R/make_der.R

In eghuang/synergy: Tools for Synergy/Antagonism Modeling

#' @title Makes a dose effect relationship function for a specified dataset.
#'
#' @description Outputs a dose effect relationship (DER) for a single ion
#'              with parameters dose and LET. The ion may be a low-LET or HZE
#'              ion and non-targeted effects may be specified.
#'
#' @param data Data.frame of single ion data.
#' @param phi Numeric constant
#' @param y_0 Numeric constant corresponding to background effect
#' @param HZE Boolean for presence of HZE ions
#' @param NTE Boolean for presence of non-targeted effects
#'
#'
#' @details data must have a numeric column "dose" and a numeric weight column
#'          "NWeight". If a paper uses dose in Gy care is needed in preceding
#'          and following lines to rescale from cGy.
#'
#' @return Function
#'
#' @examples
#' ion_data <- load_ion_data("one_ion.csv")
#'
#' LLET_der    <- make_der(ion_data, FALSE)
#' HZE_nte_der <- make_der(ion_data, TRUE, TRUE)
#' HZE_te_der  <- make_der(ion_data, TRUE, FALSE)
#'
#' @author Edward Greg Huang <eghuang@@berkeley.edu>
#' @export

make_der <- function(data, HZE, NTE = TRUE, phi = 2000, y_0 = 0.046404) {
  # Error handling in make_model
  model      <- make_model(data, HZE, NTE, phi, y_0)
  model_coef <- coef(model)

  # Swift light ================================================================
  if (!HZE) {
    # Calibrated Low LET model. Use L = 0, but maybe later will use small L > 0.
    DER <- function(dose, LET, coeff = model_coef) {
      return(1 - exp( - coeff * dose))
    }

  # HZE models =================================================================
  } else {

    if (NTE) { # HZE NTE -------------------------------------------------------
      # Calibrated hazard function.
      HZE_NTE_hazard_func <- function(dose, LET, coeff) {
        return(coeff[1] * LET * dose * exp( - coeff[2] * LET)
               + (1 - exp( - phi * dose)) * coeff[3])
      }
      # Calibrated HZE NTE DER.
      DER <- function(dose, LET, coeff = model_coef) {
        return(1 - exp( - HZE_NTE_hazard_func(dose, LET, coeff)))
      }

    } else if (!NTE) { # HZE TE ------------------------------------------------
      # Calibrated hazard function.
      HZE_TE_hazard_func <- function(dose, LET, coeff) {
        return(coeff[1] * LET * dose * exp( - coeff[2] * LET))
      }
      # Calibrated HZE TE one-ion DER.
      DER <- function(dose, LET, coeff = model_coef) {
        return(1 - exp( - HZE_TE_hazard_func(dose, LET, coeff)))
      }
    }
  }
  print(summary(model, correlation = TRUE))
  return(DER)
}


# Hidden functions =============================================================

.low_LET_slope <- function(dose, LET) { # Slope dE/dd of the low LET, low Z model.
  return(low_LET_model_coef * exp( - low_LET_model_coef * dose))
}

.HZE_NTE_slope <- function(dose, LET, alpha = 0.0000830213,
                                      beta = 0.0035474792,
                                      eta = 0.0314282300,
                                      phi = 2000) {
  return(
    (alpha * LET * exp(- beta * LET) + phi *
       eta * exp(- phi * dose)) *
         exp(- alpha * dose * LET * exp(- beta * LET) -
             eta * (1 - exp(- dose * phi)))
  )
}

.HZE_TE_slope <- function(dose, aa, pars = NULL) {
  return(aa * exp(- aa * dose))
}