R/dose.survival.R

In dcnorris/DTAT: Dose Titration Algorithm Tuning: a framework for dose individualization

# Construct a Surv object from a dose-escalation experiment,
# using interval-censoring constructs a la type='interval2'


#' Extract interval-censored dose tolerance data from a dose titration study
#' 
#' Extract interval-censored dose tolerance data from a dose titration study
#' 
#' 
#' @param de A data frame describing a dose-titration study
#' @return A \code{Surv} object of type='interval2'
#' @author David C. Norris
#' @seealso \code{\link{dose.survfit}}
#' @keywords survival
#' @importFrom stats aggregate
#' @importFrom dplyr full_join
#' @export
dose.survival <- function(de){
  suppressMessages({
    L <- stats::aggregate(dose ~ id, data=de, FUN=max, subset=!de$dlt)
    names(L)[2] <- 'doseL'
    suppressWarnings({ # expect min() to yield Inf often below
      R <- stats::aggregate(dose ~ id, data=de, FUN=min, subset=de$dlt)
      names(R)[2] <- 'doseR'
    })
    ds <- dplyr::full_join(L, R)
  })
  ds$doseL[is.na(ds$doseL)] <- 0
  ds$doseR[is.na(ds$doseR)] <- Inf
  ds <- ds[order(ds$id),]
  # Compute the Surv object from ds data frame with cols (id, doseL, doseR)
  S <- with(ds, Surv(time=doseL, time2=doseR, type='interval2'))
  S
}