R/kinfitr_SUV.R

In mathesong/kinfitr: Kinetic Modelling of PET Time Activity Curves

#' Standardised Uptake Value
#'
#' Function to calculate the standardised uptake value and its integral.
#'
#' @param tac Numeric vector of radioactivity concentrations in the target tissue for each frame. We include zero at time
#' zero: if not included, it is added.
#' @param t_tac Numeric vector of times for each frame in minutes. We use the time halfway through the frame as well as a
#' zero. If a time zero frame is not included, it will be added.
#' @param dur_tac Numeric vector of durations for each frame in minutes. This will be used instead of the middle points of the frames if provided.
#' @param injRad The injected radioactivity.  If not included, this will be set to 1 in case one is using SUV ratios.
#' @param bodymass The body mass of the participant. If not included, this will be set to 1 in case one is using SUV ratios.
#' @param frameStartEnd Optional: This allows one to specify the beginning and final frame to use for modelling, e.g. c(1,20).
#' This is to assess time stability.
#'
#' @return A list with a data frame of the calculated parameters \code{out$par} and a dataframe containing the TACs both of the
#' original data and the transformed values \code{out$tacs}
#'
#' @examples
#' data(pbr28)
#'
#' t_tac <- pbr28$tacs[[2]]$Times / 60
#' dur_tac <- pbr28$tacs[[2]]$Duration / 60
#' tac <- pbr28$tacs[[2]]$FC
#'
#'
#' fit1 <- SUV(tac, t_tac, injRad = 150, bodymass = 85)
#' fit2 <- SUV(tac, dur_tac = dur_tac, injRad = 150, bodymass = 85)
#' @author Granville J Matheson, \email{mathesong@@gmail.com}
#'
#' @export

SUV <- function(tac, t_tac = NULL, dur_tac = NULL, injRad = 1, bodymass = 1, frameStartEnd = NULL) {

  # Tidying

  if (is.null(dur_tac)) {
    tidyinput <- tidyinput_art(t_tac, tac, tac,
                               frameStartEnd) # Don't need weights, thus just set to same as tac
    t_tac <- tidyinput$t_tac
  } else {
    tidyinput <- tidyinput_art(dur_tac, tac, tac,
                               frameStartEnd) # Don't need weights, thus just set to same as tac
    dur_tac <- tidyinput$t_tac
  }


  tac <- tidyinput$tac


  # 'Model'

  denominator <- injRad / bodymass

  if (is.null(dur_tac)) {
    intSUV <- pracma::trapz(t_tac, tac) / denominator
  } else {
    intSUV <- sum((tac * dur_tac) / denominator)
  }

  suvtac <- tac / denominator


  # Output

  par <- as.data.frame(list(intSUV = intSUV))

  tacs <- data.frame(Target = tac, SUV = suvtac)

  if (is.null(dur_tac)) {
    tacs$Duration <- NA
  } else {
    tacs$Duration <- dur_tac
  }


  if (is.null(t_tac)) {
    tacs$Time <- NA
  } else {
    tacs$Time <- t_tac
  }

  out <- list(par = par, tacs = tacs)

  return(out)
}