R/nankivell_walser.R

In transplantr: Audit and Research Functions for Transplantation

#' eGFR using Nankivell formula
#'
#' A vectorised function to calculate eGFR using the Nankivell formula. By default the equation accepts
#' serum creatinine in µmol/l but can be changed to mg/dl by setting the units parameter to "US".
#' The Urea parameter is serum urea in mmol/l, but if the units parameter is set to "US",
#' Blood Urea Nitrogen (BUN) in mg/dl is used instead. It has not been possible to run automated
#' tests to confirm the
#' accuracy of this function, so please use with caution.
#'
#' Reference: Nankivell BJ, Gruenwald SM, Allen RD, Chapman JR: Predicting glomerular filtration rate
#' after renal transplantation. Transplantation 1995; 59:1683-89.
#'
#' @param SCr numeric vector of serum creatinine in µmol/l (or mg/dl if units = "US")
#' @param Urea numeric vector of serum urea in mmol/l (or BUN in mg/dl if units = "US")
#' @param Weight numeric vector of patient weights in kilograms
#' @param Height numeric vector of patient heights in centimetres
#' @param Sex character vector of sex ("F" for female, "M" for male)
#' @param Units non-vectorised optional parameter for creatinine and urea/BUN units ("SI" for µmol/l (default), "US" for mg/dl)
#'
#' @return a numeric vector of eGFR values
#' @export
#'
#' @examples
#' nankivell(SCr = 118, Urea = 13.4, Weight = 65, Height = 172, Sex = "M") # 44.55
nankivell = function(SCr, Urea, Weight, Height, Sex, Units = "SI") {
  # convert creatinine to mg/dl and BUN to urea
  if (Units == "US") {
    SCr = SCr * 88.4
    Urea = bun_to_urea(Urea)
  }

  # conversion factor for Sex
  corr = ifelse(Sex == "M", 35, 25)

  6.7 / (SCr * 88.42) + 0.25 * Weight -0.5 * Urea -100 / Height ^ 2 + corr
}

#' eGFR using Nankivell formula (US units)
#'
#' A wrapper function for the nankivell() vectorised function to calculate eGFR using the Nankivell
#' formula, but using creatinine and BUN in mg/dl rather than international units. It has not been
#' possible to run automated tests to confirm the
#' accuracy of this function, so please use with caution.
#'
#' Reference: Nankivell BJ, Gruenwald SM, Allen RD, Chapman JR: Predicting glomerular filtration rate
#' after renal transplantation. Transplantation 1995; 59:1683-89.
#'
#' @param SCr numeric vector of serum creatinine in µmol/l (or mg/dl if units = "US")
#' @param Urea numeric vector of serum urea in mmol/l (or BUN in mg/dl if units = "US")
#' @param Weight numeric vector of patient weights in kilograms
#' @param Height numeric vector of patient heights in centimetres
#' @param Sex character vector of sex ("F" for female, "M" for male)
#'
#' @return a numeric vector of eGFR values
#' @export
#'
#' @examples
#' nankivell_US(SCr = 1.33, Urea = 13.4, Weight = 65, Height = 172, Sex = "M") # 44.55
nankivell_US = function(SCr, Urea, Weight, Height, Sex) {
  nankivell(SCr, Urea, Weight, Height, Sex, Units = "US")
}

#' eGFR using the Nankivell-SPK formula
#'
#' A vectorised function to calculate the eGFR using the Nankivell-SPK formula. By default the
#' equation accepts serum creatinine in µmol/l but can be changed to
#' mg/dl by setting the units parameter to "US". To allow for serial measurements over time, such as
#' for transplant follow-up data, there is an optional offset = n parameter which increases the age
#' value used in the equation by n years. It has not been possible to run automated tests to
#' confirm the
#' accuracy of this function, so please use with caution.
#'
#' Reference: Nankivell BJ, Chapman JR, Allen RD: Predicting glomerular filtration rate after
#' simultaneous pancreas and kidney transplantation. Clin Transplant 1995; 9(2): 129-134
#'
#' @param SCr numeric vector of serum creatinine in µmol/l (or mg/dl if units = "US")
#' @param Age numeric vector of patient ages in years
#' @param Sex character vector of sex ("F" for female, "M" for male)
#' @param Weight numeric vector of patient weights in kilograms
#' @param Height numeric vector of patient heights in centimetres
#' @param Units non-vectorised optional parameter for creatinine and urea/BUN units ("SI" for µmol/l (default), "US" for mg/dl)
#' @param Offset non-vectorised optional numeric parameter for offset in years
#'
#' @return numeric vector of eGFR values
#' @export
#'
#' @examples
#' nankivell_spk(SCr = 118, Age = 74, Sex = "M", Weight = 172, Height = 172) # 48.8
nankivell_spk = function(SCr, Age, Sex, Weight, Height, Units = "SI", Offset = 0) {
  # convert creatinine to umol/l
  if (Units == "US") {
    SCr = SCr * 88.4
  }

  # conversion factor for Sex
  corr = ifelse(Sex == "M", 71.4, 50.4)

  nvspkGFR = corr + 5520 / SCr + 0.27 * Weight -
            0.50 * Age - 0.29 * Height
  nvspkGFR
}

#' eGFR using the Nankivell-SPK formula (US units)
#'
#' A wrapper function for the nankivell_spk() vectorised function to calculate the eGFR
#' using the Nankivell-SPK formula using serum creatinine in mg/dl.
#' To allow for serial measurements over time, such as
#' for transplant follow-up data, there is an optional offset = n parameter which increases the age
#' value used in the equation by n years. It has not been possible to run automated tests
#' to confirm the
#' accuracy of this function, so please use with caution.
#'
#' Reference: Nankivell BJ, Chapman JR, Allen RD: Predicting glomerular filtration rate after
#' simultaneous pancreas and kidney transplantation. Clin Transplant 1995; 9(2): 129-134
#'
#' @param SCr numeric vector of serum creatinine in µmol/l (or mg/dl if units = "US")
#' @param Age numeric vector of patient ages in years
#' @param Sex character vector of sex ("F" for female, "M" for male)
#' @param Weight numeric vector of patient weights in kilograms
#' @param Height numeric vector of patient heights in metres
#' @param Offset non-vectorised optional numeric parameter for offset in years
#'
#' @return numeric vector of eGFR values
#' @export
#'
#' @examples
#' nankivell_spk_US(SCr = 1.33, Age = 74, Sex = "M", Weight = 172, Height = 172) # 49.0
nankivell_spk_US = function(SCr, Age, Sex, Weight, Height, Offset = 0) {
  nankivell_spk(SCr, Age, Sex, Weight, Height, Offset, Units = "US")
}

#' eGFR using the Walser formula
#'
#' A vectorised function to calculate eGFR using the Walser formula. By default the equation accepts
#' serum creatinine in µmol/l but can be changed to mg/dl by setting the units parameter to "US".
#' It has not been possible to run automated tests to confirm the
#' accuracy of this function, so please use with caution.
#'
#' Reference: Walser M, Drew HH, Guldan JL. Prediction of glomerular filtration rate in advanced
#' chronic renal failure. Kidney International 1993; 44:2245-1148.
#'
#' @param SCr numeric vector of serum creatinine in µmol/l (or mg/dl if units = "US")
#' @param Age numeric vector of patient ages in years
#' @param Weight numeric vector of patient weights in kilograms
#' @param Sex character vector of sex ("F" for female, "M" for male)
#' @param Units non-vectorised optional parameter for creatinine units ("SI" for µmol/l (default), "US" for mg/dl)
#'
#' @return numeric vectors of eGFR values
#' @export
#'
#' @examples
#' walser(SCr = 118, Age = 74, Weight = 65, Sex = "M") # 56.1
walser = function(SCr, Age, Weight, Sex, Units = "SI") {
  # convert creatinine from mg/dl
  if (Units == "SI") {
    SCr = SCr / 88.4
  }

  #correction factors
  walfage = ifelse(Sex == "M", -0.103, -0.08)
  walfem = ifelse(Sex == "M", 7.57, 6.05)
  walwt = ifelse(Sex == "M", 0.096, 0.08)
  walcorr = ifelse(Sex == "M", -6.66, -4.81)

  walfem / (SCr * 0.0884) + walfage * Age + walwt * Weight + walcorr
}

#' eGFR using the Walser formula (US units)
#'
#' A wrapper function for the walser() vectorised function to calculate eGFR using the Walser formula,
#' using serum creatinine in mg/dl. It has not been possible to run automated tests to confirm the
#' accuracy of this function, so please use with caution.
#'
#' Reference: Walser M, Drew HH, Guldan JL. Prediction of glomerular filtration rate in advanced
#' chronic renal failure. Kidney International 1993; 44:2245-1148.
#'
#' @param SCr numeric vector of serum creatinine in µmol/l (or mg/dl if units = "US")
#' @param Age numeric vector of patient ages in years
#' @param Weight numeric vector of patient weights in kilograms
#' @param Sex character vector of sex ("F" for female, "M" for male)
#'
#' @return numeric vectors of eGFR values
#' @export
#'
#' @examples
#' walser_US(SCr = 1.33, Age = 74, Weight = 65, Sex = "M") # 56.3
walser_US = function(SCr, Age, Weight, Sex) {
  walser(SCr, Age, Weight, Sex, Units = "US")
}