% "AUCinf") {
    tlast <- pk.calc.tlast(conc=data$conc, time=data$time)
    clast_obs <- pk.calc.clast.obs(conc=data$conc, time=data$time)
    if (is.na(clast)) {
      # All concentrations are NA
      return(structure(NA_real_, exclude = "clast is NA"))
    } else if (clast != clast_obs & interval[2] > tlast) {
      # If using clast.pred, we need to doubly calculate at tlast.
      conc_clast <- clast
      time_clast <- tlast
    }
  }
  extrap_times <- numeric()
  if (length(missing_times) > 0) {
    if (is.null(time.dose)) {
      missing_conc <-
        interp.extrap.conc(
          conc = data$conc, time = data$time,
          time.out = missing_times,
          method = method,
          auc.type = auc.type,
          clast = clast,
          lambda.z = lambda.z,
          options = options,
          ...
        )
    } else {
      missing_conc <-
        interp.extrap.conc.dose(
          conc = data$conc, time = data$time,
          time.out = missing_times,
          method = method,
          auc.type = auc.type,
          clast = clast, lambda.z = lambda.z,
          options = options,
          # arguments specific to interp.extrap.conc.dose
          time.dose = time.dose,
          route.dose = route,
          duration.dose = duration.dose,
          out.after = FALSE,
          ...
        )
    }
    new_data <- data.frame(conc=c(data$conc, conc_clast, missing_conc),
                           time=c(data$time, time_clast, missing_times))
    tlast <- pk.calc.tlast(conc = data$conc, time = data$time, check = FALSE)
    extrap_times <- missing_times[missing_times > tlast]
    new_data <- new_data[new_data$time >= interval[1] &
                           new_data$time <= interval[2],]
    new_data <- new_data[order(new_data$time),]
    conc_interp <- new_data$conc
    time_interp <- new_data$time
    if (any(mask_na_conc <- is.na(conc_interp))) {
      missing_times <- time_interp[mask_na_conc]
      warning_message <-
        if (any(is.na(lambda.z))) {
          paste("Some interpolated/extrapolated concentration values are missing",
                "(may be due to interpolating or extrapolating over a dose with lambda.z=NA).",
                "Time points with missing data are: ",
                paste(missing_times, collapse=", "))
        } else {
          paste("Some interpolated/extrapolated concentration values are missing",
                "Time points with missing data are: ",
                paste(missing_times, collapse=", "))
        }
      warning(warning_message)
      return(NA_real_)
    }
  } else {
    mask_time <- data$time >= interval[1] & data$time <= interval[2]
    conc_interp <- data$conc[mask_time]
    time_interp <- data$time[mask_time]
  }
  # AUCinf traces an AUClast curve if the interval is finite (because
  # the interval doesn't go to infinity) while AUCall and AUClast trace
  # their own curves.  Or, they all trace their own curves.
  auc.type_map <-
    if (is.infinite(interval[2])) {
      list(
        AUClast="AUClast",
        AUCall="AUCall",
        AUCinf="AUCinf"
      )[[auc.type]]
    } else {
      list(
        AUClast="AUClast",
        AUCall="AUCall",
        AUCinf="AUClast"
      )[[auc.type]]
    }

  interval_method <-
    choose_interval_method(
      conc = conc_interp,
      time = time_interp,
      tlast = max(time_interp),
      method = method,
      auc.type = auc.type,
      options = options
    )
  if (is.finite(interval[2])) {
    interval_method[length(interval_method)] <- "zero"
  }
  if (length(extrap_times) > 0) {
    interval_method[which(time_interp == extrap_times) - 1] <- "log"
  }
  ret <-
    auc_integrate(
      conc = conc_interp, time = time_interp,
      clast = clast, tlast = tlast, lambda.z = lambda.z,
      interval_method = interval_method,
      fun_linear = aucintegrate_linear,
      fun_log = aucintegrate_log,
      fun_inf = aucintegrate_inf
    )
  ret
}

#' @describeIn pk.calc.aucint Interpolate or extrapolate concentrations for
#'   AUClast
#' @export
pk.calc.aucint.last <- function(conc, time, start=NULL, end=NULL, time.dose, ..., options=list()) {
  if (missing(time.dose))
    time.dose <- NULL
  pk.calc.aucint(conc=conc, time=time,
                 start=start, end=end,
                 options=options,
                 time.dose=time.dose,
                 ...,
                 auc.type="AUClast")
}
#' @describeIn pk.calc.aucint Interpolate or extrapolate concentrations for
#'   AUCall
#' @export
pk.calc.aucint.all <- function(conc, time, start=NULL, end=NULL, time.dose, ..., options=list()) {
  if (missing(time.dose))
    time.dose <- NULL
  pk.calc.aucint(conc=conc, time=time,
                 start=start, end=end,
                 options=options,
                 time.dose=time.dose,
                 ...,
                 auc.type="AUCall")
}
#' @describeIn pk.calc.aucint Interpolate or extrapolate concentrations for
#'   AUCinf.obs
#' @export
pk.calc.aucint.inf.obs <- function(conc, time, start=NULL, end=NULL, time.dose, lambda.z, clast.obs, ..., options=list()) {
  if (missing(time.dose))
    time.dose <- NULL
  pk.calc.aucint(conc=conc, time=time,
                 start=start, end=end,
                 time.dose=time.dose,
                 lambda.z=lambda.z, clast=clast.obs,
                 options=options, ...,
                 auc.type="AUCinf")
}
#' @describeIn pk.calc.aucint Interpolate or extrapolate concentrations for
#'   AUCinf.pred
#' @export
pk.calc.aucint.inf.pred <- function(conc, time, start=NULL, end=NULL, time.dose, lambda.z, clast.pred, ..., options=list()) {
  if (missing(time.dose))
    time.dose <- NULL
  pk.calc.aucint(conc=conc, time=time,
                 start=start, end=end,
                 time.dose=time.dose,
                 lambda.z=lambda.z, clast=clast.pred,
                 options=options, ...,
                 auc.type="AUCinf")
}

add.interval.col("aucint.last",
                 FUN="pk.calc.aucint.last",
                 values=c(FALSE, TRUE),
                 unit_type="auc",
                 pretty_name="AUCint (based on AUClast extrapolation)",
                 desc="The area under the concentration time curve in the interval extrapolating from Tlast to infinity with zeros (matching AUClast)",
                 formalsmap=list(conc="conc.group", time="time.group", time.dose=NULL))
PKNCA.set.summary(
  name="aucint.last",
  description="geometric mean and geometric coefficient of variation",
  point=business.geomean,
  spread=business.geocv
)

add.interval.col("aucint.last.dose",
                 FUN="pk.calc.aucint.last",
                 values=c(FALSE, TRUE),
                 unit_type="auc",
                 pretty_name="AUCint (based on AUClast extrapolation, dose-aware)",
                 desc="The area under the concentration time curve in the interval extrapolating from Tlast to infinity with zeros (matching AUClast) with dose-aware interpolation/extrapolation of concentrations",
                 formalsmap=list(conc="conc.group", time="time.group", time.dose="time.dose.group"))
PKNCA.set.summary(
  name="aucint.last.dose",
  description="geometric mean and geometric coefficient of variation",
  point=business.geomean,
  spread=business.geocv
)

add.interval.col("aucint.all",
                 FUN="pk.calc.aucint.all",
                 values=c(FALSE, TRUE),
                 unit_type="auc",
                 pretty_name="AUCint (based on AUCall extrapolation)",
                 desc="The area under the concentration time curve in the interval extrapolating from Tlast to infinity with the triangle from Tlast to the next point and zero thereafter (matching AUCall)",
                 formalsmap=list(conc="conc.group", time="time.group", time.dose=NULL))
PKNCA.set.summary(
  name="aucint.all",
  description="geometric mean and geometric coefficient of variation",
  point=business.geomean,
  spread=business.geocv
)

add.interval.col("aucint.all.dose",
                 FUN="pk.calc.aucint.all",
                 values=c(FALSE, TRUE),
                 unit_type="auc",
                 pretty_name="AUCint (based on AUCall extrapolation, dose-aware)",
                 desc="The area under the concentration time curve in the interval extrapolating from Tlast to infinity with the triangle from Tlast to the next point and zero thereafter (matching AUCall) with dose-aware interpolation/extrapolation of concentrations",
                 formalsmap=list(conc="conc.group", time="time.group", time.dose="time.dose.group"))
PKNCA.set.summary(
  name="aucint.all.dose",
  description="geometric mean and geometric coefficient of variation",
  point=business.geomean,
  spread=business.geocv
)

add.interval.col("aucint.inf.obs",
                 FUN="pk.calc.aucint.inf.obs",
                 values=c(FALSE, TRUE),
                 unit_type="auc",
                 pretty_name="AUCint (based on AUCinf,obs extrapolation)",
                 desc="The area under the concentration time curve in the interval extrapolating from Tlast to infinity with zeros (matching AUClast)",
                 formalsmap=list(conc="conc.group", time="time.group", time.dose=NULL),
                 depends=c("lambda.z", "clast.obs"))
PKNCA.set.summary(
  name="aucint.inf.obs",
  description="geometric mean and geometric coefficient of variation",
  point=business.geomean,
  spread=business.geocv
)

add.interval.col("aucint.inf.obs.dose",
                 FUN="pk.calc.aucint.inf.obs",
                 values=c(FALSE, TRUE),
                 unit_type="auc",
                 pretty_name="AUCint (based on AUCinf,obs extrapolation, dose-aware)",
                 desc="The area under the concentration time curve in the interval extrapolating from Tlast to infinity with zeros (matching AUClast) with dose-aware interpolation/extrapolation of concentrations",
                 formalsmap=list(conc="conc.group", time="time.group", time.dose="time.dose.group"),
                 depends=c("lambda.z", "clast.obs"))
PKNCA.set.summary(
  name="aucint.inf.obs.dose",
  description="geometric mean and geometric coefficient of variation",
  point=business.geomean,
  spread=business.geocv
)

add.interval.col("aucint.inf.pred",
                 FUN="pk.calc.aucint.inf.pred",
                 values=c(FALSE, TRUE),
                 unit_type="auc",
                 pretty_name="AUCint (based on AUCinf,pred extrapolation)",
                 desc="The area under the concentration time curve in the interval extrapolating from Tlast to infinity with the triangle from Tlast to the next point and zero thereafter (matching AUCall)",
                 formalsmap=list(conc="conc.group", time="time.group", time.dose=NULL),
                 depends=c("lambda.z", "clast.pred"))
PKNCA.set.summary(
  name="aucint.inf.pred",
  description="geometric mean and geometric coefficient of variation",
  point=business.geomean,
  spread=business.geocv
)

add.interval.col("aucint.inf.pred.dose",
                 FUN="pk.calc.aucint.inf.pred",
                 values=c(FALSE, TRUE),
                 unit_type="auc",
                 pretty_name="AUCint (based on AUCinf,pred extrapolation, dose-aware)",
                 desc="The area under the concentration time curve in the interval extrapolating from Tlast to infinity with the triangle from Tlast to the next point and zero thereafter (matching AUCall) with dose-aware interpolation/extrapolation of concentrations",
                 formalsmap=list(conc="conc.group", time="time.group", time.dose="time.dose.group"),
                 depends=c("lambda.z", "clast.pred"))
PKNCA.set.summary(
  name="aucint.inf.pred.dose",
  description="geometric mean and geometric coefficient of variation",
  point=business.geomean,
  spread=business.geocv
)