R/calc_egfr.R
In ronkeizer/clinPK: Clinical Pharmacokinetics Toolkit
#' Calculate eGFR
#'
#' Calculate the estimated glomerulal filtration rate (an estimate of renal function) based on measured serum creatinine using one of the following approaches:
#' - Cockcroft-Gault (using weight, ideal body weight, or adjusted body weight)
#' - Revised Lund-Malmo
#' - Modification of Diet in Renal Disease study (MDRD)
#' - Schwartz
#' - Schwartz revised
#' - Jelliffe
#' - Jelliffe (for unstable renal function)
#' - Wright
#'
#' Equations for estimation of eGFR from Cystatin C concentrations are available from the `calc_egfr_cystatin()` function.
#'
#' @param method eGFR estimation method, choose from `cockcroft_gault`, `cockcroft_gault_ideal`, `mdrd`, `ckd_epi`, malmo_lund_revised`, `schwartz`, `jelliffe`, `jellife_unstable`, `wright`
#' @param sex sex
#' @param age age
#' @param scr serum creatinine (mg/dL)
#' @param scr_unit, `mg/dL` or `micromol/L` (==`umol/L`)
#' @param scr_assay, `jaffe` or `enzymatic` or `idms`
#' @param race `black` or `other`
#' @param weight weight
#' @param height height, only relevant when converting to/from BSA-relative unit
#' @param bsa body surface area
#' @param bsa_method BSA estimation method, see `bsa()` for details
#' @param times vector of sampling times for creatinine (only used in Jelliffe equation for unstable patients)
#' @param ckd chronic kidney disease? (Schwartz equations only)
#' @param relative `TRUE`/`FALSE`. Report eGFR as per 1.73 m2? Requires BSA if re-calculation required. If `NULL` (=default), will choose value typical for `method`.
#' @param unit_out `ml/min` (default), `L/hr`, or `mL/hr`
#' @param preterm is patient preterm?
#' @param ... arguments passed on
#' @examples
#' calc_egfr(sex = "male", age = 50, scr = 1.1, weight = 70)
#' calc_egfr(sex = "male", age = 50, scr = 1.1, weight = 70, unit_out = "L/hr")
#' calc_egfr(sex = "male", age = 50, scr = 1.1, weight = 70, bsa = 1.8, method = "ckd_epi")
#' calc_egfr(sex = "male", age = 50, scr = c(1.1, 0.8),
#' weight = 70, height = 170, method = "jelliffe")
#' calc_egfr(sex = "male", age = 50, scr = c(1.1, 0.8),
#' weight = 70, height = 170, method = "jelliffe_unstable")
#' calc_egfr(sex = "male", age = 50, scr = 1.1,
#' weight = 70, bsa = 1.6, method = "malmo_lund_rev", relative = FALSE)
#' @export
calc_egfr <- function (
method = "cockcroft_gault",
sex = NULL,
age = NULL,
scr = NULL,
scr_unit = NULL,
scr_assay = NULL,
race = "other",
weight = NULL,
height = NULL,
bsa = NULL,
preterm = FALSE,
ckd = FALSE,
times = NULL,
bsa_method = "dubois",
relative = NULL,
unit_out = "mL/min",
...
) {
method <- gsub("-", "_", tolower(method))
method <- gsub("cockroft", "cockcroft", tolower(method)) # legacy support for typo
available_methods <- c(
"cockcroft_gault", "cockcroft_gault_ideal", "cockcroft_gault_adjusted",
"malmo_lund_revised", "malmo_lund_rev", "lund_malmo_revised", "lund_malmo_rev",
"mdrd", "ckd_epi", "schwartz", "schwartz_revised", "jelliffe", "jelliffe_unstable",
"wright")
if(!method %in% available_methods) {
stop(paste0("Sorry, eGFR calculation method not recognized! Please choose from: ", paste0(available_methods, collapse=" ")))
}
if(!is.null(scr_unit)) {
scr_units_allowed <- c("mg/dl", "micromol/l", "mumol/l", "umol/l")
if(!all(tolower(scr_unit) %in% scr_units_allowed)) {
stop("Sorry, specified serum Cr unit not recognized!")
}
}
if(method == "cockcroft_gault_ideal") {
if(is.nil(height) || is.nil(sex) || is.nil(weight) || is.nil(age)) {
stop("Cockcroft-Gault using ideal body weight requires: scr, sex, weight, height, and age as input!")
}
weight <- calc_ibw(height = height, age = age, sex = sex) # recalculate wt to ibw
}
if(method == "cockcroft_gault_adjusted") {
if(is.nil(height) || is.nil(sex) || is.nil(weight) || is.nil(age)) {
stop("Cockcroft-Gault using adjusted body weight requires: scr, sex, weight, height, and age as input!")
}
ibw <- calc_ibw(weight = weight, height = height, age = age, sex = sex)
weight <- calc_abw(weight = weight, ibw = ibw, ...) # recalculate wt to abw, potentially specify factor
}
if(is.null(scr_assay)) {
scr_assay <- "jaffe"
if(method == "schwartz_revised") {
scr_assay <- "idms"
}
message("Creatinine assay not specified, assuming ", scr_assay, ".")
}
if(is.null(scr_unit)) {
message("Creatinine unit not specified, assuming mg/dL.")
scr_unit <- "mg/dl"
}
if(!is.nil(sex)) {
sex <- tolower(sex)
}
if(is.nil(scr)) {
stop("Serum creatinine value required!")
}
if(is.nil(relative)) {
relative <- TRUE # most equations report in /1.73m2
if(method == "cockcroft_gault") { # except CG
relative <- FALSE
}
}
if(!is.nil(weight) && !is.nil(height)) {
if(is.nil(bsa)) {
bsa <- calc_bsa(weight, height, "dubois")$value
}
}
unit_out <- tolower(unit_out)
scr_unit <- gsub("%2F", "/", scr_unit)
unit_out <- gsub("%2F", "/", unit_out)
if(length(scr_unit) == 1 && length(scr) > 1) {
scr_unit <- rep(scr_unit, length(scr))
}
if(method %in% available_methods) {
crcl <- c()
unit <- unit_out
for (i in 1:length(scr)) {
if(method == "wright") {
if(is.nil(scr[i]) || is.nil(sex) || is.nil(age) || is.nil(bsa)) {
stop("Wright equation requires: scr, sex, bsa (or weight and height), and age as input!")
}
if(tolower(scr_unit[i]) == "mg/dl") {
scr[i] <- scr[i] * 88.40
}
crcl[i] = ((6580 - (38.8 * age)) * bsa * (1-(0.168*ifelse(sex == "male", 0, 1))))/scr[i]
}
if(method == "jelliffe") {
if(is.nil(scr[i]) || is.nil(sex) || is.nil(age) || is.nil(bsa)) {
stop("Jelliffe equation requires: scr, sex, bsa (or weight and height), and age as input!")
}
if(tolower(scr_unit[i]) == "mg/dl") {
scr[i] <- scr[i] * 88.40
}
crcl[i] = ((98 - 0.8*(age - 20)) * (1 - 0.01 * ifelse(sex == "male", 0, 1)) * bsa/1.73) / (scr[i]*0.0113)
}
if(method == "jelliffe_unstable") {
if(is.nil(scr[i]) || is.nil(sex) || is.nil(age) || is.nil(weight)) {
stop("Jelliffe equation requires: scr, sex, weight, and age as input!")
}
if(tolower(scr_unit[i]) %in% c("umol/l", "mumol/l", "micromol/l")) {
scr[i] <- scr[i] / 88.40
}
vol <- 0.4 * weight * 10
ifelse(sex == "male", 0.85, 0.765)
corr <- 0.85
if(sex == "female") { corr <- 0.765 }
scr1 <- scr[i]
scr2 <- scr[i]
if(i > 1) {
scr1 <- scr[i-1]
}
scr_av <- mean(c(scr1,scr2))
if(is.null(times)) {
dt <- 1 # assume 1 day difference
} else {
if(i > 1) {
dt <- times[i] - times[i-1]
if(dt <= 0) {
dt <- 1
}
} else {
dt <- 1 # doesn't matter, for first obs we're not looking at a previous sample anyhow
}
}
cr_prod <- (29.305-(0.203*age)) * weight * (1.037-(0.0338 * scr_av)) * ifelse(sex == "male", 0.85, 0.765)
crcl[i] <- ((vol * (scr1 - scr2)/dt + cr_prod) * 100) / (1440 * scr_av)
}
if(method == "mdrd") {
if(is.nil(scr[i]) || is.nil(sex) || is.nil(race) || is.nil(age)) {
stop("MDRD equation requires: scr, sex, race, and age as input!")
}
if(tolower(scr_unit[i]) %in% c("umol/l", "mumol/l", "micromol/l")) {
scr[i] <- scr[i] / 88.40
}
f_sex <- 1
f_race <- 1
if (sex == "female") { f_sex <- 0.762 }
if (race == "black") { f_race <- 1.210 }
crcl[i] <- 186 * scr[i]^(-1.154) * f_sex * f_race * age^(-0.203)
if(!relative) {
if(is.nil(bsa)) {
stop("Error: bsa not specified, or weight and height not specified! Can't convert between absolute and relative eGFR!")
} else {
crcl[i] <- crcl[i] * (bsa/1.73)
unit <- unit
}
} else {
unit <- paste0(unit_out, "/1.73m^2")
}
}
if(method == "ckd_epi") {
if(is.nil(scr[i]) || is.nil(sex) || is.nil(race) || is.nil(age)) {
stop("MDRD equation requires: scr, sex, race, and age as input!")
}
if(tolower(scr_unit[i]) %in% c("umol/l", "mumol/l", "micromol/l")) {
scr[i] <- scr[i] / 88.40
}
f_sex <- 1
f_race <- 1
if (sex == "female") { f_sex <- 1.018 }
if (race == "black") { f_race <- 1.159 }
crcl[i] <- 141 * min(scr[i], 1)^(-0.329) * max(scr[i], 1)^(-1.209) * 0.993^age * f_sex * f_race
if(!relative) {
if(is.nil(bsa)) {
stop("Error: bsa not specified, or weight and height not specified! Can't convert between absolute and relative eGFR!")
} else {
crcl[i] <- crcl[i] * (bsa/1.73)
unit <- unit
}
} else {
unit <- paste0(unit_out, "/1.73m^2")
}
}
if(method %in% c("cockcroft_gault", "cockcroft_gault_ideal", "cockcroft_gault_adjusted")) {
if(is.nil(scr[i]) || is.nil(sex) || is.nil(weight) || is.nil(age)) {
stop("cockcroft-Gault equation requires: scr, sex, weight, and age as input!")
}
if(tolower(scr_unit[i]) %in% c("umol/l", "mumol/l", "micromol/l")) {
scr[i] <- scr[i] / 88.40
}
f_sex <- 1
if (sex == "female") {
f_sex <- 0.85
}
crcl[i] <- f_sex * (140-age) / scr[i] * (weight/72)
if(relative) {
if(is.nil(bsa)) {
stop("Error: bsa not specified, or weight and height not specified! Can't convert between absolute and relative eGFR!")
} else {
crcl[i] <- crcl[i] / (bsa/1.73)
unit <- paste0(unit_out, "/1.73m^2")
}
}
}
if(method == "malmo_lund_revised" || method == "lund_malmo_revised" || method == "lund_malmo_rev" || method == "malmo_lund_rev") {
if(is.nil(scr) || is.nil(sex) || is.nil(age)) {
stop("Revised Lund-Malmo equation requires: scr, sex, and age as input!")
}
if(tolower(scr_unit[i]) == "mg/dl") {
scr[i] <- scr[i] * 88.40
}
if(sex == "female") {
if(scr[i] < 150) {
x <- 2.50 + 0.0121 * (150-scr[i])
} else {
x <- 2.50 - 0.926 * log(scr[i]/150)
}
} else { # male
if(scr[i] < 180) {
x <- 2.56 + 0.00968 * (180-scr[i])
} else {
x <- 2.56 - 0.926 * log(scr[i]/150)
}
}
crcl[i] <- exp(x - 0.0158*age + 0.438*log(age))
if(!relative) {
if(is.nil(bsa)) {
stop("Error: bsa not specified, or weight and height not specified! Can't convert between absolute and relative eGFR!")
} else {
crcl[i] <- crcl[i] * (bsa/1.73)
}
} else {
unit <- paste0(unit_out, "/1.73m^2")
}
}
if(method == "schwartz" || method == "schwartz_revised") {
if(is.nil(scr[i]) || is.nil(age) || is.nil(sex) || is.nil(height) || is.nil(preterm)) {
stop("Schwartz equation requires: scr, sex, height, preterm, and age as input!")
}
if(tolower(scr_unit[i]) %in% c("umol/l", "mumol/l", "micromol/l")) {
scr[i] <- scr[i] / 88.40
}
if(method == "schwartz") {
scr[i] <- convert_creat_assay(scr[i], from = scr_assay, to = "jaffe")
}
if(method == "schwartz_revised") {
scr[i] <- convert_creat_assay(scr[i], from = scr_assay, to = "idms")
}
if(method == "schwartz_revised") {
k <- 0.413
} else {
k <- 0.55
if (age < 1) {
k <- 0.45
if(age < (40/52)) {
k <- 0.33
}
} else {
if(sex == "male") {
k <- 0.7
}
if(ckd) {
k <- 0.413
}
}
}
crcl[i] <- (k * height) / scr
if(!relative) {
if(is.nil(bsa)) {
stop("Error: bsa not specified, or weight and height not specified! Can't convert between absolute and relative eGFR!")
} else {
crcl[i] <- crcl[i] * (bsa/1.73)
message("eGFR from Schwartz commonly reported as relative to 1.73m^2 BSA. Consider using 'relative=TRUE' argument.")
}
} else {
unit <- paste0(unit_out, "/1.73m^2")
}
}
if (length(grep("^l/hr", tolower(unit_out))) > 0) {
crcl[i] <- crcl[i] * 60 / 1000
}
if (length(grep("^ml/hr", tolower(unit_out))) > 0) {
crcl[i] <- crcl[i] * 60
}
}
return(list(
value = crcl,
unit = unit
))
} else {
return(FALSE)
}
}
ronkeizer/clinPK documentation built on May 20, 2019, 5:07 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
#' Calculate eGFR
#'
#' Calculate the estimated glomerulal filtration rate (an estimate of renal function) based on measured serum creatinine using one of the following approaches:
#' - Cockcroft-Gault (using weight, ideal body weight, or adjusted body weight)
#' - Revised Lund-Malmo
#' - Modification of Diet in Renal Disease study (MDRD)
#' - Schwartz
#' - Schwartz revised
#' - Jelliffe
#' - Jelliffe (for unstable renal function)
#' - Wright
#'
#' Equations for estimation of eGFR from Cystatin C concentrations are available from the `calc_egfr_cystatin()` function.
#'
#' @param method eGFR estimation method, choose from `cockcroft_gault`, `cockcroft_gault_ideal`, `mdrd`, `ckd_epi`, malmo_lund_revised`, `schwartz`, `jelliffe`, `jellife_unstable`, `wright`
#' @param sex sex
#' @param age age
#' @param scr serum creatinine (mg/dL)
#' @param scr_unit, `mg/dL` or `micromol/L` (==`umol/L`)
#' @param scr_assay, `jaffe` or `enzymatic` or `idms`
#' @param race `black` or `other`
#' @param weight weight
#' @param height height, only relevant when converting to/from BSA-relative unit
#' @param bsa body surface area
#' @param bsa_method BSA estimation method, see `bsa()` for details
#' @param times vector of sampling times for creatinine (only used in Jelliffe equation for unstable patients)
#' @param ckd chronic kidney disease? (Schwartz equations only)
#' @param relative `TRUE`/`FALSE`. Report eGFR as per 1.73 m2? Requires BSA if re-calculation required. If `NULL` (=default), will choose value typical for `method`.
#' @param unit_out `ml/min` (default), `L/hr`, or `mL/hr`
#' @param preterm is patient preterm?
#' @param ... arguments passed on
#' @examples
#' calc_egfr(sex = "male", age = 50, scr = 1.1, weight = 70)
#' calc_egfr(sex = "male", age = 50, scr = 1.1, weight = 70, unit_out = "L/hr")
#' calc_egfr(sex = "male", age = 50, scr = 1.1, weight = 70, bsa = 1.8, method = "ckd_epi")
#' calc_egfr(sex = "male", age = 50, scr = c(1.1, 0.8),
#' weight = 70, height = 170, method = "jelliffe")
#' calc_egfr(sex = "male", age = 50, scr = c(1.1, 0.8),
#' weight = 70, height = 170, method = "jelliffe_unstable")
#' calc_egfr(sex = "male", age = 50, scr = 1.1,
#' weight = 70, bsa = 1.6, method = "malmo_lund_rev", relative = FALSE)
#' @export
calc_egfr <- function (
method = "cockcroft_gault",
sex = NULL,
age = NULL,
scr = NULL,
scr_unit = NULL,
scr_assay = NULL,
race = "other",
weight = NULL,
height = NULL,
bsa = NULL,
preterm = FALSE,
ckd = FALSE,
times = NULL,
bsa_method = "dubois",
relative = NULL,
unit_out = "mL/min",
...
) {
method <- gsub("-", "_", tolower(method))
method <- gsub("cockroft", "cockcroft", tolower(method)) # legacy support for typo
available_methods <- c(
"cockcroft_gault", "cockcroft_gault_ideal", "cockcroft_gault_adjusted",
"malmo_lund_revised", "malmo_lund_rev", "lund_malmo_revised", "lund_malmo_rev",
"mdrd", "ckd_epi", "schwartz", "schwartz_revised", "jelliffe", "jelliffe_unstable",
"wright")
if(!method %in% available_methods) {
stop(paste0("Sorry, eGFR calculation method not recognized! Please choose from: ", paste0(available_methods, collapse=" ")))
}
if(!is.null(scr_unit)) {
scr_units_allowed <- c("mg/dl", "micromol/l", "mumol/l", "umol/l")
if(!all(tolower(scr_unit) %in% scr_units_allowed)) {
stop("Sorry, specified serum Cr unit not recognized!")
}
}
if(method == "cockcroft_gault_ideal") {
if(is.nil(height) || is.nil(sex) || is.nil(weight) || is.nil(age)) {
stop("Cockcroft-Gault using ideal body weight requires: scr, sex, weight, height, and age as input!")
}
weight <- calc_ibw(height = height, age = age, sex = sex) # recalculate wt to ibw
}
if(method == "cockcroft_gault_adjusted") {
if(is.nil(height) || is.nil(sex) || is.nil(weight) || is.nil(age)) {
stop("Cockcroft-Gault using adjusted body weight requires: scr, sex, weight, height, and age as input!")
}
ibw <- calc_ibw(weight = weight, height = height, age = age, sex = sex)
weight <- calc_abw(weight = weight, ibw = ibw, ...) # recalculate wt to abw, potentially specify factor
}
if(is.null(scr_assay)) {
scr_assay <- "jaffe"
if(method == "schwartz_revised") {
scr_assay <- "idms"
}
message("Creatinine assay not specified, assuming ", scr_assay, ".")
}
if(is.null(scr_unit)) {
message("Creatinine unit not specified, assuming mg/dL.")
scr_unit <- "mg/dl"
}
if(!is.nil(sex)) {
sex <- tolower(sex)
}
if(is.nil(scr)) {
stop("Serum creatinine value required!")
}
if(is.nil(relative)) {
relative <- TRUE # most equations report in /1.73m2
if(method == "cockcroft_gault") { # except CG
relative <- FALSE
}
}
if(!is.nil(weight) && !is.nil(height)) {
if(is.nil(bsa)) {
bsa <- calc_bsa(weight, height, "dubois")$value
}
}
unit_out <- tolower(unit_out)
scr_unit <- gsub("%2F", "/", scr_unit)
unit_out <- gsub("%2F", "/", unit_out)
if(length(scr_unit) == 1 && length(scr) > 1) {
scr_unit <- rep(scr_unit, length(scr))
}
if(method %in% available_methods) {
crcl <- c()
unit <- unit_out
for (i in 1:length(scr)) {
if(method == "wright") {
if(is.nil(scr[i]) || is.nil(sex) || is.nil(age) || is.nil(bsa)) {
stop("Wright equation requires: scr, sex, bsa (or weight and height), and age as input!")
}
if(tolower(scr_unit[i]) == "mg/dl") {
scr[i] <- scr[i] * 88.40
}
crcl[i] = ((6580 - (38.8 * age)) * bsa * (1-(0.168*ifelse(sex == "male", 0, 1))))/scr[i]
}
if(method == "jelliffe") {
if(is.nil(scr[i]) || is.nil(sex) || is.nil(age) || is.nil(bsa)) {
stop("Jelliffe equation requires: scr, sex, bsa (or weight and height), and age as input!")
}
if(tolower(scr_unit[i]) == "mg/dl") {
scr[i] <- scr[i] * 88.40
}
crcl[i] = ((98 - 0.8*(age - 20)) * (1 - 0.01 * ifelse(sex == "male", 0, 1)) * bsa/1.73) / (scr[i]*0.0113)
}
if(method == "jelliffe_unstable") {
if(is.nil(scr[i]) || is.nil(sex) || is.nil(age) || is.nil(weight)) {
stop("Jelliffe equation requires: scr, sex, weight, and age as input!")
}
if(tolower(scr_unit[i]) %in% c("umol/l", "mumol/l", "micromol/l")) {
scr[i] <- scr[i] / 88.40
}
vol <- 0.4 * weight * 10
ifelse(sex == "male", 0.85, 0.765)
corr <- 0.85
if(sex == "female") { corr <- 0.765 }
scr1 <- scr[i]
scr2 <- scr[i]
if(i > 1) {
scr1 <- scr[i-1]
}
scr_av <- mean(c(scr1,scr2))
if(is.null(times)) {
dt <- 1 # assume 1 day difference
} else {
if(i > 1) {
dt <- times[i] - times[i-1]
if(dt <= 0) {
dt <- 1
}
} else {
dt <- 1 # doesn't matter, for first obs we're not looking at a previous sample anyhow
}
}
cr_prod <- (29.305-(0.203*age)) * weight * (1.037-(0.0338 * scr_av)) * ifelse(sex == "male", 0.85, 0.765)
crcl[i] <- ((vol * (scr1 - scr2)/dt + cr_prod) * 100) / (1440 * scr_av)
}
if(method == "mdrd") {
if(is.nil(scr[i]) || is.nil(sex) || is.nil(race) || is.nil(age)) {
stop("MDRD equation requires: scr, sex, race, and age as input!")
}
if(tolower(scr_unit[i]) %in% c("umol/l", "mumol/l", "micromol/l")) {
scr[i] <- scr[i] / 88.40
}
f_sex <- 1
f_race <- 1
if (sex == "female") { f_sex <- 0.762 }
if (race == "black") { f_race <- 1.210 }
crcl[i] <- 186 * scr[i]^(-1.154) * f_sex * f_race * age^(-0.203)
if(!relative) {
if(is.nil(bsa)) {
stop("Error: bsa not specified, or weight and height not specified! Can't convert between absolute and relative eGFR!")
} else {
crcl[i] <- crcl[i] * (bsa/1.73)
unit <- unit
}
} else {
unit <- paste0(unit_out, "/1.73m^2")
}
}
if(method == "ckd_epi") {
if(is.nil(scr[i]) || is.nil(sex) || is.nil(race) || is.nil(age)) {
stop("MDRD equation requires: scr, sex, race, and age as input!")
}
if(tolower(scr_unit[i]) %in% c("umol/l", "mumol/l", "micromol/l")) {
scr[i] <- scr[i] / 88.40
}
f_sex <- 1
f_race <- 1
if (sex == "female") { f_sex <- 1.018 }
if (race == "black") { f_race <- 1.159 }
crcl[i] <- 141 * min(scr[i], 1)^(-0.329) * max(scr[i], 1)^(-1.209) * 0.993^age * f_sex * f_race
if(!relative) {
if(is.nil(bsa)) {
stop("Error: bsa not specified, or weight and height not specified! Can't convert between absolute and relative eGFR!")
} else {
crcl[i] <- crcl[i] * (bsa/1.73)
unit <- unit
}
} else {
unit <- paste0(unit_out, "/1.73m^2")
}
}
if(method %in% c("cockcroft_gault", "cockcroft_gault_ideal", "cockcroft_gault_adjusted")) {
if(is.nil(scr[i]) || is.nil(sex) || is.nil(weight) || is.nil(age)) {
stop("cockcroft-Gault equation requires: scr, sex, weight, and age as input!")
}
if(tolower(scr_unit[i]) %in% c("umol/l", "mumol/l", "micromol/l")) {
scr[i] <- scr[i] / 88.40
}
f_sex <- 1
if (sex == "female") {
f_sex <- 0.85
}
crcl[i] <- f_sex * (140-age) / scr[i] * (weight/72)
if(relative) {
if(is.nil(bsa)) {
stop("Error: bsa not specified, or weight and height not specified! Can't convert between absolute and relative eGFR!")
} else {
crcl[i] <- crcl[i] / (bsa/1.73)
unit <- paste0(unit_out, "/1.73m^2")
}
}
}
if(method == "malmo_lund_revised" || method == "lund_malmo_revised" || method == "lund_malmo_rev" || method == "malmo_lund_rev") {
if(is.nil(scr) || is.nil(sex) || is.nil(age)) {
stop("Revised Lund-Malmo equation requires: scr, sex, and age as input!")
}
if(tolower(scr_unit[i]) == "mg/dl") {
scr[i] <- scr[i] * 88.40
}
if(sex == "female") {
if(scr[i] < 150) {
x <- 2.50 + 0.0121 * (150-scr[i])
} else {
x <- 2.50 - 0.926 * log(scr[i]/150)
}
} else { # male
if(scr[i] < 180) {
x <- 2.56 + 0.00968 * (180-scr[i])
} else {
x <- 2.56 - 0.926 * log(scr[i]/150)
}
}
crcl[i] <- exp(x - 0.0158*age + 0.438*log(age))
if(!relative) {
if(is.nil(bsa)) {
stop("Error: bsa not specified, or weight and height not specified! Can't convert between absolute and relative eGFR!")
} else {
crcl[i] <- crcl[i] * (bsa/1.73)
}
} else {
unit <- paste0(unit_out, "/1.73m^2")
}
}
if(method == "schwartz" || method == "schwartz_revised") {
if(is.nil(scr[i]) || is.nil(age) || is.nil(sex) || is.nil(height) || is.nil(preterm)) {
stop("Schwartz equation requires: scr, sex, height, preterm, and age as input!")
}
if(tolower(scr_unit[i]) %in% c("umol/l", "mumol/l", "micromol/l")) {
scr[i] <- scr[i] / 88.40
}
if(method == "schwartz") {
scr[i] <- convert_creat_assay(scr[i], from = scr_assay, to = "jaffe")
}
if(method == "schwartz_revised") {
scr[i] <- convert_creat_assay(scr[i], from = scr_assay, to = "idms")
}
if(method == "schwartz_revised") {
k <- 0.413
} else {
k <- 0.55
if (age < 1) {
k <- 0.45
if(age < (40/52)) {
k <- 0.33
}
} else {
if(sex == "male") {
k <- 0.7
}
if(ckd) {
k <- 0.413
}
}
}
crcl[i] <- (k * height) / scr
if(!relative) {
if(is.nil(bsa)) {
stop("Error: bsa not specified, or weight and height not specified! Can't convert between absolute and relative eGFR!")
} else {
crcl[i] <- crcl[i] * (bsa/1.73)
message("eGFR from Schwartz commonly reported as relative to 1.73m^2 BSA. Consider using 'relative=TRUE' argument.")
}
} else {
unit <- paste0(unit_out, "/1.73m^2")
}
}
if (length(grep("^l/hr", tolower(unit_out))) > 0) {
crcl[i] <- crcl[i] * 60 / 1000
}
if (length(grep("^ml/hr", tolower(unit_out))) > 0) {
crcl[i] <- crcl[i] * 60
}
}
return(list(
value = crcl,
unit = unit
))
} else {
return(FALSE)
}
}
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.