R/LifecoursePhysiology.R
In sahu27/sahu: Population Life Course Exposure to Health Effects Modeling
# Small utility function for linear interpolation
# Used internally
interp2 <- function(x1, x2, y1, y2, x)
{
m = (y2 - y1)/(x2 - x1)
y = y1 + m*(x - x1)
return(y)
}
#' Get volumes for tissues provided on the basis of age and gender
#'
#' @param age Age of the organism in years
#' @param gender The gender of the organism "M" for Male or "F" for Female
#' @param perf_frct fraction of perfused tissue. default to 0.85
#' @param tissues List of tissues for which the volumes are needed. The tissues can be one of the following
#' liver,
#' blood,
#' fat,
#' bone,
#' brain,
#' gonad,
#' heart,
#' intestine,
#' kidney,
#' lung,
#' pancreas,
#' skin,
#' spleen,
#' stomach,
#' thymus,
#' remaining,
#' muscle
#' @return
#' list containing volumes for age, gender and tissues.
#' @export
#'
getLifecourseTissueVolumes<- function(age = 25, gender = "M",perf_frct = 0.85,
tissues=list()){
tissue_vol_list <- NULL
available_tissues <- c("blood","fat","skin","muscle","bone","brain","lung",
"heart","gi","kidney","liver","rpf","spf")
spf_tissues <- c("fat","skin","muscle","bone")
rpf_tissues <- available_tissues[!(available_tissues %in% c(spf_tissues,"rpf","spf"))]
inactive_tissues <- dplyr::setdiff(available_tissues,tissues)
rpf_inactive_tissues <- inactive_tissues[inactive_tissues %in% rpf_tissues]
spf_inactive_tissues <- inactive_tissues[inactive_tissues %in% spf_tissues]
if(is.na(age)) return
tissue_vol_list[["gi"]]<-getLifecourseGutVolume(age,gender)
tissue_vol_list[["liver"]]<-getLifecourseLiverVolume(age,gender)
tissue_vol_list[["blood"]]<-getLifecourseBloodVolume(age,gender)
tissue_vol_list[["fat"]]<-getLifecourseAdiposeVolume(age,gender)
tissue_vol_list[["bone"]]<-getLifecourseBoneVolume(age,gender)
tissue_vol_list[["brain"]]<-getLifecourseBrainVolume(age,gender)
tissue_vol_list[["heart"]]<-getLifecourseHeartVolume(age,gender)
tissue_vol_list[["kidney"]]<-getLifecourseKidneyVolume(age,gender)
tissue_vol_list[["lung"]]<-getLifecourseLungVolume(age,gender)
tissue_vol_list[["skin"]]<-getLifecourseSkinVolume(age,gender)
tissue_vol_list[["muscle"]]<-getLifecourseMuscleVolume(age,gender)
# for richly perfused get value
#from equation and add inactive tissue volumes
vol <- getLifecourseRapidlyPerfusedVolume(age,gender)
rpf_inact_vol <- sum(tissue_vol_list[rpf_inactive_tissues])
tissue_vol_list[["rpf"]]<-vol+rpf_inact_vol
# for slowly perfused get value
#from equation and add inactive tissue volumes
vol <- getLifecourseSlowlyPerfusedVolume(age,gender,perf_frct)
spf_inact_vol <- sum(tissue_vol_list[spf_inactive_tissues])
tissue_vol_list[["spf"]]<-vol+spf_inact_vol
#print(tissue_vol_list[tissues])
return(tissue_vol_list[tissues])
}
#' Get perfusion for tissues provided on the basis of age and gender
#'
#' @param age Age of the organism in years
#' @param gender The gender of the organism "M" for Male or "F" for Female
#' @param source source of the equation. defaults to "sciv" for scitovation
#' @param tissues List of tissues for which blood perfusion is needed. The
#' tissues can be any of the following
#' liver,
#' fat,
#' bone,
#' brain,
#' gonad,
#' heart,
#' intestine,
#' kidney,
#' lung,
#' pancreas,
#' skin,
#' spleen,
#' stomach,
#' thymus,
#' muscle,
#' remaining.
#'
#' @return list containing blood perfusion of tissues for the given age and
#' gender.
#' @export
getLifecourseTissuePerfusion<- function(age = 25, gender = "M", tissues = list(),source = "sciv"){
if(is.na(age)) return(NA)
if (source == "sciv"){
#get scaling factor for cardiac output calculated as sum(qc) or from SCIV equation
qc_scaling <- 1
}else{
qc_scaling <- 1.164749
}
tissue_perf_list <- NULL
available_tissues <- c("fat","skin","muscle","bone","brain","lung",
"heart","gi","kidney","liver","rpf","spf")
spf_tissues <- c("fat","skin","muscle")
rpf_tissues <- available_tissues[!(available_tissues %in% c(spf_tissues,"rpf","spf"))]
inactive_tissues <- dplyr::setdiff(available_tissues,tissues)
rpf_inactive_tissues <- inactive_tissues[inactive_tissues %in% rpf_tissues]
spf_inactive_tissues <- inactive_tissues[inactive_tissues %in% spf_tissues]
if ("gi" %in% tissues){
tissue_perf_list[["gi"]] <- (getLifecourseGutPerfusion(age,gender)) * qc_scaling
tissue_perf_list[["liver_art"]]<- getLifecourseLiverArterialPerfusion(age,gender) * qc_scaling
tissue_perf_list[["liver_ven"]]<- (tissue_perf_list[["liver_art"]] +
tissue_perf_list[["gi"]])
}else{
tissue_perf_list[["liver_art"]]<- (getLifecourseLiverArterialPerfusion(age,gender)+
getLifecourseGutPerfusion(age,gender)) * qc_scaling
tissue_perf_list[["liver_ven"]]<- tissue_perf_list[["liver_art"]]
}
if (!("liver" %in% tissues)){
rpf_inactive_tissues <- c(inactive_tissues,"liver")
tissue_perf_list[["liver"]]<- getLifecourseLiverArterialPerfusion(age,gender)* qc_scaling
}
tissue_perf_list[["fat"]]<- getLifecourseAdiposePerfusion(age,gender)* qc_scaling
tissue_perf_list[["bone"]]<- getLifecourseBonePerfusion(age,gender)* qc_scaling
tissue_perf_list[["brain"]]<-getLifecourseBrainPerfusion(age,gender)* qc_scaling
# tissue_perf_list[["gonad"]]<- getLifecourseGonadPerfusion(age,gender)* qc_scaling
tissue_perf_list[["heart"]]<- getLifecourseHeartPerfusion(age,gender)* qc_scaling
tissue_perf_list[["kidney"]]<-getLifecourseKidneyPerfusion(age,gender)* qc_scaling
tissue_perf_list[["lung"]]<- getLifecourseLungPerfusion(age,gender)* qc_scaling
# tissue_perf_list[["pancreas"]]<- getLifecoursePancreasPerfusion(age,gender)* qc_scaling
tissue_perf_list[["skin"]]<- getLifecourseSkinPerfusion(age,gender)* qc_scaling
# tissue_perf_list[["spleen"]]<- getLifecourseSpleenPerfusion(age,gender)* qc_scaling
# tissue_perf_list[["thymus"]]<- getLifecourseThymusPerfusion(age,gender)* qc_scaling
tissue_perf_list[["muscle"]]<- getLifecourseMusclePerfusion(age,gender)* qc_scaling
# for rapidly perfused tissue flow
rpf_perf <- getLifecourseRichlyPerfusedTissuePerfusion(age,gender)* qc_scaling
inact_perf <- sum(tissue_perf_list[rpf_inactive_tissues])
tissue_perf_list[["rpf"]]<- rpf_perf+inact_perf
# for slowly perfused tissue flow
spf_perf <- getLifecourseSlowlyPerfusedTissuePerfusion(age,gender)* qc_scaling
inact_perf <- sum(tissue_perf_list[spf_inactive_tissues])
tissue_perf_list[["spf"]]<- spf_perf+inact_perf
if("liver" %in% tissues){
tissues <- tissues[tissues != "liver"]
tissues <- c(tissues,"liver_art","liver_ven")
}
return(tissue_perf_list[tissues])
}
#' Get average body weight using the life course equation
#' @description The function is used to calculate the average body weight in kgs for humans based on age and gender.
#' The function uses life course equations developed by Scitovation.
#' @param age age in years
#' @param gender Either "M" for male or "F" for female
#' @return Body Weight in kgs
#' @export
getLifecourseBodyWeight <- function(age, gender){
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseBodyWeightMale(age))
}else if(gender == "F") {
return(getLifecourseBodyWeightFemale(age))
}
}
#' Calculate body weight in kg of average human male using the lifecourse
#' equation
#' @description This function is not called directly by the user. See
#' \code{getLifeCourseBodyWeight}
#' @param age age in years
#' @return Body weight in kg
getLifecourseBodyWeightMale <- function(age){
mwbirth = 4
mwchild = 28
mwadult = 56
half = 6
k = 70
theta = 14.85
diff_bh_bw = -1.46
mbw25 = 81.208
wa = diff_bh_bw + theta
lambda = log(k**2) / (2.0 * wa * mwadult)
bw = NA
if(age >= 0 && age < 26) {
bw = mwbirth + (mwchild*age)/(half + age) + (mwadult/(1.0 + k*exp(-lambda*mwadult*age)))
}else if(age >= 26) {
months = age*12
bw = ((2.19e-08 * months**3.0) - (1.22e-04 * months**2.0) + (0.120*months) + 50.824)*mbw25/76.6
}
return(bw)
}
#' Calculate body weight in kg of average human female using the lifecourse
#' equation
#' @description This function is not called directly by the user. See
#' \code{getLifeCourseBodyWeight}
#' @param age age in years
#' @return Body weight in kg
getLifecourseBodyWeightFemale <- function(age){
mwbirth = 3.4
mwchild = 22
mwadult = 42.854
wadult = 42.668
half = 3
mbwadult = 65.236
k = 142
lambda = 0.010279
theta = 11.5
h1 = 163
bw = NA
if(age >= 0 && age < 22.3333) {
bw = 3.4 +(mwchild*age)/(3.0 + age) + (mwadult/(1.0 + 142.11536*exp(-0.01028*mwadult*age)))
}else if(age >= 22.3333) {
months = age*12
bw = ((6.17*10^-09*months^3)-(9.68*10^-5*months^2)+(0.109*months)+43.790)*mbwadult/66.17
}
return(bw)
}
#' Get average body height using the life course equation
#' @description The function is used to calculate the average body height for humans based on age and gender.
#' The function uses life course equations developed by Scitovation.
#' @param age age in years
#' @param gender Either "M" for male or "F" for female
#' @return Body Height
#' @export
getLifecourseBodyHeight <- function(age, gender){
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseBodyHeightMale(age))
}
else if(gender == "F") {
return(getLifecourseBodyHeightFemale(age))
}
}
#' Calculate body height of average human male using the lifecourse
#' equation
#' @description This function is not called directly by the user.
#' @param age age in years
#' @return Body height
getLifecourseBodyHeightMale <- function(age){
if(is.na(age)) return(NA)
h1 = 177
theta = 14.85
s0 = 0.135
s1 = 1.5
c1 = 0.9
d1 = 0.5
mht = 168.6
mbht3 = h1 - 2.0*(h1 - mht)/(exp(s0*(age - theta)) + exp(s1*(age - theta)))
mbhtj3 = h1*(1.0 - 1.0/(1.0 + ((age + 0.75)/d1)^c1))
bh = NA
if(age >= 0 && age < 3) {
bh = h1*(1.0 - 1.0/(1.0 + ((age + 0.75)/d1)^c1))*mbht3/mbhtj3
} else if(age >= 3) {
bh = 177.0 - 2.0*(177.0 - mht)/(exp(s0*(age - theta)) + exp(s1*(age - theta)))
}
return(bh)
}
#====================================================================================================
getLifecourseBodyHeightFemale <- function(age)
#====================================================================================================
{
if(is.na(age)) return(NA)
h1 = 162.15
theta = 11.2536
s0 = 0.135
s1 = 1.27
mht = 151
mbht = 94.2
mbhtj = 94.81
bh = NA
if(age >= 0 && age <= 3) {
bh = h1*(1 - 1/(1 + ((age + 0.75)/2.3)^0.7))*mbht/mbhtj
} else if(age >= 3) {
bh = h1 - 2*(h1 - mht)/(exp(s0*(age - theta)) + exp(s1*(age - theta)))
}
return(bh)
}
#====================================================================================================
getLifecourseBodySurfaceArea <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseBodySurfaceAreaMale(age))
}
else if(gender == "F") {
return(getLifecourseBodySurfaceAreaFemale(age))
}
}
#====================================================================================================
getLifecourseBodySurfaceAreaMale <- function(age)
#====================================================================================================
{
mbw = getLifecourseBodyWeightMale(age)
mbh = getLifecourseBodyHeightMale(age)
bsa = exp(-3.751 + 0.422*log(mbh) + 0.515*log(mbw))
return(bsa)
}
#====================================================================================================
getLifecourseBodySurfaceAreaFemale <- function(age)
#====================================================================================================
{
mbw = getLifecourseBodyWeightFemale(age)
mbh = getLifecourseBodyHeightFemale(age)
bsa = exp(-3.751 + 0.422*log(mbh) + 0.515*log(mbw))
return(bsa)
}
#====================================================================================================
getLifecourseBodyMassIndex <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseBodyMassIndexMale(age))
}
else if(gender == "F") {
return(getLifecourseBodyMassIndexFemale(age))
}
}
#====================================================================================================
getLifecourseBodyMassIndexMale <- function(age)
#====================================================================================================
{
mbw = getLifecourseBodyWeightMale(age)
mbh = getLifecourseBodyHeightMale(age)
bmi = mbw/((mbh/100)**2)
return(bmi)
}
#====================================================================================================
getLifecourseBodyMassIndexFemale <- function(age)
#====================================================================================================
{
mbw = getLifecourseBodyWeightFemale(age)
mbh = getLifecourseBodyHeightFemale(age)
bmi = mbw/((mbh/100)**2)
return(bmi)
}
#====================================================================================================
getLifecourseHematocrit <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseHematocritMale(age))
}
else if(gender == "F") {
return(getLifecourseHematocritFemale(age))
}
}
#====================================================================================================
getLifecourseHematocritMale <- function(age)
#====================================================================================================
{
hct = NA;
if(age >= 0 && age < 2) {
hct = 0.359
} else if(age >= 2) {
hct = (((1.12815e-06)*(age**3.0)) - (1.72362e-04*(age**2.0)) + (8.15264e-03*age) + 0.327363)
}
return(hct)
}
#====================================================================================================
getLifecourseHematocritFemale <- function(age)
#====================================================================================================
{
hct = NA;
# Note: this is same as male equation
if(age >= 0 && age < 2) {
hct = 0.359
} else if(age >= 2) {
hct = (((1.12815e-06)*(age**3.0)) - (1.72362e-04*(age**2.0)) + (8.15264e-03*age) + 0.327363)
}
return(hct)
}
#====================================================================================================
getLifecourseBloodVolume <- function(age, gender, source = "sciv")
#====================================================================================================
{
if(is.na(age)) return(NA)
if (source == "bosgra"){
if(gender == "M") {
return(getLifecourseBloodVolumeMale(age))
}
else if(gender == "F") {
return(getLifecourseBloodVolumeFemale(age))
}
}else if(source == "sciv"){
if(gender == "M") {
return(getLifecourseBloodVolumeMaleSciV(age))
}
else if(gender == "F") {
return(getLifecourseBloodVolumeFemaleSciV(age))
}
}
}
#====================================================================================================
getLifecourseBloodVolumeMale <- function(age)
#====================================================================================================
{
bsa = getLifecourseBodySurfaceAreaMale(age)
vblood = 3.33*bsa - 0.81
return(vblood)
}
getLifecourseBloodVolumeMaleSciV<- function(age){
mbsa <- getLifecourseBodySurfaceAreaMale(age)
hct <- getLifecourseHematocritMale(age)
bw <- getLifecourseBodyWeightMale(age)
#constants:
a <- 10.0
b <- 1.2082
c <- 3.2869
d <- 0.0
e <- 1000.0
vpls <- (a^(b *log10(mbsa) + c)) * (1 + d) * ((1 - hct) / e)
vbldc <- (vpls/bw)/(1-hct)
vblood <- vbldc*bw
return(vblood)
}
getLifecourseBloodVolumeFemaleSciV<- function(age){
mbsa <- getLifecourseBodySurfaceAreaFemale(age)
hct <- getLifecourseHematocritFemale(age)
bw <- getLifecourseBodyWeightFemale(age)
#constants:
a <- 10.0
b <- 1.2082
c <- 3.2869
e <- 1000.0
#equations
vpls <- (a^(b *log10(mbsa) + c)) *((1 - hct) / e)
vbldc <- (vpls/bw)/(1-hct)
vblood <- vbldc*bw
return(vblood)
}
#====================================================================================================
getLifecourseBloodVolumeFemale <- function(age)
#====================================================================================================
{
bsa = getLifecourseBodySurfaceAreaFemale(age)
vblood = 2.66*bsa - 0.46
return(vblood)
}
#====================================================================================================
getLifecourseAdiposeVolume <- function(age, gender, source = "sciv")
#====================================================================================================
{
if(is.na(age)) return(NA)
if(source=="bosgra"){
if(gender == "M") {
return(getLifecourseAdiposeVolumeMaleSciV(age))
}
else if(gender == "F") {
return(getLifecourseAdiposeVolumeFemaleSciV(age))
}
}else if(source == "sciv"){
if(gender == "M") {
return(getLifecourseAdiposeVolumeMaleSciV(age))
}
else if(gender == "F") {
return(getLifecourseAdiposeVolumeFemaleSciV(age))
}
}
}
#====================================================================================================
getLifecourseAdiposeVolumeMaleSciV <- function(age)
#====================================================================================================
{
vadipose = NA
# Note, these are not the Bosgra equations. Those eqns apparently have some errors,
# so I'm using the Scitovation eqns here.
mbw25 = 81.21
mbmi25 = 25.92
mbmi20 = 24.07
bw = getLifecourseBodyWeightMale(age)
bmi = getLifecourseBodyMassIndexMale(age)
mvfatadult = 18.02
mperfat20a = 22
mperfat20b = 23.1
if(age >= 0 && age < 20) {
vadipose = bw*((2.9875*exp(-0.129*age) + 0.67)*bmi + 0.2635*age - 4.843)/100.0
}
else if(age >= 20) {
vadipose = bw*(-5.33798*bmi + 0.11149*(bmi**2.0) + 0.09795*age + 85.24521)*(mperfat20a/mperfat20b)/100.0
}
return(vadipose)
}
#====================================================================================================
getLifecourseAdiposeVolumeFemaleSciV <- function(age)
#====================================================================================================
{
vadipose = NA
# Note, these are not the Bosgra equations. Those eqns apparently have some errors,
# so I'm using the Scitovation eqns here.
mbw25 = 81.21
mbmi25 = 25.92
mbmi20 = 24.07
bw = getLifecourseBodyWeightFemale(age)
bmi = getLifecourseBodyMassIndexFemale(age)
mvfatadult = 24.15
mperfat25a = 36.51
mperfat25b = 37.32
if(age >= 0 && age < 25) {
vadipose = bw*((1.5334*exp(-0.103*age) + 0.67)*bmi + 0.6276*age + 1.0301)/100.0
}
else if(age >= 25) {
vadipose = bw*(1.9224*bmi - 0.018517*(bmi**2.0) + 0.05537*age - 0.794894)*(mperfat25a/mperfat25b)/100.0
}
return(vadipose)
}
#====================================================================================================
getLifecourseBoneVolume <- function(age, gender, source = "sciv")
#====================================================================================================
{
if(is.na(age)) return(NA)
if (source == "Bosgra"){
if(gender == "M") {
return(getLifecourseBoneVolumeMale(age))
}
else if(gender == "F") {
return(getLifecourseBoneVolumeFemale(age))
}
}else if (source == "sciv"){
if(gender == "M") {
return(getLifecourseBoneVolumeMaleSciV(age))
}
else if(gender == "F") {
return(getLifecourseBoneVolumeFemaleSciV(age))
}
}
}
#====================================================================================================
getLifecourseBoneVolumeMale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightMale(age)
vbone = exp(0.0689)*((h/100)**2.67)
return(vbone)
}
#====================================================================================================
getLifecourseBoneVolumeFemale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightFemale(age)
vbone = exp(0.0689)*((h/100)**2.67)
return(vbone)
}
getLifecourseBoneVolumeMaleSciV<- function(age){
# calculated using linear interpolation
x <- c(0,1,5,10,15,25)
y <- c(0.05,0.15,0.34,0.63,1.08,1.17)
vals <- approx(x,y,age,"linear",rule = 2)
return(vals$y)
}
getLifecourseBoneVolumeFemaleSciV<- function(age){
# calculated using linear interpolation
x <- c(0,1,5,10,15,25)
y <- c(0.5,0.15,0.34,0.63,1,0.9)
vals <- approx(x,y,age,"linear",rule = 2)
return(vals$y)
}
#====================================================================================================
getLifecourseBrainVolume <- function(age, gender, source = "sciv")
#====================================================================================================
{
if(is.na(age)) return(NA)
if(source=="bosgra"){
if(gender == "M") {
return(getLifecourseBrainVolumeMale(age))
}
else if(gender == "F") {
return(getLifecourseBrainVolumeFemale(age))
}
}else if(source=="sciv"){
if(gender == "M") {
return(getLifecourseBrainVolumeMaleSciV(age))
}
else if(gender == "F") {
return(getLifecourseBrainVolumeFemaleSciV(age))
}
}
}
#====================================================================================================
getLifecourseBrainVolumeMale <- function(age)
#====================================================================================================
{
v0 = 0.405
vbrain = v0*(3.68 - 2.68*exp(-age/0.89))*(exp(-age/629))
return(vbrain)
}
#====================================================================================================
getLifecourseBrainVolumeFemale <- function(age)
#====================================================================================================
{
v0 = 0.373
vbrain = v0*(3.68 - 2.68*exp(-age/0.89))*(exp(-age/629))
return(vbrain)
}
getLifecourseBrainVolumeMaleSciV <- function(age){
#constants
a <- 10.0
b <- 0.315
c <- 9.0
d <- 6.92
vbrain <- a*(age+b)/(c+d*age)
return(vbrain)
}
getLifecourseBrainVolumeFemaleSciV <- function(age){
#constants
a <- 10.0
b <- 0.315
c <- 9.0
d <- 6.92
vbrain <- a*(age+b)/(c+d*age)
return(vbrain)
}
#====================================================================================================
getLifecourseGonadVolume <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseGonadVolumeMale(age))
}
else if(gender == "F") {
return(getLifecourseGonadVolumeFemale(age))
}
}
#====================================================================================================
getLifecourseGonadVolumeMale <- function(age)
#====================================================================================================
{
vgon = (3.3 + 53*(1 - exp(-(age/17.5)**5.4)))/1000 # Convert to kg
return(vgon)
}
#====================================================================================================
getLifecourseGonadVolumeFemale <- function(age)
#====================================================================================================
{
vgon = (3.3 + 90*(1 - exp(-(age/16.8)**6.7)))/1000 # Convert to kg
return(vgon)
}
#====================================================================================================
getLifecourseHeartVolume <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseHeartVolumeMale(age))
}
else if(gender == "F") {
return(getLifecourseHeartVolumeFemale(age))
}
}
#====================================================================================================
getLifecourseHeartVolumeMale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightMale(age)
vhrt = exp(-2.502)*((h/100)**2.13)
return(vhrt)
}
#====================================================================================================
getLifecourseHeartVolumeFemale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightFemale(age)
vhrt = exp(-2.502)*((h/100)**2.13)
return(vhrt)
}
#the gut volume comes from internal gut equations. Will be used for the GI compartment in the model
# if volume for individual compartments is needed use bosgra equations for individual compartments
getLifecourseGutVolume <- function(age,gender){
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseGutVolumeMale(age))
}
else if(gender == "F") {
return(getLifecourseGutVolumeFemale(age))
}
}
getLifecourseGutVolumeMale <- function(age){
mbw <- getLifecourseBodyWeightMale(age)
vfat <- getLifecourseAdiposeVolumeMaleSciV(age)
lbw <- mbw - vfat
vgut <- 0.021*lbw
return(vgut)
}
getLifecourseGutVolumeFemale <- function(age){
mbw <- getLifecourseBodyWeightFemale(age)
vfat <- getLifecourseAdiposeVolumeFemaleSciV(age)
lbw <- mbw - vfat
vgut <- 0.027*lbw
return(vgut)
}
#====================================================================================================
getLifecourseIntestineVolume <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseIntestineVolumeMale(age))
}
else if(gender == "F") {
return(getLifecourseIntestineVolumeFemale(age))
}
}
#====================================================================================================
getLifecourseIntestineVolumeMale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightMale(age)
vint = exp(-1.351)*((h/100)**2.47)
return(vint)
}
#====================================================================================================
getLifecourseIntestineVolumeFemale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightFemale(age)
vint = exp(-1.351)*((h/100)**2.47)
return(vint)
}
#====================================================================================================
getLifecourseKidneyVolume <- function(age, gender, source = "sciv")
#====================================================================================================
{
if(is.na(age)) return(NA)
# remove this block once we have scitovation equations
if (source == "sciv"){
warning("Scitovation equations not found, Using bosgra equations instead")
source = "bosgra"
}
if(source == "bosgra"){
if(gender == "M") {
return(getLifecourseKidneyVolumeMale(age))
}
else if(gender == "F") {
return(getLifecourseKidneyVolumeFemale(age))
}
}else if(source == "sciv"){
stop("No Scitovation Equations found")
}
}
#====================================================================================================
getLifecourseKidneyVolumeMale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightMale(age)
vkid = exp(-2.306)*((h/100)**1.93)
return(vkid)
}
#====================================================================================================
getLifecourseKidneyVolumeFemale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightFemale(age)
vkid = exp(-2.306)*((h/100)**1.93)
return(vkid)
}
#====================================================================================================
getLifecourseLiverVolume <- function(age, gender, source = "sciv")
#====================================================================================================
{
if(is.na(age)) return(NA)
if (source == "bosgra"){
if(gender == "M") {
return(getLifecourseLiverVolumeMale(age))
}
else if(gender == "F") {
return(getLifecourseLiverVolumeFemale(age))
}
}else if(source == "sciv"){
if(gender == "M") {
return(getLifecourseLiverVolumeMaleSciV(age))
}
else if(gender == "F") {
return(getLifecourseLiverVolumeFemaleSciV(age))
}
}
}
#====================================================================================================
getLifecourseLiverVolumeMale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightMale(age)
vliv = exp(-0.6786)*((h/100)**1.98)
return(vliv)
}
#====================================================================================================
getLifecourseLiverVolumeFemale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightFemale(age)
vliv = exp(-0.6786)*((h/100)**1.98)
return(vliv)
}
getLifecourseLiverVolumeMaleSciV<- function(age){
mbw <- getLifecourseBodyWeightMale(age)
mbsa <- getLifecourseBodySurfaceAreaMale(age)
if (age < 23){
a <- 0.05012
b <- 0.78
vliv <- a*mbw^b
}else{
# mean adult (25y) liver weight
mliv268 <- 0.0512*getLifecourseBodyWeightMale(25)^0.78
# mean adult (25y) body surface area
mbsa268 <- 2.01
a <- 1.0728
b <- 0.3457
vliv <- (a * mbsa - b) * mliv268 / (a * mbsa268 - b)
}
}
getLifecourseLiverVolumeFemaleSciV<- function(age){
mbw <- getLifecourseBodyWeightFemale(age)
mbsa <- getLifecourseBodySurfaceAreaFemale(age)
if (age < 23){
a <- 0.05012
b <- 0.78
vliv <- a*mbw^b
}else{
# mean adult (25y) liver weight
mliv268 <- 0.0512*getLifecourseBodyWeightFemale(25)^0.78
# mean adult (25y) body surface area
mbsa268 <- 1.75
a <- 1.0728
b <- 0.3457
vliv <- (a * mbsa - b) * mliv268 / (a * mbsa268 - b)
}
}
#====================================================================================================
getLifecourseLungVolume <- function(age, gender,source = "bosgra")
#====================================================================================================
{
if(is.na(age)) return(NA)
# remove this block once we have scitovation equations
if (source == "sciv"){
warning("Scitovation equations not found, Using bosgra equations instead")
source = "bosgra"
}
if(source=="bosgra"){
if(gender == "M") {
return(getLifecourseLungVolumeMale(age))
}
else if(gender == "F") {
return(getLifecourseLungVolumeFemale(age))
}
}
}
#====================================================================================================
getLifecourseLungVolumeMale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightMale(age)
vliv = exp(-2.092)*((h/100)**2.1)
return(vliv)
}
#====================================================================================================
getLifecourseLungVolumeFemale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightFemale(age)
vliv = exp(-2.092)*((h/100)**2.1)
return(vliv)
}
#====================================================================================================
getLifecoursePancreasVolume <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecoursePancreasVolumeMale(age))
}
else if(gender == "F") {
return(getLifecoursePancreasVolumeFemale(age))
}
}
#====================================================================================================
getLifecoursePancreasVolumeMale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightMale(age)
vpan = exp(-3.431)*((h/100)**2.43)
return(vpan)
}
#====================================================================================================
getLifecoursePancreasVolumeFemale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightFemale(age)
vpan = exp(-3.431)*((h/100)**2.43)
return(vpan)
}
#====================================================================================================
getLifecourseSkinVolume <- function(age, gender,source = "sciv")
#====================================================================================================
{
if(is.na(age)) return(NA)
if(source == "bosgra"){
if(gender == "M") {
return(getLifecourseSkinVolumeMale(age))
}
else if(gender == "F") {
return(getLifecourseSkinVolumeFemale(age))
}
}else if(source == "sciv"){
if(gender == "M") {
return(getLifecourseSkinVolumeMaleSciV(age))
}
else if(gender == "F") {
return(getLifecourseSkinVolumeFemaleSciV(age))
}
}
}
#====================================================================================================
getLifecourseSkinVolumeMale <- function(age)
#====================================================================================================
{
bsa = getLifecourseBodySurfaceAreaMale(age)
vskn = exp(1.64*bsa - 1.93)
return(vskn)
}
#====================================================================================================
getLifecourseSkinVolumeFemale <- function(age)
#====================================================================================================
{
bsa = getLifecourseBodySurfaceAreaFemale(age)
vskn = exp(1.64*bsa - 1.93)
return(vskn)
}
getLifecourseSkinVolumeMaleSciV <- function(age){
mbsa <- getLifecourseBodySurfaceAreaMale(age) # in m^2
mbsa <- mbsa*10000
depth <- 0.15 #in cm
vskin <- (mbsa*depth)/1000
return(vskin)
}
getLifecourseSkinVolumeFemaleSciV <- function(age){
mbsa <- getLifecourseBodySurfaceAreaFemale(age) # in m^2
mbsa <- mbsa*10000
depth <- 0.15 #in cm
vskin <- (mbsa*depth)/1000
return(vskin)
}
#====================================================================================================
getLifecourseSpleenVolume <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseSpleenVolumeMale(age))
}
else if(gender == "F") {
return(getLifecourseSpleenVolumeFemale(age))
}
}
#====================================================================================================
getLifecourseSpleenVolumeMale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightMale(age)
vspl = exp(-3.123)*((h/100)**2.16)
return(vspl)
}
#====================================================================================================
getLifecourseSpleenVolumeFemale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightFemale(age)
vspl = exp(-3.123)*((h/100)**2.16)
return(vspl)
}
#====================================================================================================
getLifecourseStomachVolume <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseStomachVolumeMale(age))
}
else if(gender == "F") {
return(getLifecourseStomachVolumeFemale(age))
}
}
#====================================================================================================
getLifecourseStomachVolumeMale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightMale(age)
vsto = exp(-3.266)*((h/100)**2.45)
return(vsto)
}
#====================================================================================================
getLifecourseStomachVolumeFemale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightFemale(age)
vsto = exp(-3.266)*((h/100)**2.45)
return(vsto)
}
#====================================================================================================
getLifecourseThymusVolume <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseThymusVolumeMale(age))
}
else if(gender == "F") {
return(getLifecourseThymusVolumeFemale(age))
}
}
#====================================================================================================
getLifecourseThymusVolumeMale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightMale(age)
vthy = 14*((7.1 - 6.1*exp(-age/11.9))*(0.14 + 0.86*exp(-age/10.3)))/1000 # convert to kg
return(vthy)
}
#====================================================================================================
getLifecourseThymusVolumeFemale <- function(age)
#====================================================================================================
{
# Note, same as male eqn
h = getLifecourseBodyHeightFemale(age)
vthy = 14*((7.1 - 6.1*exp(-age/11.9))*(0.14 + 0.86*exp(-age/10.3)))/1000 # convert to kg
return(vthy)
}
#====================================================================================================
getLifecourseRemainingVolume <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseRemainingVolumeMale(age))
}
else if(gender == "F") {
return(getLifecourseRemainingVolumeFemale(age))
}
}
#====================================================================================================
getLifecourseRemainingVolumeMale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightMale(age)
vrem = exp(-0.072)*((h/100)**1.95)
return(vrem)
}
#====================================================================================================
getLifecourseRemainingVolumeFemale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightFemale(age)
vrem = exp(-0.072)*((h/100)**1.95)
return(vrem)
}
#====================================================================================================
getLifecourseRapidlyPerfusedVolume <- function(age, gender,source = "sciv")
#====================================================================================================
{
if(is.na(age)) return(NA)
# remove this block once we have bosgra equations
if (source == "bosgra"){
warning("Bosgra equations not found, Using ScitoVation equations instead")
source = "sciv"
}
if(source == "sciv"){
if(gender == "M") {
return(getLifecourseRapidlyPerfusedVolumeMaleSciV(age))
}else if(gender == "F") {
return(getLifecourseRapidlyPerfusedVolumeFemaleSciV(age))
}
}
}
getLifecourseRapidlyPerfusedVolumeMaleSciV<- function(age){
vgut <- getLifecourseGutVolumeMale(age)
vrpf <- 2.596*vgut
return(vrpf)
}
getLifecourseRapidlyPerfusedVolumeFemaleSciV<- function(age){
vgut <- getLifecourseGutVolumeFemale(age)
vrpf <- 2.464*vgut
return(vrpf)
}
#====================================================================================================
getLifecourseMuscleVolume <- function(age, gender,source="sciv")
#====================================================================================================
{
if(is.na(age)) return(NA)
if (source == "bosgra"){
if(gender == "M") {
return(getLifecourseMuscleVolumeMale(age))
}
else if(gender == "F") {
return(getLifecourseMuscleVolumeFemale(age))
}
}else if (source == "sciv"){
if (gender == "M"){
return(getLifecourseMuscleVolumeMaleSciV(age))
}else if (gender == "F"){
return(getLifecourseMuscleVolumeFemaleSciV(age))
}
}
}
#====================================================================================================
getLifecourseMuscleVolumeMale <- function(age)
#====================================================================================================
{
vmus = getLifecourseBodyWeightMale(age) -
getLifecourseAdiposeVolumeMaleSciV(age) -
getLifecourseBloodVolumeMale(age) -
getLifecourseBoneVolumeMale(age) -
getLifecourseBrainVolumeMale(age) -
getLifecourseGonadVolumeMale(age) -
getLifecourseHeartVolumeMale(age) -
getLifecourseIntestineVolumeMale(age) -
getLifecourseKidneyVolumeMale(age) -
getLifecourseLiverVolumeMale(age) -
getLifecourseLungVolumeMale(age) -
getLifecoursePancreasVolumeMale(age) -
getLifecourseRemainingVolumeMale(age) -
getLifecourseSkinVolumeMale(age) -
getLifecourseSpleenVolumeMale(age) -
getLifecourseStomachVolumeMale(age) -
getLifecourseThymusVolumeMale(age)
return(vmus)
}
#====================================================================================================
getLifecourseMuscleVolumeFemale <- function(age)
#====================================================================================================
{
vmus = getLifecourseBodyWeightMale(age) -
getLifecourseAdiposeVolumeFemaleSciV(age) -
getLifecourseBloodVolumeFemale(age) -
getLifecourseBoneVolumeFemale(age) -
getLifecourseBrainVolumeFemale(age) -
getLifecourseGonadVolumeFemale(age) -
getLifecourseHeartVolumeFemale(age) -
getLifecourseIntestineVolumeFemale(age) -
getLifecourseKidneyVolumeFemale(age) -
getLifecourseLiverVolumeFemale(age) -
getLifecourseLungVolumeFemale(age) -
getLifecoursePancreasVolumeFemale(age) -
getLifecourseRemainingVolumeFemale(age) -
getLifecourseSkinVolumeFemale(age) -
getLifecourseSpleenVolumeFemale(age) -
getLifecourseStomachVolumeFemale(age) -
getLifecourseThymusVolumeFemale(age)
return(vmus)
}
#====================================================================================================
getLifecourseSlowlyPerfusedVolume <- function(age, gender,perf_frct=0.85)
#====================================================================================================
{
if(is.na(age)) return(NA)
if (gender == "M"){
return(getLifecourseSlowlyPerfusedVolumeMale(age,perf_frct))
}else if (gender == "F"){
return(getLifecourseSlowlyPerfusedVolumeFemale(age,perf_frct))
}
}
getLifecourseSlowlyPerfusedVolumeMale <- function(age,perf_frct=0.85){
bw <- getLifecourseBodyWeightMale(age)
perfused_bw <- perf_frct*bw
total_volume <- (getLifecourseGutVolume(age,"M")+
getLifecourseIntestineVolume(age,"M")+
getLifecourseLiverVolume(age,"M")+
getLifecourseBloodVolume(age,"M")+
getLifecourseAdiposeVolume(age,"M")+
getLifecourseBoneVolume(age,"M")+
getLifecourseBrainVolume(age,"M")+
getLifecourseHeartVolume(age,"M")+
getLifecourseKidneyVolume(age,"M")+
getLifecourseLungVolume(age,"M")+
getLifecourseSkinVolume(age,"M")+
getLifecourseMuscleVolume(age,"M")+
getLifecourseRapidlyPerfusedVolume(age,"M"))
vol <- perfused_bw- total_volume
vol <- ifelse(vol < 0, 1e-5,vol)
return(vol)
}
getLifecourseSlowlyPerfusedVolumeFemale <- function(age,perf_frct=0.85){
bw <- getLifecourseBodyWeightFemale(age)
perfused_bw <- perf_frct*bw
total_volume <- (getLifecourseGutVolume(age,"F")+
getLifecourseIntestineVolume(age,"F")+
getLifecourseLiverVolume(age,"F")+
getLifecourseBloodVolume(age,"F")+
getLifecourseAdiposeVolume(age,"F")+
getLifecourseBoneVolume(age,"F")+
getLifecourseBrainVolume(age,"F")+
getLifecourseHeartVolume(age,"F")+
getLifecourseKidneyVolume(age,"F")+
getLifecourseLungVolume(age,"F")+
getLifecourseSkinVolume(age,"F")+
getLifecourseMuscleVolume(age,"F")+
getLifecourseRapidlyPerfusedVolume(age,"F"))
vol <- perfused_bw- total_volume
vol <- ifelse(vol < 0, 1e-5,vol)
return(vol)
}
#====================================================================================================
getLifecourseMuscleVolumeMale <- function(age)
#====================================================================================================
{
vmus = getLifecourseBodyWeightMale(age) -
getLifecourseAdiposeVolumeMaleSciV(age) -
getLifecourseBloodVolumeMale(age) -
getLifecourseBoneVolumeMale(age) -
getLifecourseBrainVolumeMale(age) -
getLifecourseGonadVolumeMale(age) -
getLifecourseHeartVolumeMale(age) -
getLifecourseIntestineVolumeMale(age) -
getLifecourseKidneyVolumeMale(age) -
getLifecourseLiverVolumeMale(age) -
getLifecourseLungVolumeMale(age) -
getLifecoursePancreasVolumeMale(age) -
getLifecourseRemainingVolumeMale(age) -
getLifecourseSkinVolumeMale(age) -
getLifecourseSpleenVolumeMale(age) -
getLifecourseStomachVolumeMale(age) -
getLifecourseThymusVolumeMale(age)
return(vmus)
}
#====================================================================================================
getLifecourseMuscleVolumeFemale <- function(age)
#====================================================================================================
{
vmus = getLifecourseBodyWeightMale(age) -
getLifecourseAdiposeVolumeFemaleSciV(age) -
getLifecourseBloodVolumeFemale(age) -
getLifecourseBoneVolumeFemale(age) -
getLifecourseBrainVolumeFemale(age) -
getLifecourseGonadVolumeFemale(age) -
getLifecourseHeartVolumeFemale(age) -
getLifecourseIntestineVolumeFemale(age) -
getLifecourseKidneyVolumeFemale(age) -
getLifecourseLiverVolumeFemale(age) -
getLifecourseLungVolumeFemale(age) -
getLifecoursePancreasVolumeFemale(age) -
getLifecourseRemainingVolumeFemale(age) -
getLifecourseSkinVolumeFemale(age) -
getLifecourseSpleenVolumeFemale(age) -
getLifecourseStomachVolumeFemale(age) -
getLifecourseThymusVolumeFemale(age)
return(vmus)
}
getLifecourseMuscleVolumeMaleSciV<- function(age){
# calculated using linear interpolation
x <- c(0,1,5,10,15,25)
y <- c(0.8,1.9,5.6,11,24,29)
vals <- approx(x,y,age,"linear",rule = 2)
return(vals$y)
}
getLifecourseMuscleVolumeFemaleSciV<- function(age){
# calculated using linear interpolation
x <- c(0,1,5,10,15,25)
y <- c(0.8,1.9,5.6,11,17,17.5)
vals <- approx(x,y,age,"linear",rule = 2)
return(vals$y)
}
#====================================================================================================
getLifecourseTissueVolumeSum <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseTissueVolumeSumMale(age))
}
else if(gender == "F") {
return(getLifecourseTissueVolumeSumFemale(age))
}
}
#====================================================================================================
getLifecourseTissueVolumeSumMale <- function(age)
#====================================================================================================
{
vall = +
getLifecourseAdiposeVolumeMaleSciV(age) +
getLifecourseBloodVolumeMale(age) +
getLifecourseBoneVolumeMale(age) +
getLifecourseBrainVolumeMale(age) +
getLifecourseGonadVolumeMale(age) +
getLifecourseHeartVolumeMale(age) +
getLifecourseIntestineVolumeMale(age) +
getLifecourseKidneyVolumeMale(age) +
getLifecourseLiverVolumeMale(age) +
getLifecourseLungVolumeMale(age) +
getLifecoursePancreasVolumeMale(age) +
getLifecourseRemainingVolumeMale(age) +
getLifecourseSkinVolumeMale(age) +
getLifecourseSpleenVolumeMale(age) +
getLifecourseStomachVolumeMale(age) +
getLifecourseThymusVolumeMale(age) +
getLifecourseMuscleVolumeMale(age)
return(vall)
}
#====================================================================================================
getLifecourseTissueVolumeSumFemale <- function(age)
#====================================================================================================
{
vall = +
getLifecourseAdiposeVolumeFemaleSciV(age) +
getLifecourseBloodVolumeFemale(age) +
getLifecourseBoneVolumeFemale(age) +
getLifecourseBrainVolumeFemale(age) +
getLifecourseGonadVolumeFemale(age) +
getLifecourseHeartVolumeFemale(age) +
getLifecourseIntestineVolumeFemale(age) +
getLifecourseKidneyVolumeFemale(age) +
getLifecourseLiverVolumeFemale(age) +
getLifecourseLungVolumeFemale(age) +
getLifecoursePancreasVolumeFemale(age) +
getLifecourseRemainingVolumeFemale(age) +
getLifecourseSkinVolumeFemale(age) +
getLifecourseSpleenVolumeFemale(age) +
getLifecourseStomachVolumeFemale(age) +
getLifecourseThymusVolumeFemale(age) +
getLifecourseMuscleVolumeFemale(age)
return(vall)
}
#====================================================================================================
getLifecourseAdiposePerfusion <- function(age, gender, source = "sciv")
#====================================================================================================
{
if(is.na(age)) return(NA)
if(source == "bosgra"){
if(gender == "M") {
return(getLifecourseAdiposePerfusionMale(age))
}
else if(gender == "F") {
return(getLifecourseAdiposePerfusionFemale(age))
}
}else if(source == "sciv"){
if(gender == "M") {
return(getLifecourseAdiposePerfusionMaleSciV(age))
}
else if(gender == "F") {
return(getLifecourseAdiposePerfusionFemaleSciV(age))
}
}
}
getLifecourseAdiposePerfusionMaleSciV<- function(age){
vfatc25 = 0.238
qfatc25 = 0.05
vfat <- getLifecourseAdiposeVolumeMaleSciV(age)
bw <- getLifecourseBodyWeightMale(age)
qc <- getLifecourseCardiacOutput(age,"M")
vfatc <- vfat/bw
qfatc <- (vfatc/vfatc25)*qfatc25
qfat <- qfatc*qc
return(qfat)
}
getLifecourseAdiposePerfusionFemaleSciV<- function(age){
vfatc25 = 0.368
qfatc25 = 0.085
vfat <- getLifecourseAdiposeVolumeFemaleSciV(age)
bw <- getLifecourseBodyWeightFemale(age)
qc <- getLifecourseCardiacOutput(age,"F")
vfatc <- vfat/bw
qfatc <- (vfatc/vfatc25)*qfatc25
qfat <- qfatc*qc
return(qfat)
}
#====================================================================================================
getLifecourseAdiposePerfusionMale <- function(age)
#====================================================================================================
{
m = getLifecourseAdiposeVolumeMaleSciV(age)
m35 = getLifecourseAdiposeVolumeMaleSciV(35)
q = m*19.5/m35
return(q)
}
#====================================================================================================
getLifecourseAdiposePerfusionFemale <- function(age)
#====================================================================================================
{
m = getLifecourseAdiposeVolumeFemaleSciV(age)
m35 = getLifecourseAdiposeVolumeFemaleSciV(35)
q = m*30.1/m35
return(q)
}
#====================================================================================================
getLifecourseBonePerfusion <- function(age, gender, source = "sciv")
#====================================================================================================
{
if(is.na(age)) return(NA)
if(source == "bosgra"){
if(gender == "M") {
return(getLifecourseBonePerfusionMale(age))
}
else if(gender == "F") {
return(getLifecourseBonePerfusionFemale(age))
}
}else if(source == "sciv"){
if(gender == "M") {
return(getLifecourseBonePerfusionMaleSciV(age))
}
else if(gender == "F") {
return(getLifecourseBonePerfusionFemaleSciV(age))
}
}
}
getLifecourseBonePerfusionMaleSciV<- function(age){
qbone25c <- 0.03
qc <- getLifecourseCardiacOutput(age,"M")
bw25 <- getLifecourseBodyWeightMale(25)
bw <- getLifecourseBodyWeightMale(age)
vbonec25 <- getLifecourseBoneVolumeMaleSciV(25)/bw25
vbonec <- getLifecourseBoneVolumeMaleSciV(age)/bw
qbone <- qc*(vbonec/vbonec25)*qbone25c
return(qbone)
}
getLifecourseBonePerfusionFemaleSciV<- function(age){
qbone25c <- 0.03
qc <- getLifecourseCardiacOutput(age,"F")
bw25 <- getLifecourseBodyWeightFemale(25)
bw <- getLifecourseBodyWeightFemale(age)
vbonec25 <- getLifecourseBoneVolumeFemaleSciV(25)/bw25
vbonec <- getLifecourseBoneVolumeFemaleSciV(age)/bw
qbone <- qc*(vbonec/vbonec25)*qbone25c
return(qbone)
}
#====================================================================================================
getLifecourseBonePerfusionMale <- function(age)
#====================================================================================================
{
m = getLifecourseBoneVolumeMale(age)
m35 = getLifecourseBoneVolumeMale(35)
q = m*7.8/m35
return(q)
}
#====================================================================================================
getLifecourseBonePerfusionFemale <- function(age)
#====================================================================================================
{
m = getLifecourseBoneVolumeFemale(age)
m35 = getLifecourseBoneVolumeFemale(35)
q = m*7.1/m35
return(q)
}
#====================================================================================================
getLifecourseBrainPerfusion <- function(age, gender,source = "sciv")
#====================================================================================================
{
if(is.na(age)) return(NA)
if(source == "bosgra"){
if(gender == "M") {
return(getLifecourseBrainPerfusionMale(age))
}
else if(gender == "F") {
return(getLifecourseBrainPerfusionFemale(age))
}
}else if (source == "sciv"){
if(gender == "M") {
return(getLifecourseBrainPerfusionMaleSciV(age))
}
else if(gender == "F") {
return(getLifecourseBrainPerfusionFemaleSciV(age))
}
}
}
#====================================================================================================
getLifecourseBrainPerfusionMale <- function(age)
#====================================================================================================
{
m = getLifecourseBrainVolumeMale(age)
m35 = getLifecourseBrainVolumeMale(35)
q = m*46.8/m35
return(q)
}
#====================================================================================================
getLifecourseBrainPerfusionFemale <- function(age)
#====================================================================================================
{
m = getLifecourseBrainVolumeFemale(age)
m35 = getLifecourseBrainVolumeFemale(35)
q = m*42.5/m35
return(q)
}
getLifecourseBrainPerfusionMaleSciV<- function(age){
qc <- getLifecourseCardiacOutput(age,"M")
qbrnc <- (3/age)*exp(-0.5*(log(age/41.92)/1.876)^2)
qbrn <- qbrnc*qc
return(qbrn)
}
getLifecourseBrainPerfusionFemaleSciV<- function(age){
qc <- getLifecourseCardiacOutput(age,"F")
qbrnc <- (3.064/age)*exp(-0.5*(log(age/47.57)/1.94)^2)
qbrn <- qbrnc*qc
return(qbrn)
}
#====================================================================================================
getLifecourseGonadPerfusion <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseGonadPerfusionMale(age))
}
else if(gender == "F") {
return(getLifecourseGonadPerfusionFemale(age))
}
}
#====================================================================================================
getLifecourseGonadPerfusionMale <- function(age)
#====================================================================================================
{
m = getLifecourseGonadVolumeMale(age)
m35 = getLifecourseGonadVolumeMale(35)
q = m*0.195/m35
return(q)
}
#====================================================================================================
getLifecourseGonadPerfusionFemale <- function(age)
#====================================================================================================
{
m = getLifecourseGonadVolumeFemale(age)
m35 = getLifecourseGonadVolumeFemale(35)
q = m*0.071/m35
return(q)
}
#====================================================================================================
getLifecourseHeartPerfusion <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseHeartPerfusionMale(age))
}
else if(gender == "F") {
return(getLifecourseHeartPerfusionFemale(age))
}
}
#====================================================================================================
getLifecourseHeartPerfusionMale <- function(age)
#====================================================================================================
{
m = getLifecourseHeartVolumeMale(age)
m35 = getLifecourseHeartVolumeMale(35)
q = m*15.6/m35
return(q)
}
#====================================================================================================
getLifecourseHeartPerfusionFemale <- function(age)
#====================================================================================================
{
m = getLifecourseHeartVolumeFemale(age)
m35 = getLifecourseHeartVolumeFemale(35)
q = m*17.7/m35
return(q)
}
#====================================================================================================
getLifecourseIntestinePerfusion <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseIntestinePerfusionMale(age))
}
else if(gender == "F") {
return(getLifecourseIntestinePerfusionFemale(age))
}
}
#====================================================================================================
getLifecourseIntestinePerfusionMale <- function(age)
#====================================================================================================
{
m = getLifecourseIntestineVolumeMale(age)
m35 = getLifecourseIntestineVolumeMale(35)
q = m*54.6/m35
return(q)
}
#====================================================================================================
getLifecourseIntestinePerfusionFemale <- function(age)
#====================================================================================================
{
m = getLifecourseIntestineVolumeFemale(age)
m35 = getLifecourseIntestineVolumeFemale(35)
q = m*56.6/m35
return(q)
}
#====================================================================================================
getLifecourseKidneyPerfusion <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseKidneyPerfusionMale(age))
}
else if(gender == "F") {
return(getLifecourseKidneyPerfusionFemale(age))
}
}
#====================================================================================================
getLifecourseKidneyPerfusionMale <- function(age)
#====================================================================================================
{
m = getLifecourseKidneyVolumeMale(age)
m35 = getLifecourseKidneyVolumeMale(35)
q = m*74.1/m35
return(q)
}
#====================================================================================================
getLifecourseKidneyPerfusionFemale <- function(age)
#====================================================================================================
{
m = getLifecourseKidneyVolumeFemale(age)
m35 = getLifecourseKidneyVolumeFemale(35)
q = m*60.2/m35
return(q)
}
#====================================================================================================
getLifecourseLiverArterialPerfusion <- function(age, gender, source = "sciv")
#====================================================================================================
{
if(is.na(age)) return(NA)
if(source == "bosgra"){
if(gender == "M") {
return(getLifecourseLiverArterialPerfusionMale(age))
}
else if(gender == "F") {
return(getLifecourseLiverArterialPerfusionFemale(age))
}
}else if (source == "sciv"){
if(gender == "M") {
return(getLifecourseLiverArterialPerfusionMaleSciV(age))
}
else if(gender == "F") {
return(getLifecourseLiverArterialPerfusionFemaleSciV(age))
}
}
}
#====================================================================================================
getLifecourseLiverArterialPerfusionMale <- function(age)
#====================================================================================================
{
m = getLifecourseLiverVolumeMale(age)
m35 = getLifecourseLiverVolumeMale(35)
q = m*25.35/m35
return(q)
}
#====================================================================================================
getLifecourseLiverArterialPerfusionFemale <- function(age)
#====================================================================================================
{
m = getLifecourseLiverVolumeFemale(age)
m35 = getLifecourseLiverVolumeFemale(35)
q = m*23.0/m35
return(q)
}
getLifecourseLiverArterialPerfusionMaleSciV<- function(age){
vliv <- getLifecourseLiverVolumeMaleSciV(age)
bw <- getLifecourseBodyWeightMale(age)
qc <- getLifecourseCardiacOutput(age,"M")
vlivc <- vliv/bw
qlivartc <- (vlivc/0.0199)*0.065
qlivart <- qlivartc*qc
return(qlivart)
}
getLifecourseLiverArterialPerfusionFemaleSciV<- function(age){
vliv <- getLifecourseLiverVolumeFemaleSciV(age)
bw <- getLifecourseBodyWeightFemale(age)
qc <- getLifecourseCardiacOutput(age,"F")
vlivc <- vliv/bw
qlivartc <- (vlivc/0.0199)*0.065
qlivart <- qlivartc*qc
return(qlivart)
}
getLifecourseGutPerfusion<- function(age,gender){
if(is.na(age)) return(NA)
if(gender == "M"){
return(getLifecourseGutPerfusionMale(age))
}else if(gender == "F"){
return(getLifecourseGutPerfusionFemale(age))
}
}
getLifecourseGutPerfusionMale<- function(age){
vgutc25 <- 0.016
qgutc25 <- 0.15
vgut <- getLifecourseGutVolumeMale(age)
bw <- getLifecourseBodyWeightMale(age)
qc <- getLifecourseCardiacOutput(age,"M")
vgutc <- vgut/bw
qgutc <- (vgutc/vgutc25)*qgutc25
qgut <- qgutc *qc
return(qgut)
}
getLifecourseGutPerfusionFemale<- function(age){
vgutc25 <- 0.0170660419467526
qgutc25 <- 0.17
vgut <- getLifecourseGutVolumeFemale(age)
bw <- getLifecourseBodyWeightFemale(age)
qc <- getLifecourseCardiacOutput(age,"F")
vgutc <- vgut/bw
qgutc <- (vgutc/vgutc25)*qgutc25
qgut <- qgutc *qc
return(qgut)
}
#====================================================================================================
getLifecourseLiverSplancnicPerfusion <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseLiverSplancnicPerfusionMale(age))
}
else if(gender == "F") {
return(getLifecourseLiverSplancnicPerfusionFemale(age))
}
}
#====================================================================================================
getLifecourseLiverSplancnicPerfusionMale <- function(age)
#====================================================================================================
{
q = getLifecoursePancreasPerfusionMale(age) +
getLifecourseSpleenPerfusionMale(age) +
getLifecourseStomachPerfusionMale(age) +
getLifecourseIntestinePerfusionMale(age)
return(q)
}
#====================================================================================================
getLifecourseLiverSplancnicPerfusionFemale <- function(age)
#====================================================================================================
{
q = getLifecoursePancreasPerfusionFemale(age) +
getLifecourseSpleenPerfusionFemale(age) +
getLifecourseStomachPerfusionFemale(age) +
getLifecourseIntestinePerfusionFemale(age)
return(q)
}
#====================================================================================================
getLifecourseLiverTotalPerfusion <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseLiverTotalPerfusionMale(age))
}
else if(gender == "F") {
return(getLifecourseLiverTotalPerfusionFemale(age))
}
}
#====================================================================================================
getLifecourseLiverTotalPerfusionMale <- function(age)
#====================================================================================================
{
q = getLifecourseLiverArterialPerfusionMale(age) +
getLifecourseLiverSplancnicPerfusionMale(age)
return(q)
}
#====================================================================================================
getLifecourseLiverTotalPerfusionFemale <- function(age)
#====================================================================================================
{
q = getLifecourseLiverArterialPerfusionFemale(age) +
getLifecourseLiverSplancnicPerfusionFemale(age)
return(q)
}
#====================================================================================================
getLifecourseMusclePerfusion <- function(age, gender, source = "sciv")
#====================================================================================================
{
if(is.na(age)) return(NA)
if(source == "sciv"){
if(gender == "M") {
return(getLifecourseMusclePerfusionMaleSciV(age))
}
else if(gender == "F") {
return(getLifecourseMusclePerfusionFemaleSciV(age))
}
}else if(source == "bosgra"){
if(gender == "M") {
return(getLifecourseMusclePerfusionMale(age))
}
else if(gender == "F") {
return(getLifecourseMusclePerfusionFemale(age))
}
}
}
getLifecourseMusclePerfusionMaleSciV <- function(age){
vmuscc25 <- getLifecourseMuscleVolumeMaleSciV(25)/getLifecourseBodyWeightMale(25)
qmuscc25 <- 0.17
vmusc <- getLifecourseMuscleVolumeMaleSciV(age)
bw <- getLifecourseBodyWeightMale(age)
qc <- getLifecourseCardiacOutput(age,"M")
vmuscc <- vmusc/bw
qmuscc <- (vmuscc/vmuscc25)*qmuscc25
qmusc <- qmuscc *qc
return(qmusc)
}
getLifecourseMusclePerfusionFemaleSciV <- function(age){
vmuscc25 <- getLifecourseMuscleVolumeFemaleSciV(25)/getLifecourseBodyWeightFemale(25)
qmuscc25 <- 0.12
vmusc <- getLifecourseMuscleVolumeFemaleSciV(age)
bw <- getLifecourseBodyWeightFemale(age)
qc <- getLifecourseCardiacOutput(age,"F")
vmuscc <- vmusc/bw
qmuscc <- (vmuscc/vmuscc25)*qmuscc25
qmusc <- qmuscc *qc
return(qmusc)
}
#====================================================================================================
getLifecourseMusclePerfusionMale <- function(age)
#====================================================================================================
{
m = getLifecourseMuscleVolumeMaleSciV(age)
m35 = getLifecourseMuscleVolumeMaleSciV(35)
q = m*66.3/m35
return(q)
}
#====================================================================================================
getLifecourseMusclePerfusionFemale <- function(age)
#====================================================================================================
{
m = getLifecourseMuscleVolumeFemaleSciV(age)
m35 = getLifecourseMuscleVolumeFemaleSciV(35)
q = m*42.5/m35
return(q)
}
#====================================================================================================
getLifecoursePancreasPerfusion <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecoursePancreasPerfusionMale(age))
}
else if(gender == "F") {
return(getLifecoursePancreasPerfusionFemale(age))
}
}
#====================================================================================================
getLifecoursePancreasPerfusionMale <- function(age)
#====================================================================================================
{
m = getLifecoursePancreasVolumeMale(age)
m35 = getLifecoursePancreasVolumeMale(35)
q = m*3.9/m35
return(q)
}
#====================================================================================================
getLifecoursePancreasPerfusionFemale <- function(age)
#====================================================================================================
{
m = getLifecoursePancreasVolumeFemale(age)
m35 = getLifecoursePancreasVolumeFemale(35)
q = m*3.54/m35
return(q)
}
#====================================================================================================
getLifecourseSkinPerfusion <- function(age, gender, source = "sciv")
#====================================================================================================
{
if(is.na(age)) return(NA)
if (source == "bosgra"){
if(gender == "M") {
return(getLifecourseSkinPerfusionMale(age))
}
else if(gender == "F") {
return(getLifecourseSkinPerfusionFemale(age))
}
}else if(source == "sciv"){
if(gender == "M") {
return(getLifecourseSkinPerfusionMaleSciV(age))
}
else if(gender == "F") {
return(getLifecourseSkinPerfusionFemaleSciV(age))
}
}
}
#====================================================================================================
getLifecourseSkinPerfusionMale <- function(age)
#====================================================================================================
{
m = getLifecourseSkinVolumeMale(age)
m35 = getLifecourseSkinVolumeMale(35)
q = m*19.5/m35
return(q)
}
getLifecourseSkinPerfusionMaleSciV<- function(age){
vsknc25 <- getLifecourseSkinVolumeMaleSciV(25)/getLifecourseBodyWeightMale(25)
qsknc25 <- 0.058
vskn <- getLifecourseSkinVolumeMaleSciV(age)
bw <- getLifecourseBodyWeightMale(age)
qc <- getLifecourseCardiacOutput(age,"M")
vsknc <- vskn/bw
qsknc <- (vsknc/vsknc25)*qsknc25
qskn <- qsknc *qc
return(qskn)
}
getLifecourseSkinPerfusionFemaleSciV<- function(age){
vsknc25 <- getLifecourseSkinVolumeFemaleSciV(25)/getLifecourseBodyWeightFemale(25)
qsknc25 <- 0.058
vskn <- getLifecourseSkinVolumeFemaleSciV(age)
bw <- getLifecourseBodyWeightFemale(age)
qc <- getLifecourseCardiacOutput(age,"F")
vsknc <- vskn/bw
qsknc <- (vsknc/vsknc25)*qsknc25
qskn <- qsknc *qc
return(qskn)
}
#====================================================================================================
getLifecourseSkinPerfusionFemale <- function(age)
#====================================================================================================
{
m = getLifecourseSkinVolumeFemale(age)
m35 = getLifecourseSkinVolumeFemale(35)
q = m*17.7/m35
return(q)
}
#====================================================================================================
getLifecourseSpleenPerfusion <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseSpleenPerfusionMale(age))
}
else if(gender == "F") {
return(getLifecourseSpleenPerfusionFemale(age))
}
}
#====================================================================================================
getLifecourseSpleenPerfusionMale <- function(age)
#====================================================================================================
{
m = getLifecourseSpleenVolumeMale(age)
m35 = getLifecourseSpleenVolumeMale(35)
q = m*11.7/m35
return(q)
}
#====================================================================================================
getLifecourseSpleenPerfusionFemale <- function(age)
#====================================================================================================
{
m = getLifecourseSpleenVolumeFemale(age)
m35 = getLifecourseSpleenVolumeFemale(35)
q = m*10.6/m35
return(q)
}
#====================================================================================================
getLifecourseStomachPerfusion <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseStomachPerfusionMale(age))
}
else if(gender == "F") {
return(getLifecourseStomachPerfusionFemale(age))
}
}
#====================================================================================================
getLifecourseStomachPerfusionMale <- function(age)
#====================================================================================================
{
m = getLifecourseStomachVolumeMale(age)
m35 = getLifecourseStomachVolumeMale(35)
q = m*3.9/m35
return(q)
}
#====================================================================================================
getLifecourseStomachPerfusionFemale <- function(age)
#====================================================================================================
{
m = getLifecourseStomachVolumeFemale(age)
m35 = getLifecourseStomachVolumeFemale(35)
q = m*3.54/m35
return(q)
}
#====================================================================================================
getLifecourseThymusPerfusion <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseThymusPerfusionMale(age))
}
else if(gender == "F") {
return(getLifecourseThymusPerfusionFemale(age))
}
}
#====================================================================================================
getLifecourseThymusPerfusionMale <- function(age)
#====================================================================================================
{
m = getLifecourseThymusVolumeMale(age)
m35 = getLifecourseThymusVolumeMale(35)
q = m*0.39/m35
return(q)
}
#====================================================================================================
getLifecourseThymusPerfusionFemale <- function(age)
#====================================================================================================
{
m = getLifecourseThymusVolumeFemale(age)
m35 = getLifecourseThymusVolumeFemale(35)
q = m*0.37/m35
return(q)
}
#====================================================================================================
getLifecourseRemainingPerfusion <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseRemainingPerfusionMale(age))
}
else if(gender == "F") {
return(getLifecourseRemainingPerfusionFemale(age))
}
}
#====================================================================================================
getLifecourseRemainingPerfusionMale <- function(age)
#====================================================================================================
{
m = getLifecourseRemainingVolumeMale(age)
m35 = getLifecourseRemainingVolumeMale(35)
q = m*21.8/m35
return(q)
}
#====================================================================================================
getLifecourseRemainingPerfusionFemale <- function(age)
#====================================================================================================
{
m = getLifecourseRemainingVolumeFemale(age)
m35 = getLifecourseRemainingVolumeFemale(35)
q = m*20.5/m35
return(q)
}
#====================================================================================================
getLifecourseLungPerfusion <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseLungPerfusionMale(age))
}
else if(gender == "F") {
return(getLifecourseLungPerfusionFemale(age))
}
}
#====================================================================================================
getLifecourseLungPerfusionMale <- function(age)
#====================================================================================================
{
# Using data from Jongeneelen...
# Their reported lung perfusion is not cardiac output,
# but a small arterial flow (fraction of their reported CO)
q0 = 390*0.03 # They report CO as 390 L/h, their perfusion fraction if 0.03
m = getLifecourseRemainingVolumeMale(age)
m35 = getLifecourseRemainingVolumeMale(35)
q = m*q0/m35
return(q)
}
#====================================================================================================
getLifecourseLungPerfusionFemale <- function(age)
#====================================================================================================
{
# Using data from Joneneelen...
# Their reported lung perfusion is not cardiac output,
# but a small arterial flow (fraction of their reported CO)
q0 = 390*0.03 # They report CO as 390 L/h, their perfusion fraction if 0.03
m = getLifecourseRemainingVolumeFemale(age)
m35 = getLifecourseRemainingVolumeFemale(35)
q = m*q0/m35
return(q)
}
#===========
getLifecourseRichlyPerfusedTissuePerfusion<- function(age,gender){
if (is.na(age)) return(NA)
if(gender == "M"){
getLifecourseRichlyPerfusedTissuePerfusionMale(age)
}else if(gender == "F"){
getLifecourseRichlyPerfusedTissuePerfusionFemale(age)
}
}
getLifecourseRichlyPerfusedTissuePerfusionMale <- function(age){
vrpfc25 <- 0.042
qrpfc25 <- 0.215
vrpf <- getLifecourseRapidlyPerfusedVolumeMaleSciV(age)
bw <- getLifecourseBodyWeightMale(age)
qc <- getLifecourseCardiacOutput(age,"M")
vrpfc <- vrpf/bw
qrpfc <- (vrpfc/vrpfc25)*qrpfc25
qrpf <- qrpfc *qc
return(qrpf)
}
getLifecourseRichlyPerfusedTissuePerfusionFemale <- function(age){
vrpfc25 <- 0.042
qrpfc25 <- 0.215
vrpf <- getLifecourseRapidlyPerfusedVolumeFemaleSciV(age)
bw <- getLifecourseBodyWeightFemale(age)
qc <- getLifecourseCardiacOutput(age,"F")
vrpfc <- vrpf/bw
qrpfc <- (vrpfc/vrpfc25)*qrpfc25
qrpf <- qrpfc *qc
return(qrpf)
}
#===========
getLifecourseSlowlyPerfusedTissuePerfusion<- function(age,gender){
if (is.na(age)) return(NA)
if(gender == "M"){
getLifecourseSlowlyPerfusedTissuePerfusionMale(age)
}else if(gender == "F"){
getLifecourseSlowlyPerfusedTissuePerfusionFemale(age)
}
}
getLifecourseSlowlyPerfusedTissuePerfusionMale <- function(age){
vspfc25 <- getLifecourseSlowlyPerfusedVolumeMale(25)/getLifecourseBodyWeightMale(25)
qspfc25 <- 0.190 - 0.058 # 0.058 was fractional skin perfion
vspf <- getLifecourseSlowlyPerfusedVolumeMale(age)
bw <- getLifecourseBodyWeightMale(age)
qc <- getLifecourseCardiacOutput(age,"M")
vspfc <- vspf/bw
qspfc <- (vspfc/vspfc25)*qspfc25
qspf <- qspfc *qc
return(qspf)
}
getLifecourseSlowlyPerfusedTissuePerfusionFemale <- function(age){
vspfc25 <- getLifecourseSlowlyPerfusedVolumeFemale(25)/getLifecourseBodyWeightFemale(25)
qspfc25 <- 0.190 - 0.058 # 0.058 was fractional skin perfion
vspf <- getLifecourseSlowlyPerfusedVolumeFemale(age)
bw <- getLifecourseBodyWeightFemale(age)
qc <- getLifecourseCardiacOutput(age,"F")
vspfc <- vspf/bw
qspfc <- (vspfc/vspfc25)*qspfc25
qspf <- qspfc *qc
return(qspf)
}
#' Get the cardiac output based on the life course equations
#' @description Get the cardiac output for a specific age and gender. Uses either Bosgra or ScitoVation equations
#' @param age Age in years
#' @param gender Gender can be either "M" for male or "F" for female
#' @param source Source of the equations. Either from Bosgra et al. "bosgra" or from ScitoVation publications as "sciv"
#' @param qc_var variability for cardiac output. Used to account for exercise level. Can only be used when source = "sciv"
#' @export
#'
getLifecourseCardiacOutput <- function(age, gender, source = "sciv",qc_var= 0)
#====================================================================================================
{
if(is.na(age)) return(NA)
if (source == "bosgra"){
if(gender == "M") {
return(getLifecourseCardiacOutputMale(age))
}
else if(gender == "F") {
return(getLifecourseCardiacOutputFemale(age))
}
}else if(source == "sciv"){
if(gender == "M") {
return(getLifecourseCardiacOutputMaleSciV(age,qc_var))
}
else if(gender == "F") {
return(getLifecourseCardiacOutputFemaleSciV(age,qc_var))
}
}
}
#============================
getLifecourseCardiacOutputMaleSciV<- function(age,qc_var){
mbsa <- getLifecourseBodySurfaceAreaMale(age)
# scaling factor for body surface area to cardiac output
bsa_qc_scaling <- 3.5
# QC min is variability factor for inter individual variation in QC,
# can be also used to adjust cardiac output based on activity level
qc <- mbsa*bsa_qc_scaling*(1+qc_var)*60
}
#============================
getLifecourseCardiacOutputFemaleSciV<- function(age,qc_var){
mbsa <- getLifecourseBodySurfaceAreaFemale(age)
# scaling factor for body surface area to cardiac output
bsa_qc_scaling <- 3.5
# QC min is variability factor for inter individual variation in QC,
# can be also used to adjust cardiac output based on activity level
qc <- mbsa*bsa_qc_scaling*(1+qc_var)*60
}
#====================================================================================================
getLifecourseCardiacOutputMale <- function(age)
#====================================================================================================
{
q = getLifecourseAdiposePerfusionMale(age) +
getLifecourseBonePerfusionMale(age) +
getLifecourseBrainPerfusionMale(age) +
getLifecourseGonadPerfusionMale(age) +
getLifecourseHeartPerfusionMale(age) +
getLifecourseKidneyPerfusionMale(age) +
getLifecourseLiverArterialPerfusionMale(age) +
getLifecourseMusclePerfusionMale(age) +
getLifecourseRemainingPerfusionMale(age) +
getLifecourseSkinPerfusionMale(age) +
getLifecourseThymusPerfusionMale(age) +
getLifecourseIntestinePerfusionMale(age) +
getLifecoursePancreasPerfusionMale(age) +
getLifecourseSpleenPerfusionMale(age) +
getLifecourseStomachPerfusionMale(age)
return(q)
}
#====================================================================================================
getLifecourseCardiacOutputFemale <- function(age)
#====================================================================================================
{
q = getLifecourseAdiposePerfusionFemale(age) +
getLifecourseBonePerfusionFemale(age) +
getLifecourseBrainPerfusionFemale(age) +
getLifecourseGonadPerfusionFemale(age)+
getLifecourseHeartPerfusionFemale(age) +
getLifecourseKidneyPerfusionFemale(age) +
getLifecourseLiverArterialPerfusionFemale(age) +
getLifecourseMusclePerfusionFemale(age) +
getLifecourseRemainingPerfusionFemale(age) +
getLifecourseSkinPerfusionFemale(age) +
getLifecourseThymusPerfusionFemale(age) +
getLifecourseIntestinePerfusionFemale(age) +
getLifecoursePancreasPerfusionFemale(age) +
getLifecourseSpleenPerfusionFemale(age) +
getLifecourseStomachPerfusionFemale(age)
return(q)
}
#' Get the ventilation rate for a given age and gender
#' @description Uses life course equation to calculate a ventilation rate for a specific age and gender
#' @param age Age in years
#' @param gender Either "M" for Male for "F" for Female
#' @param activity Activity level. Can be "rest" or "light exercise"
#' @param source source of equations either "sciv" or "bosgra"
#' @export
getLifecourseVentilationRate <- function(age, gender,activity="rest",source="sciv")
#====================================================================================================
{
if(is.na(age)) return(NA)
if (source == "bosgra"){
if (activity != "rest"){
warning(sprintf(
"The source does not have valid equations for activity type '%s'.
Using the default 'rest' activity instead",activity)
)
}
if(gender == "M") {
return(getLifecourseVentilationRateMale(age))
}
else if(gender == "F") {
return(getLifecourseVentilationRateFemale(age))
}
} else if(source == "sciv") {
if(gender == "M"){
return(getLifecourseVentilationRateMaleSCIV(age,activity))
}else if(gender == "F"){
return(getLifecourseVentilationRateFemaleSCIV(age,activity))
}
}
}
#=====
getLifecourseVentilationRateMaleSCIV <- function(age,activity){
if (activity == "rest"){
return(0.4493*exp(log(0.09919/0.4493)*exp(-0.175*age))*1000)
}
}
#=======
getLifecourseVentilationRateFemaleSCIV<- function(age,activity){
if (activity == "rest"){
return(0.3255*exp(log(0.08771/0.3255)*exp(-0.3731*age))*1000)
}
}
#====================================================================================================
getLifecourseVentilationRateMale <- function(age)
#====================================================================================================
{
co = getLifecourseCardiacOutputMale(age)
qp = 0.96*co + 58
return(qp)
}
#====================================================================================================
getLifecourseVentilationRateFemale <- function(age)
#====================================================================================================
{
co = getLifecourseCardiacOutputFemale(age)
qp = 0.62*co + 82
return(qp)
}
#'Get the Lung Dead Space for a given age and gender
#' @description Uses life course equation to calculate the lung dead space for a specific age and gender
#' @param age Age in years
#' @param gender Either "M" for Male for "F" for Female
#' @export
getLifecourseLungDeadSpace<- function(age,gender){
if(is.na(age)) return(NA)
if(gender == "M"){
return(getLifecourseLungDeadSpaceMale(age))
}else if(gender == "F"){
return(getLifecourseLungDeadSpaceFemale(age))
}
}
#=========
getLifecourseLungDeadSpaceMale <- function(age){
return(0.17*exp(log(0.01371/0.17)*exp(-0.13*age)))
}
#=========
getLifecourseLungDeadSpaceFemale <- function(age){
return(0.1274*exp(log(0.01345/0.1274)*exp(-0.1609*age)))
}
#' Get the tidal volume for a given age and gender
#' @description Uses life course equation to calculate the tidal volume for a specific age and gender
#' @param age Age in years
#' @param gender Either "M" for Male for "F" for Female
#' @param activity Activity level. Can be "rest" or "light activity"
#' @export
getLifecourseTidalVolume <- function(age,gender,activity ="rest"){
if(is.na(age)) return(NA)
if (gender=="M"){
return(getLifecourseTidalVolumeMale(age,activity))
}else if(gender=="F"){
return(getLifecourseTidalVolumeFemale(age,activity))
}
}
#======
getLifecourseTidalVolumeMale<- function(age,activity){
if (activity == "rest"){
return(0.6842*exp(log(0.04306/0.6842)*exp(-0.1357*age)))
}else if(activity == "light exercise"){
if(age <= 1){
return(1.661*exp(log(0.07428/1.661)*exp(-0.1095*age)))
}else{
return(0.1041+(age^2.727)*(1.478-0.1041)/(age^2.727+12.23^2.727))
}
}
}
#=======
getLifecourseTidalVolumeFemale<- function(age,activity){
if (activity == "rest"){
return(0.02712+(age^0.9173)*(0.9599-0.02712)/(age^0.9173+27.01^0.9173))
}else if(activity == "light exercise"){
if (age <= 1){
return(1.159*exp(log(0.07248/1.159)*exp(-0.1362*age)))
}else{
return(0.1036+(age^3.064)*(1.055-0.1036)/(age^3.064+9.58^3.064))
}
}
}
#' Get the urine production rate for a given age and gender
#' @description Uses life course equation to calculate a urine production rate for a specific age and gender
#' @param age Age in years
#' @param gender Either "M" for Male for "F" for Female
#' @export
getLifecourseUrineProductionRate <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseUrineProductionRateMale(age))
}
else if(gender == "F") {
return(getLifecourseUrineProductionRateFemale(age))
}
}
#====================================================================================================
getLifecourseUrineProductionRateMale <- function(age)
#====================================================================================================
{
ur = -2.96538E-06*age^4 + 7.71852E-04*age^3 - 7.54327E-02*age^2 + 3.04687E+00*age + 1.26931E+01
return(ur)
}
#====================================================================================================
getLifecourseUrineProductionRateFemale <- function(age)
#====================================================================================================
{
ur = 1.59275E-04*age^3 - 3.09917E-02*age^2 + 1.70013E+00*age + 2.07921E+01
return(ur)
}
#' Get the Glomerular Filteration Rate for a given age and gender
#' @description Uses life course equation to calculate a GFR for a specific age and gender
#' @param age Age in years
#' @param gender Either "M" for Male for "F" for Female
#' @export
getLifecourseGlomerularFiltrationRate <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseGlomerularFiltrationRateMale(age))
}
else if(gender == "F") {
return(getLifecourseGlomerularFiltrationRateFemale(age))
}
}
#====================================================================================================
getLifecourseGlomerularFiltrationRateMale <- function(age)
#====================================================================================================
{
gfr = NA
bw = getLifecourseBodyWeightMale(age)
mbw10d = getLifecourseBodyWeightMale(1/365)
mbw1 = getLifecourseBodyWeightMale(1)
bsa = getLifecourseBodySurfaceAreaMale(age)
bsa1 = getLifecourseBodySurfaceAreaMale(1)
bsa30 = getLifecourseBodySurfaceAreaMale(30)
gfr_bsa = 7.62
days = age/365
if(age >= 0 && age <= 1/365) # 1 day
{
gfr = 0.12 * (1.0 + 1.0) * (-0.0013 * mbw10d**2.0 + 0.2025 * mbw10d - 0.1363) * (gfr_bsa * bsa1 / 1.73) / ((-0.0013 * mbw1**2.0 + 0.2025 * mbw1 - 0.1363) * (0.48 + (0.0571 * (10.0 - 3.0))))
}
else if (age > 1/365 && age <= 3/365) # 3 days
{
gfr = 0.12 * (1.0 + days) * (-0.0013 * mbw10d**2.0 + 0.2025 * mbw10d - 0.1363) * (gfr_bsa * bsa1 / 1.73) / ((-0.0013 * mbw1**2.0 + 0.2025 * mbw1 - 0.1363) * (0.48 + (0.0571 * (10.0 - 3.0))))
}
else if (age > 3/365 && age <= 10/365) # 10 days
{
gfr = (0.48 + (0.0571 * (days - 3))) * (-0.0013 * mbw10d**2.0 + 0.2025 * mbw10d - 0.1363) * (gfr_bsa * bsa1 / 1.73) / ((-0.0013 * mbw1**2.0 + 0.2025 * mbw1 - 0.1363) * (0.48 + (0.0571 * (10.0 - 3.0))))
}
else if (age > 10/365 && age <= 1)
{
gfr = (-0.0013 * bw**2.0 + 0.2025 * bw - 0.1363) * (gfr_bsa * bsa1 / 1.73) / (-0.0013 * mbw1**2.0 + 0.2025 * mbw1 - 0.1363)
}
else if (age > 1 && age <= 30)
{
gfr = gfr_bsa * bsa / 1.73
}
else if (age > 30)
{
gfr = gfr_bsa * bsa30 / 1.73 - (0.0066 * (7.62 * bsa30 / 1.73) * (age - 30))
}
return(gfr)
}
#====================================================================================================
getLifecourseGlomerularFiltrationRateFemale <- function(age)
#====================================================================================================
{
gfr = NA
bw = getLifecourseBodyWeightFemale(age)
mbw10d = getLifecourseBodyWeightFemale(1/365)
mbw1 = getLifecourseBodyWeightFemale(1)
bsa = getLifecourseBodySurfaceAreaFemale(age)
bsa1 = getLifecourseBodySurfaceAreaFemale(1)
bsa30 = getLifecourseBodySurfaceAreaFemale(30)
gfr_bsa = 7.62
days = age/365
if(age >= 0 && age <= 1/365) # 1 day
{
gfr = 0.12 * (1.0 + 1.0) * (-0.0013 * mbw10d**2.0 + 0.2025 * mbw10d - 0.1363) * (gfr_bsa * bsa1 / 1.73) / ((-0.0013 * mbw1**2.0 + 0.2025 * mbw1 - 0.1363) * (0.48 + (0.0571 * (10.0 - 3.0))))
}
else if (age > 1/365 && age <= 3/365) # 3 days
{
gfr = 0.12 * (1.0 + days) * (-0.0013 * mbw10d**2.0 + 0.2025 * mbw10d - 0.1363) * (gfr_bsa * bsa1 / 1.73) / ((-0.0013 * mbw1**2.0 + 0.2025 * mbw1 - 0.1363) * (0.48 + (0.0571 * (10.0 - 3.0))))
}
else if (age > 3/365 && age <= 10/365) # 10 days
{
gfr = (0.48 + (0.0571 * (days - 3))) * (-0.0013 * mbw10d**2.0 + 0.2025 * mbw10d - 0.1363) * (gfr_bsa * bsa1 / 1.73) / ((-0.0013 * mbw1**2.0 + 0.2025 * mbw1 - 0.1363) * (0.48 + (0.0571 * (10.0 - 3.0))))
}
else if (age > 10/365 && age <= 1)
{
gfr = (-0.0013 * bw**2.0 + 0.2025 * bw - 0.1363) * (gfr_bsa * bsa1 / 1.73) / (-0.0013 * mbw1**2.0 + 0.2025 * mbw1 - 0.1363)
}
else if (age > 1 && age <= 30)
{
gfr = gfr_bsa * bsa / 1.73
}
else if (age > 30)
{
gfr = gfr_bsa * bsa30 / 1.73 - (0.0062 * (7.62 * bsa30 / 1.73) * (age - 30))
}
return(gfr)
}
sahu27/sahu documentation built on May 30, 2019, 2:06 a.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.
# Small utility function for linear interpolation
# Used internally
interp2 <- function(x1, x2, y1, y2, x)
{
m = (y2 - y1)/(x2 - x1)
y = y1 + m*(x - x1)
return(y)
}
#' Get volumes for tissues provided on the basis of age and gender
#'
#' @param age Age of the organism in years
#' @param gender The gender of the organism "M" for Male or "F" for Female
#' @param perf_frct fraction of perfused tissue. default to 0.85
#' @param tissues List of tissues for which the volumes are needed. The tissues can be one of the following
#' liver,
#' blood,
#' fat,
#' bone,
#' brain,
#' gonad,
#' heart,
#' intestine,
#' kidney,
#' lung,
#' pancreas,
#' skin,
#' spleen,
#' stomach,
#' thymus,
#' remaining,
#' muscle
#' @return
#' list containing volumes for age, gender and tissues.
#' @export
#'
getLifecourseTissueVolumes<- function(age = 25, gender = "M",perf_frct = 0.85,
tissues=list()){
tissue_vol_list <- NULL
available_tissues <- c("blood","fat","skin","muscle","bone","brain","lung",
"heart","gi","kidney","liver","rpf","spf")
spf_tissues <- c("fat","skin","muscle","bone")
rpf_tissues <- available_tissues[!(available_tissues %in% c(spf_tissues,"rpf","spf"))]
inactive_tissues <- dplyr::setdiff(available_tissues,tissues)
rpf_inactive_tissues <- inactive_tissues[inactive_tissues %in% rpf_tissues]
spf_inactive_tissues <- inactive_tissues[inactive_tissues %in% spf_tissues]
if(is.na(age)) return
tissue_vol_list[["gi"]]<-getLifecourseGutVolume(age,gender)
tissue_vol_list[["liver"]]<-getLifecourseLiverVolume(age,gender)
tissue_vol_list[["blood"]]<-getLifecourseBloodVolume(age,gender)
tissue_vol_list[["fat"]]<-getLifecourseAdiposeVolume(age,gender)
tissue_vol_list[["bone"]]<-getLifecourseBoneVolume(age,gender)
tissue_vol_list[["brain"]]<-getLifecourseBrainVolume(age,gender)
tissue_vol_list[["heart"]]<-getLifecourseHeartVolume(age,gender)
tissue_vol_list[["kidney"]]<-getLifecourseKidneyVolume(age,gender)
tissue_vol_list[["lung"]]<-getLifecourseLungVolume(age,gender)
tissue_vol_list[["skin"]]<-getLifecourseSkinVolume(age,gender)
tissue_vol_list[["muscle"]]<-getLifecourseMuscleVolume(age,gender)
# for richly perfused get value
#from equation and add inactive tissue volumes
vol <- getLifecourseRapidlyPerfusedVolume(age,gender)
rpf_inact_vol <- sum(tissue_vol_list[rpf_inactive_tissues])
tissue_vol_list[["rpf"]]<-vol+rpf_inact_vol
# for slowly perfused get value
#from equation and add inactive tissue volumes
vol <- getLifecourseSlowlyPerfusedVolume(age,gender,perf_frct)
spf_inact_vol <- sum(tissue_vol_list[spf_inactive_tissues])
tissue_vol_list[["spf"]]<-vol+spf_inact_vol
#print(tissue_vol_list[tissues])
return(tissue_vol_list[tissues])
}
#' Get perfusion for tissues provided on the basis of age and gender
#'
#' @param age Age of the organism in years
#' @param gender The gender of the organism "M" for Male or "F" for Female
#' @param source source of the equation. defaults to "sciv" for scitovation
#' @param tissues List of tissues for which blood perfusion is needed. The
#' tissues can be any of the following
#' liver,
#' fat,
#' bone,
#' brain,
#' gonad,
#' heart,
#' intestine,
#' kidney,
#' lung,
#' pancreas,
#' skin,
#' spleen,
#' stomach,
#' thymus,
#' muscle,
#' remaining.
#'
#' @return list containing blood perfusion of tissues for the given age and
#' gender.
#' @export
getLifecourseTissuePerfusion<- function(age = 25, gender = "M", tissues = list(),source = "sciv"){
if(is.na(age)) return(NA)
if (source == "sciv"){
#get scaling factor for cardiac output calculated as sum(qc) or from SCIV equation
qc_scaling <- 1
}else{
qc_scaling <- 1.164749
}
tissue_perf_list <- NULL
available_tissues <- c("fat","skin","muscle","bone","brain","lung",
"heart","gi","kidney","liver","rpf","spf")
spf_tissues <- c("fat","skin","muscle")
rpf_tissues <- available_tissues[!(available_tissues %in% c(spf_tissues,"rpf","spf"))]
inactive_tissues <- dplyr::setdiff(available_tissues,tissues)
rpf_inactive_tissues <- inactive_tissues[inactive_tissues %in% rpf_tissues]
spf_inactive_tissues <- inactive_tissues[inactive_tissues %in% spf_tissues]
if ("gi" %in% tissues){
tissue_perf_list[["gi"]] <- (getLifecourseGutPerfusion(age,gender)) * qc_scaling
tissue_perf_list[["liver_art"]]<- getLifecourseLiverArterialPerfusion(age,gender) * qc_scaling
tissue_perf_list[["liver_ven"]]<- (tissue_perf_list[["liver_art"]] +
tissue_perf_list[["gi"]])
}else{
tissue_perf_list[["liver_art"]]<- (getLifecourseLiverArterialPerfusion(age,gender)+
getLifecourseGutPerfusion(age,gender)) * qc_scaling
tissue_perf_list[["liver_ven"]]<- tissue_perf_list[["liver_art"]]
}
if (!("liver" %in% tissues)){
rpf_inactive_tissues <- c(inactive_tissues,"liver")
tissue_perf_list[["liver"]]<- getLifecourseLiverArterialPerfusion(age,gender)* qc_scaling
}
tissue_perf_list[["fat"]]<- getLifecourseAdiposePerfusion(age,gender)* qc_scaling
tissue_perf_list[["bone"]]<- getLifecourseBonePerfusion(age,gender)* qc_scaling
tissue_perf_list[["brain"]]<-getLifecourseBrainPerfusion(age,gender)* qc_scaling
# tissue_perf_list[["gonad"]]<- getLifecourseGonadPerfusion(age,gender)* qc_scaling
tissue_perf_list[["heart"]]<- getLifecourseHeartPerfusion(age,gender)* qc_scaling
tissue_perf_list[["kidney"]]<-getLifecourseKidneyPerfusion(age,gender)* qc_scaling
tissue_perf_list[["lung"]]<- getLifecourseLungPerfusion(age,gender)* qc_scaling
# tissue_perf_list[["pancreas"]]<- getLifecoursePancreasPerfusion(age,gender)* qc_scaling
tissue_perf_list[["skin"]]<- getLifecourseSkinPerfusion(age,gender)* qc_scaling
# tissue_perf_list[["spleen"]]<- getLifecourseSpleenPerfusion(age,gender)* qc_scaling
# tissue_perf_list[["thymus"]]<- getLifecourseThymusPerfusion(age,gender)* qc_scaling
tissue_perf_list[["muscle"]]<- getLifecourseMusclePerfusion(age,gender)* qc_scaling
# for rapidly perfused tissue flow
rpf_perf <- getLifecourseRichlyPerfusedTissuePerfusion(age,gender)* qc_scaling
inact_perf <- sum(tissue_perf_list[rpf_inactive_tissues])
tissue_perf_list[["rpf"]]<- rpf_perf+inact_perf
# for slowly perfused tissue flow
spf_perf <- getLifecourseSlowlyPerfusedTissuePerfusion(age,gender)* qc_scaling
inact_perf <- sum(tissue_perf_list[spf_inactive_tissues])
tissue_perf_list[["spf"]]<- spf_perf+inact_perf
if("liver" %in% tissues){
tissues <- tissues[tissues != "liver"]
tissues <- c(tissues,"liver_art","liver_ven")
}
return(tissue_perf_list[tissues])
}
#' Get average body weight using the life course equation
#' @description The function is used to calculate the average body weight in kgs for humans based on age and gender.
#' The function uses life course equations developed by Scitovation.
#' @param age age in years
#' @param gender Either "M" for male or "F" for female
#' @return Body Weight in kgs
#' @export
getLifecourseBodyWeight <- function(age, gender){
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseBodyWeightMale(age))
}else if(gender == "F") {
return(getLifecourseBodyWeightFemale(age))
}
}
#' Calculate body weight in kg of average human male using the lifecourse
#' equation
#' @description This function is not called directly by the user. See
#' \code{getLifeCourseBodyWeight}
#' @param age age in years
#' @return Body weight in kg
getLifecourseBodyWeightMale <- function(age){
mwbirth = 4
mwchild = 28
mwadult = 56
half = 6
k = 70
theta = 14.85
diff_bh_bw = -1.46
mbw25 = 81.208
wa = diff_bh_bw + theta
lambda = log(k**2) / (2.0 * wa * mwadult)
bw = NA
if(age >= 0 && age < 26) {
bw = mwbirth + (mwchild*age)/(half + age) + (mwadult/(1.0 + k*exp(-lambda*mwadult*age)))
}else if(age >= 26) {
months = age*12
bw = ((2.19e-08 * months**3.0) - (1.22e-04 * months**2.0) + (0.120*months) + 50.824)*mbw25/76.6
}
return(bw)
}
#' Calculate body weight in kg of average human female using the lifecourse
#' equation
#' @description This function is not called directly by the user. See
#' \code{getLifeCourseBodyWeight}
#' @param age age in years
#' @return Body weight in kg
getLifecourseBodyWeightFemale <- function(age){
mwbirth = 3.4
mwchild = 22
mwadult = 42.854
wadult = 42.668
half = 3
mbwadult = 65.236
k = 142
lambda = 0.010279
theta = 11.5
h1 = 163
bw = NA
if(age >= 0 && age < 22.3333) {
bw = 3.4 +(mwchild*age)/(3.0 + age) + (mwadult/(1.0 + 142.11536*exp(-0.01028*mwadult*age)))
}else if(age >= 22.3333) {
months = age*12
bw = ((6.17*10^-09*months^3)-(9.68*10^-5*months^2)+(0.109*months)+43.790)*mbwadult/66.17
}
return(bw)
}
#' Get average body height using the life course equation
#' @description The function is used to calculate the average body height for humans based on age and gender.
#' The function uses life course equations developed by Scitovation.
#' @param age age in years
#' @param gender Either "M" for male or "F" for female
#' @return Body Height
#' @export
getLifecourseBodyHeight <- function(age, gender){
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseBodyHeightMale(age))
}
else if(gender == "F") {
return(getLifecourseBodyHeightFemale(age))
}
}
#' Calculate body height of average human male using the lifecourse
#' equation
#' @description This function is not called directly by the user.
#' @param age age in years
#' @return Body height
getLifecourseBodyHeightMale <- function(age){
if(is.na(age)) return(NA)
h1 = 177
theta = 14.85
s0 = 0.135
s1 = 1.5
c1 = 0.9
d1 = 0.5
mht = 168.6
mbht3 = h1 - 2.0*(h1 - mht)/(exp(s0*(age - theta)) + exp(s1*(age - theta)))
mbhtj3 = h1*(1.0 - 1.0/(1.0 + ((age + 0.75)/d1)^c1))
bh = NA
if(age >= 0 && age < 3) {
bh = h1*(1.0 - 1.0/(1.0 + ((age + 0.75)/d1)^c1))*mbht3/mbhtj3
} else if(age >= 3) {
bh = 177.0 - 2.0*(177.0 - mht)/(exp(s0*(age - theta)) + exp(s1*(age - theta)))
}
return(bh)
}
#====================================================================================================
getLifecourseBodyHeightFemale <- function(age)
#====================================================================================================
{
if(is.na(age)) return(NA)
h1 = 162.15
theta = 11.2536
s0 = 0.135
s1 = 1.27
mht = 151
mbht = 94.2
mbhtj = 94.81
bh = NA
if(age >= 0 && age <= 3) {
bh = h1*(1 - 1/(1 + ((age + 0.75)/2.3)^0.7))*mbht/mbhtj
} else if(age >= 3) {
bh = h1 - 2*(h1 - mht)/(exp(s0*(age - theta)) + exp(s1*(age - theta)))
}
return(bh)
}
#====================================================================================================
getLifecourseBodySurfaceArea <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseBodySurfaceAreaMale(age))
}
else if(gender == "F") {
return(getLifecourseBodySurfaceAreaFemale(age))
}
}
#====================================================================================================
getLifecourseBodySurfaceAreaMale <- function(age)
#====================================================================================================
{
mbw = getLifecourseBodyWeightMale(age)
mbh = getLifecourseBodyHeightMale(age)
bsa = exp(-3.751 + 0.422*log(mbh) + 0.515*log(mbw))
return(bsa)
}
#====================================================================================================
getLifecourseBodySurfaceAreaFemale <- function(age)
#====================================================================================================
{
mbw = getLifecourseBodyWeightFemale(age)
mbh = getLifecourseBodyHeightFemale(age)
bsa = exp(-3.751 + 0.422*log(mbh) + 0.515*log(mbw))
return(bsa)
}
#====================================================================================================
getLifecourseBodyMassIndex <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseBodyMassIndexMale(age))
}
else if(gender == "F") {
return(getLifecourseBodyMassIndexFemale(age))
}
}
#====================================================================================================
getLifecourseBodyMassIndexMale <- function(age)
#====================================================================================================
{
mbw = getLifecourseBodyWeightMale(age)
mbh = getLifecourseBodyHeightMale(age)
bmi = mbw/((mbh/100)**2)
return(bmi)
}
#====================================================================================================
getLifecourseBodyMassIndexFemale <- function(age)
#====================================================================================================
{
mbw = getLifecourseBodyWeightFemale(age)
mbh = getLifecourseBodyHeightFemale(age)
bmi = mbw/((mbh/100)**2)
return(bmi)
}
#====================================================================================================
getLifecourseHematocrit <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseHematocritMale(age))
}
else if(gender == "F") {
return(getLifecourseHematocritFemale(age))
}
}
#====================================================================================================
getLifecourseHematocritMale <- function(age)
#====================================================================================================
{
hct = NA;
if(age >= 0 && age < 2) {
hct = 0.359
} else if(age >= 2) {
hct = (((1.12815e-06)*(age**3.0)) - (1.72362e-04*(age**2.0)) + (8.15264e-03*age) + 0.327363)
}
return(hct)
}
#====================================================================================================
getLifecourseHematocritFemale <- function(age)
#====================================================================================================
{
hct = NA;
# Note: this is same as male equation
if(age >= 0 && age < 2) {
hct = 0.359
} else if(age >= 2) {
hct = (((1.12815e-06)*(age**3.0)) - (1.72362e-04*(age**2.0)) + (8.15264e-03*age) + 0.327363)
}
return(hct)
}
#====================================================================================================
getLifecourseBloodVolume <- function(age, gender, source = "sciv")
#====================================================================================================
{
if(is.na(age)) return(NA)
if (source == "bosgra"){
if(gender == "M") {
return(getLifecourseBloodVolumeMale(age))
}
else if(gender == "F") {
return(getLifecourseBloodVolumeFemale(age))
}
}else if(source == "sciv"){
if(gender == "M") {
return(getLifecourseBloodVolumeMaleSciV(age))
}
else if(gender == "F") {
return(getLifecourseBloodVolumeFemaleSciV(age))
}
}
}
#====================================================================================================
getLifecourseBloodVolumeMale <- function(age)
#====================================================================================================
{
bsa = getLifecourseBodySurfaceAreaMale(age)
vblood = 3.33*bsa - 0.81
return(vblood)
}
getLifecourseBloodVolumeMaleSciV<- function(age){
mbsa <- getLifecourseBodySurfaceAreaMale(age)
hct <- getLifecourseHematocritMale(age)
bw <- getLifecourseBodyWeightMale(age)
#constants:
a <- 10.0
b <- 1.2082
c <- 3.2869
d <- 0.0
e <- 1000.0
vpls <- (a^(b *log10(mbsa) + c)) * (1 + d) * ((1 - hct) / e)
vbldc <- (vpls/bw)/(1-hct)
vblood <- vbldc*bw
return(vblood)
}
getLifecourseBloodVolumeFemaleSciV<- function(age){
mbsa <- getLifecourseBodySurfaceAreaFemale(age)
hct <- getLifecourseHematocritFemale(age)
bw <- getLifecourseBodyWeightFemale(age)
#constants:
a <- 10.0
b <- 1.2082
c <- 3.2869
e <- 1000.0
#equations
vpls <- (a^(b *log10(mbsa) + c)) *((1 - hct) / e)
vbldc <- (vpls/bw)/(1-hct)
vblood <- vbldc*bw
return(vblood)
}
#====================================================================================================
getLifecourseBloodVolumeFemale <- function(age)
#====================================================================================================
{
bsa = getLifecourseBodySurfaceAreaFemale(age)
vblood = 2.66*bsa - 0.46
return(vblood)
}
#====================================================================================================
getLifecourseAdiposeVolume <- function(age, gender, source = "sciv")
#====================================================================================================
{
if(is.na(age)) return(NA)
if(source=="bosgra"){
if(gender == "M") {
return(getLifecourseAdiposeVolumeMaleSciV(age))
}
else if(gender == "F") {
return(getLifecourseAdiposeVolumeFemaleSciV(age))
}
}else if(source == "sciv"){
if(gender == "M") {
return(getLifecourseAdiposeVolumeMaleSciV(age))
}
else if(gender == "F") {
return(getLifecourseAdiposeVolumeFemaleSciV(age))
}
}
}
#====================================================================================================
getLifecourseAdiposeVolumeMaleSciV <- function(age)
#====================================================================================================
{
vadipose = NA
# Note, these are not the Bosgra equations. Those eqns apparently have some errors,
# so I'm using the Scitovation eqns here.
mbw25 = 81.21
mbmi25 = 25.92
mbmi20 = 24.07
bw = getLifecourseBodyWeightMale(age)
bmi = getLifecourseBodyMassIndexMale(age)
mvfatadult = 18.02
mperfat20a = 22
mperfat20b = 23.1
if(age >= 0 && age < 20) {
vadipose = bw*((2.9875*exp(-0.129*age) + 0.67)*bmi + 0.2635*age - 4.843)/100.0
}
else if(age >= 20) {
vadipose = bw*(-5.33798*bmi + 0.11149*(bmi**2.0) + 0.09795*age + 85.24521)*(mperfat20a/mperfat20b)/100.0
}
return(vadipose)
}
#====================================================================================================
getLifecourseAdiposeVolumeFemaleSciV <- function(age)
#====================================================================================================
{
vadipose = NA
# Note, these are not the Bosgra equations. Those eqns apparently have some errors,
# so I'm using the Scitovation eqns here.
mbw25 = 81.21
mbmi25 = 25.92
mbmi20 = 24.07
bw = getLifecourseBodyWeightFemale(age)
bmi = getLifecourseBodyMassIndexFemale(age)
mvfatadult = 24.15
mperfat25a = 36.51
mperfat25b = 37.32
if(age >= 0 && age < 25) {
vadipose = bw*((1.5334*exp(-0.103*age) + 0.67)*bmi + 0.6276*age + 1.0301)/100.0
}
else if(age >= 25) {
vadipose = bw*(1.9224*bmi - 0.018517*(bmi**2.0) + 0.05537*age - 0.794894)*(mperfat25a/mperfat25b)/100.0
}
return(vadipose)
}
#====================================================================================================
getLifecourseBoneVolume <- function(age, gender, source = "sciv")
#====================================================================================================
{
if(is.na(age)) return(NA)
if (source == "Bosgra"){
if(gender == "M") {
return(getLifecourseBoneVolumeMale(age))
}
else if(gender == "F") {
return(getLifecourseBoneVolumeFemale(age))
}
}else if (source == "sciv"){
if(gender == "M") {
return(getLifecourseBoneVolumeMaleSciV(age))
}
else if(gender == "F") {
return(getLifecourseBoneVolumeFemaleSciV(age))
}
}
}
#====================================================================================================
getLifecourseBoneVolumeMale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightMale(age)
vbone = exp(0.0689)*((h/100)**2.67)
return(vbone)
}
#====================================================================================================
getLifecourseBoneVolumeFemale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightFemale(age)
vbone = exp(0.0689)*((h/100)**2.67)
return(vbone)
}
getLifecourseBoneVolumeMaleSciV<- function(age){
# calculated using linear interpolation
x <- c(0,1,5,10,15,25)
y <- c(0.05,0.15,0.34,0.63,1.08,1.17)
vals <- approx(x,y,age,"linear",rule = 2)
return(vals$y)
}
getLifecourseBoneVolumeFemaleSciV<- function(age){
# calculated using linear interpolation
x <- c(0,1,5,10,15,25)
y <- c(0.5,0.15,0.34,0.63,1,0.9)
vals <- approx(x,y,age,"linear",rule = 2)
return(vals$y)
}
#====================================================================================================
getLifecourseBrainVolume <- function(age, gender, source = "sciv")
#====================================================================================================
{
if(is.na(age)) return(NA)
if(source=="bosgra"){
if(gender == "M") {
return(getLifecourseBrainVolumeMale(age))
}
else if(gender == "F") {
return(getLifecourseBrainVolumeFemale(age))
}
}else if(source=="sciv"){
if(gender == "M") {
return(getLifecourseBrainVolumeMaleSciV(age))
}
else if(gender == "F") {
return(getLifecourseBrainVolumeFemaleSciV(age))
}
}
}
#====================================================================================================
getLifecourseBrainVolumeMale <- function(age)
#====================================================================================================
{
v0 = 0.405
vbrain = v0*(3.68 - 2.68*exp(-age/0.89))*(exp(-age/629))
return(vbrain)
}
#====================================================================================================
getLifecourseBrainVolumeFemale <- function(age)
#====================================================================================================
{
v0 = 0.373
vbrain = v0*(3.68 - 2.68*exp(-age/0.89))*(exp(-age/629))
return(vbrain)
}
getLifecourseBrainVolumeMaleSciV <- function(age){
#constants
a <- 10.0
b <- 0.315
c <- 9.0
d <- 6.92
vbrain <- a*(age+b)/(c+d*age)
return(vbrain)
}
getLifecourseBrainVolumeFemaleSciV <- function(age){
#constants
a <- 10.0
b <- 0.315
c <- 9.0
d <- 6.92
vbrain <- a*(age+b)/(c+d*age)
return(vbrain)
}
#====================================================================================================
getLifecourseGonadVolume <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseGonadVolumeMale(age))
}
else if(gender == "F") {
return(getLifecourseGonadVolumeFemale(age))
}
}
#====================================================================================================
getLifecourseGonadVolumeMale <- function(age)
#====================================================================================================
{
vgon = (3.3 + 53*(1 - exp(-(age/17.5)**5.4)))/1000 # Convert to kg
return(vgon)
}
#====================================================================================================
getLifecourseGonadVolumeFemale <- function(age)
#====================================================================================================
{
vgon = (3.3 + 90*(1 - exp(-(age/16.8)**6.7)))/1000 # Convert to kg
return(vgon)
}
#====================================================================================================
getLifecourseHeartVolume <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseHeartVolumeMale(age))
}
else if(gender == "F") {
return(getLifecourseHeartVolumeFemale(age))
}
}
#====================================================================================================
getLifecourseHeartVolumeMale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightMale(age)
vhrt = exp(-2.502)*((h/100)**2.13)
return(vhrt)
}
#====================================================================================================
getLifecourseHeartVolumeFemale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightFemale(age)
vhrt = exp(-2.502)*((h/100)**2.13)
return(vhrt)
}
#the gut volume comes from internal gut equations. Will be used for the GI compartment in the model
# if volume for individual compartments is needed use bosgra equations for individual compartments
getLifecourseGutVolume <- function(age,gender){
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseGutVolumeMale(age))
}
else if(gender == "F") {
return(getLifecourseGutVolumeFemale(age))
}
}
getLifecourseGutVolumeMale <- function(age){
mbw <- getLifecourseBodyWeightMale(age)
vfat <- getLifecourseAdiposeVolumeMaleSciV(age)
lbw <- mbw - vfat
vgut <- 0.021*lbw
return(vgut)
}
getLifecourseGutVolumeFemale <- function(age){
mbw <- getLifecourseBodyWeightFemale(age)
vfat <- getLifecourseAdiposeVolumeFemaleSciV(age)
lbw <- mbw - vfat
vgut <- 0.027*lbw
return(vgut)
}
#====================================================================================================
getLifecourseIntestineVolume <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseIntestineVolumeMale(age))
}
else if(gender == "F") {
return(getLifecourseIntestineVolumeFemale(age))
}
}
#====================================================================================================
getLifecourseIntestineVolumeMale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightMale(age)
vint = exp(-1.351)*((h/100)**2.47)
return(vint)
}
#====================================================================================================
getLifecourseIntestineVolumeFemale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightFemale(age)
vint = exp(-1.351)*((h/100)**2.47)
return(vint)
}
#====================================================================================================
getLifecourseKidneyVolume <- function(age, gender, source = "sciv")
#====================================================================================================
{
if(is.na(age)) return(NA)
# remove this block once we have scitovation equations
if (source == "sciv"){
warning("Scitovation equations not found, Using bosgra equations instead")
source = "bosgra"
}
if(source == "bosgra"){
if(gender == "M") {
return(getLifecourseKidneyVolumeMale(age))
}
else if(gender == "F") {
return(getLifecourseKidneyVolumeFemale(age))
}
}else if(source == "sciv"){
stop("No Scitovation Equations found")
}
}
#====================================================================================================
getLifecourseKidneyVolumeMale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightMale(age)
vkid = exp(-2.306)*((h/100)**1.93)
return(vkid)
}
#====================================================================================================
getLifecourseKidneyVolumeFemale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightFemale(age)
vkid = exp(-2.306)*((h/100)**1.93)
return(vkid)
}
#====================================================================================================
getLifecourseLiverVolume <- function(age, gender, source = "sciv")
#====================================================================================================
{
if(is.na(age)) return(NA)
if (source == "bosgra"){
if(gender == "M") {
return(getLifecourseLiverVolumeMale(age))
}
else if(gender == "F") {
return(getLifecourseLiverVolumeFemale(age))
}
}else if(source == "sciv"){
if(gender == "M") {
return(getLifecourseLiverVolumeMaleSciV(age))
}
else if(gender == "F") {
return(getLifecourseLiverVolumeFemaleSciV(age))
}
}
}
#====================================================================================================
getLifecourseLiverVolumeMale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightMale(age)
vliv = exp(-0.6786)*((h/100)**1.98)
return(vliv)
}
#====================================================================================================
getLifecourseLiverVolumeFemale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightFemale(age)
vliv = exp(-0.6786)*((h/100)**1.98)
return(vliv)
}
getLifecourseLiverVolumeMaleSciV<- function(age){
mbw <- getLifecourseBodyWeightMale(age)
mbsa <- getLifecourseBodySurfaceAreaMale(age)
if (age < 23){
a <- 0.05012
b <- 0.78
vliv <- a*mbw^b
}else{
# mean adult (25y) liver weight
mliv268 <- 0.0512*getLifecourseBodyWeightMale(25)^0.78
# mean adult (25y) body surface area
mbsa268 <- 2.01
a <- 1.0728
b <- 0.3457
vliv <- (a * mbsa - b) * mliv268 / (a * mbsa268 - b)
}
}
getLifecourseLiverVolumeFemaleSciV<- function(age){
mbw <- getLifecourseBodyWeightFemale(age)
mbsa <- getLifecourseBodySurfaceAreaFemale(age)
if (age < 23){
a <- 0.05012
b <- 0.78
vliv <- a*mbw^b
}else{
# mean adult (25y) liver weight
mliv268 <- 0.0512*getLifecourseBodyWeightFemale(25)^0.78
# mean adult (25y) body surface area
mbsa268 <- 1.75
a <- 1.0728
b <- 0.3457
vliv <- (a * mbsa - b) * mliv268 / (a * mbsa268 - b)
}
}
#====================================================================================================
getLifecourseLungVolume <- function(age, gender,source = "bosgra")
#====================================================================================================
{
if(is.na(age)) return(NA)
# remove this block once we have scitovation equations
if (source == "sciv"){
warning("Scitovation equations not found, Using bosgra equations instead")
source = "bosgra"
}
if(source=="bosgra"){
if(gender == "M") {
return(getLifecourseLungVolumeMale(age))
}
else if(gender == "F") {
return(getLifecourseLungVolumeFemale(age))
}
}
}
#====================================================================================================
getLifecourseLungVolumeMale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightMale(age)
vliv = exp(-2.092)*((h/100)**2.1)
return(vliv)
}
#====================================================================================================
getLifecourseLungVolumeFemale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightFemale(age)
vliv = exp(-2.092)*((h/100)**2.1)
return(vliv)
}
#====================================================================================================
getLifecoursePancreasVolume <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecoursePancreasVolumeMale(age))
}
else if(gender == "F") {
return(getLifecoursePancreasVolumeFemale(age))
}
}
#====================================================================================================
getLifecoursePancreasVolumeMale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightMale(age)
vpan = exp(-3.431)*((h/100)**2.43)
return(vpan)
}
#====================================================================================================
getLifecoursePancreasVolumeFemale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightFemale(age)
vpan = exp(-3.431)*((h/100)**2.43)
return(vpan)
}
#====================================================================================================
getLifecourseSkinVolume <- function(age, gender,source = "sciv")
#====================================================================================================
{
if(is.na(age)) return(NA)
if(source == "bosgra"){
if(gender == "M") {
return(getLifecourseSkinVolumeMale(age))
}
else if(gender == "F") {
return(getLifecourseSkinVolumeFemale(age))
}
}else if(source == "sciv"){
if(gender == "M") {
return(getLifecourseSkinVolumeMaleSciV(age))
}
else if(gender == "F") {
return(getLifecourseSkinVolumeFemaleSciV(age))
}
}
}
#====================================================================================================
getLifecourseSkinVolumeMale <- function(age)
#====================================================================================================
{
bsa = getLifecourseBodySurfaceAreaMale(age)
vskn = exp(1.64*bsa - 1.93)
return(vskn)
}
#====================================================================================================
getLifecourseSkinVolumeFemale <- function(age)
#====================================================================================================
{
bsa = getLifecourseBodySurfaceAreaFemale(age)
vskn = exp(1.64*bsa - 1.93)
return(vskn)
}
getLifecourseSkinVolumeMaleSciV <- function(age){
mbsa <- getLifecourseBodySurfaceAreaMale(age) # in m^2
mbsa <- mbsa*10000
depth <- 0.15 #in cm
vskin <- (mbsa*depth)/1000
return(vskin)
}
getLifecourseSkinVolumeFemaleSciV <- function(age){
mbsa <- getLifecourseBodySurfaceAreaFemale(age) # in m^2
mbsa <- mbsa*10000
depth <- 0.15 #in cm
vskin <- (mbsa*depth)/1000
return(vskin)
}
#====================================================================================================
getLifecourseSpleenVolume <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseSpleenVolumeMale(age))
}
else if(gender == "F") {
return(getLifecourseSpleenVolumeFemale(age))
}
}
#====================================================================================================
getLifecourseSpleenVolumeMale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightMale(age)
vspl = exp(-3.123)*((h/100)**2.16)
return(vspl)
}
#====================================================================================================
getLifecourseSpleenVolumeFemale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightFemale(age)
vspl = exp(-3.123)*((h/100)**2.16)
return(vspl)
}
#====================================================================================================
getLifecourseStomachVolume <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseStomachVolumeMale(age))
}
else if(gender == "F") {
return(getLifecourseStomachVolumeFemale(age))
}
}
#====================================================================================================
getLifecourseStomachVolumeMale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightMale(age)
vsto = exp(-3.266)*((h/100)**2.45)
return(vsto)
}
#====================================================================================================
getLifecourseStomachVolumeFemale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightFemale(age)
vsto = exp(-3.266)*((h/100)**2.45)
return(vsto)
}
#====================================================================================================
getLifecourseThymusVolume <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseThymusVolumeMale(age))
}
else if(gender == "F") {
return(getLifecourseThymusVolumeFemale(age))
}
}
#====================================================================================================
getLifecourseThymusVolumeMale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightMale(age)
vthy = 14*((7.1 - 6.1*exp(-age/11.9))*(0.14 + 0.86*exp(-age/10.3)))/1000 # convert to kg
return(vthy)
}
#====================================================================================================
getLifecourseThymusVolumeFemale <- function(age)
#====================================================================================================
{
# Note, same as male eqn
h = getLifecourseBodyHeightFemale(age)
vthy = 14*((7.1 - 6.1*exp(-age/11.9))*(0.14 + 0.86*exp(-age/10.3)))/1000 # convert to kg
return(vthy)
}
#====================================================================================================
getLifecourseRemainingVolume <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseRemainingVolumeMale(age))
}
else if(gender == "F") {
return(getLifecourseRemainingVolumeFemale(age))
}
}
#====================================================================================================
getLifecourseRemainingVolumeMale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightMale(age)
vrem = exp(-0.072)*((h/100)**1.95)
return(vrem)
}
#====================================================================================================
getLifecourseRemainingVolumeFemale <- function(age)
#====================================================================================================
{
h = getLifecourseBodyHeightFemale(age)
vrem = exp(-0.072)*((h/100)**1.95)
return(vrem)
}
#====================================================================================================
getLifecourseRapidlyPerfusedVolume <- function(age, gender,source = "sciv")
#====================================================================================================
{
if(is.na(age)) return(NA)
# remove this block once we have bosgra equations
if (source == "bosgra"){
warning("Bosgra equations not found, Using ScitoVation equations instead")
source = "sciv"
}
if(source == "sciv"){
if(gender == "M") {
return(getLifecourseRapidlyPerfusedVolumeMaleSciV(age))
}else if(gender == "F") {
return(getLifecourseRapidlyPerfusedVolumeFemaleSciV(age))
}
}
}
getLifecourseRapidlyPerfusedVolumeMaleSciV<- function(age){
vgut <- getLifecourseGutVolumeMale(age)
vrpf <- 2.596*vgut
return(vrpf)
}
getLifecourseRapidlyPerfusedVolumeFemaleSciV<- function(age){
vgut <- getLifecourseGutVolumeFemale(age)
vrpf <- 2.464*vgut
return(vrpf)
}
#====================================================================================================
getLifecourseMuscleVolume <- function(age, gender,source="sciv")
#====================================================================================================
{
if(is.na(age)) return(NA)
if (source == "bosgra"){
if(gender == "M") {
return(getLifecourseMuscleVolumeMale(age))
}
else if(gender == "F") {
return(getLifecourseMuscleVolumeFemale(age))
}
}else if (source == "sciv"){
if (gender == "M"){
return(getLifecourseMuscleVolumeMaleSciV(age))
}else if (gender == "F"){
return(getLifecourseMuscleVolumeFemaleSciV(age))
}
}
}
#====================================================================================================
getLifecourseMuscleVolumeMale <- function(age)
#====================================================================================================
{
vmus = getLifecourseBodyWeightMale(age) -
getLifecourseAdiposeVolumeMaleSciV(age) -
getLifecourseBloodVolumeMale(age) -
getLifecourseBoneVolumeMale(age) -
getLifecourseBrainVolumeMale(age) -
getLifecourseGonadVolumeMale(age) -
getLifecourseHeartVolumeMale(age) -
getLifecourseIntestineVolumeMale(age) -
getLifecourseKidneyVolumeMale(age) -
getLifecourseLiverVolumeMale(age) -
getLifecourseLungVolumeMale(age) -
getLifecoursePancreasVolumeMale(age) -
getLifecourseRemainingVolumeMale(age) -
getLifecourseSkinVolumeMale(age) -
getLifecourseSpleenVolumeMale(age) -
getLifecourseStomachVolumeMale(age) -
getLifecourseThymusVolumeMale(age)
return(vmus)
}
#====================================================================================================
getLifecourseMuscleVolumeFemale <- function(age)
#====================================================================================================
{
vmus = getLifecourseBodyWeightMale(age) -
getLifecourseAdiposeVolumeFemaleSciV(age) -
getLifecourseBloodVolumeFemale(age) -
getLifecourseBoneVolumeFemale(age) -
getLifecourseBrainVolumeFemale(age) -
getLifecourseGonadVolumeFemale(age) -
getLifecourseHeartVolumeFemale(age) -
getLifecourseIntestineVolumeFemale(age) -
getLifecourseKidneyVolumeFemale(age) -
getLifecourseLiverVolumeFemale(age) -
getLifecourseLungVolumeFemale(age) -
getLifecoursePancreasVolumeFemale(age) -
getLifecourseRemainingVolumeFemale(age) -
getLifecourseSkinVolumeFemale(age) -
getLifecourseSpleenVolumeFemale(age) -
getLifecourseStomachVolumeFemale(age) -
getLifecourseThymusVolumeFemale(age)
return(vmus)
}
#====================================================================================================
getLifecourseSlowlyPerfusedVolume <- function(age, gender,perf_frct=0.85)
#====================================================================================================
{
if(is.na(age)) return(NA)
if (gender == "M"){
return(getLifecourseSlowlyPerfusedVolumeMale(age,perf_frct))
}else if (gender == "F"){
return(getLifecourseSlowlyPerfusedVolumeFemale(age,perf_frct))
}
}
getLifecourseSlowlyPerfusedVolumeMale <- function(age,perf_frct=0.85){
bw <- getLifecourseBodyWeightMale(age)
perfused_bw <- perf_frct*bw
total_volume <- (getLifecourseGutVolume(age,"M")+
getLifecourseIntestineVolume(age,"M")+
getLifecourseLiverVolume(age,"M")+
getLifecourseBloodVolume(age,"M")+
getLifecourseAdiposeVolume(age,"M")+
getLifecourseBoneVolume(age,"M")+
getLifecourseBrainVolume(age,"M")+
getLifecourseHeartVolume(age,"M")+
getLifecourseKidneyVolume(age,"M")+
getLifecourseLungVolume(age,"M")+
getLifecourseSkinVolume(age,"M")+
getLifecourseMuscleVolume(age,"M")+
getLifecourseRapidlyPerfusedVolume(age,"M"))
vol <- perfused_bw- total_volume
vol <- ifelse(vol < 0, 1e-5,vol)
return(vol)
}
getLifecourseSlowlyPerfusedVolumeFemale <- function(age,perf_frct=0.85){
bw <- getLifecourseBodyWeightFemale(age)
perfused_bw <- perf_frct*bw
total_volume <- (getLifecourseGutVolume(age,"F")+
getLifecourseIntestineVolume(age,"F")+
getLifecourseLiverVolume(age,"F")+
getLifecourseBloodVolume(age,"F")+
getLifecourseAdiposeVolume(age,"F")+
getLifecourseBoneVolume(age,"F")+
getLifecourseBrainVolume(age,"F")+
getLifecourseHeartVolume(age,"F")+
getLifecourseKidneyVolume(age,"F")+
getLifecourseLungVolume(age,"F")+
getLifecourseSkinVolume(age,"F")+
getLifecourseMuscleVolume(age,"F")+
getLifecourseRapidlyPerfusedVolume(age,"F"))
vol <- perfused_bw- total_volume
vol <- ifelse(vol < 0, 1e-5,vol)
return(vol)
}
#====================================================================================================
getLifecourseMuscleVolumeMale <- function(age)
#====================================================================================================
{
vmus = getLifecourseBodyWeightMale(age) -
getLifecourseAdiposeVolumeMaleSciV(age) -
getLifecourseBloodVolumeMale(age) -
getLifecourseBoneVolumeMale(age) -
getLifecourseBrainVolumeMale(age) -
getLifecourseGonadVolumeMale(age) -
getLifecourseHeartVolumeMale(age) -
getLifecourseIntestineVolumeMale(age) -
getLifecourseKidneyVolumeMale(age) -
getLifecourseLiverVolumeMale(age) -
getLifecourseLungVolumeMale(age) -
getLifecoursePancreasVolumeMale(age) -
getLifecourseRemainingVolumeMale(age) -
getLifecourseSkinVolumeMale(age) -
getLifecourseSpleenVolumeMale(age) -
getLifecourseStomachVolumeMale(age) -
getLifecourseThymusVolumeMale(age)
return(vmus)
}
#====================================================================================================
getLifecourseMuscleVolumeFemale <- function(age)
#====================================================================================================
{
vmus = getLifecourseBodyWeightMale(age) -
getLifecourseAdiposeVolumeFemaleSciV(age) -
getLifecourseBloodVolumeFemale(age) -
getLifecourseBoneVolumeFemale(age) -
getLifecourseBrainVolumeFemale(age) -
getLifecourseGonadVolumeFemale(age) -
getLifecourseHeartVolumeFemale(age) -
getLifecourseIntestineVolumeFemale(age) -
getLifecourseKidneyVolumeFemale(age) -
getLifecourseLiverVolumeFemale(age) -
getLifecourseLungVolumeFemale(age) -
getLifecoursePancreasVolumeFemale(age) -
getLifecourseRemainingVolumeFemale(age) -
getLifecourseSkinVolumeFemale(age) -
getLifecourseSpleenVolumeFemale(age) -
getLifecourseStomachVolumeFemale(age) -
getLifecourseThymusVolumeFemale(age)
return(vmus)
}
getLifecourseMuscleVolumeMaleSciV<- function(age){
# calculated using linear interpolation
x <- c(0,1,5,10,15,25)
y <- c(0.8,1.9,5.6,11,24,29)
vals <- approx(x,y,age,"linear",rule = 2)
return(vals$y)
}
getLifecourseMuscleVolumeFemaleSciV<- function(age){
# calculated using linear interpolation
x <- c(0,1,5,10,15,25)
y <- c(0.8,1.9,5.6,11,17,17.5)
vals <- approx(x,y,age,"linear",rule = 2)
return(vals$y)
}
#====================================================================================================
getLifecourseTissueVolumeSum <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseTissueVolumeSumMale(age))
}
else if(gender == "F") {
return(getLifecourseTissueVolumeSumFemale(age))
}
}
#====================================================================================================
getLifecourseTissueVolumeSumMale <- function(age)
#====================================================================================================
{
vall = +
getLifecourseAdiposeVolumeMaleSciV(age) +
getLifecourseBloodVolumeMale(age) +
getLifecourseBoneVolumeMale(age) +
getLifecourseBrainVolumeMale(age) +
getLifecourseGonadVolumeMale(age) +
getLifecourseHeartVolumeMale(age) +
getLifecourseIntestineVolumeMale(age) +
getLifecourseKidneyVolumeMale(age) +
getLifecourseLiverVolumeMale(age) +
getLifecourseLungVolumeMale(age) +
getLifecoursePancreasVolumeMale(age) +
getLifecourseRemainingVolumeMale(age) +
getLifecourseSkinVolumeMale(age) +
getLifecourseSpleenVolumeMale(age) +
getLifecourseStomachVolumeMale(age) +
getLifecourseThymusVolumeMale(age) +
getLifecourseMuscleVolumeMale(age)
return(vall)
}
#====================================================================================================
getLifecourseTissueVolumeSumFemale <- function(age)
#====================================================================================================
{
vall = +
getLifecourseAdiposeVolumeFemaleSciV(age) +
getLifecourseBloodVolumeFemale(age) +
getLifecourseBoneVolumeFemale(age) +
getLifecourseBrainVolumeFemale(age) +
getLifecourseGonadVolumeFemale(age) +
getLifecourseHeartVolumeFemale(age) +
getLifecourseIntestineVolumeFemale(age) +
getLifecourseKidneyVolumeFemale(age) +
getLifecourseLiverVolumeFemale(age) +
getLifecourseLungVolumeFemale(age) +
getLifecoursePancreasVolumeFemale(age) +
getLifecourseRemainingVolumeFemale(age) +
getLifecourseSkinVolumeFemale(age) +
getLifecourseSpleenVolumeFemale(age) +
getLifecourseStomachVolumeFemale(age) +
getLifecourseThymusVolumeFemale(age) +
getLifecourseMuscleVolumeFemale(age)
return(vall)
}
#====================================================================================================
getLifecourseAdiposePerfusion <- function(age, gender, source = "sciv")
#====================================================================================================
{
if(is.na(age)) return(NA)
if(source == "bosgra"){
if(gender == "M") {
return(getLifecourseAdiposePerfusionMale(age))
}
else if(gender == "F") {
return(getLifecourseAdiposePerfusionFemale(age))
}
}else if(source == "sciv"){
if(gender == "M") {
return(getLifecourseAdiposePerfusionMaleSciV(age))
}
else if(gender == "F") {
return(getLifecourseAdiposePerfusionFemaleSciV(age))
}
}
}
getLifecourseAdiposePerfusionMaleSciV<- function(age){
vfatc25 = 0.238
qfatc25 = 0.05
vfat <- getLifecourseAdiposeVolumeMaleSciV(age)
bw <- getLifecourseBodyWeightMale(age)
qc <- getLifecourseCardiacOutput(age,"M")
vfatc <- vfat/bw
qfatc <- (vfatc/vfatc25)*qfatc25
qfat <- qfatc*qc
return(qfat)
}
getLifecourseAdiposePerfusionFemaleSciV<- function(age){
vfatc25 = 0.368
qfatc25 = 0.085
vfat <- getLifecourseAdiposeVolumeFemaleSciV(age)
bw <- getLifecourseBodyWeightFemale(age)
qc <- getLifecourseCardiacOutput(age,"F")
vfatc <- vfat/bw
qfatc <- (vfatc/vfatc25)*qfatc25
qfat <- qfatc*qc
return(qfat)
}
#====================================================================================================
getLifecourseAdiposePerfusionMale <- function(age)
#====================================================================================================
{
m = getLifecourseAdiposeVolumeMaleSciV(age)
m35 = getLifecourseAdiposeVolumeMaleSciV(35)
q = m*19.5/m35
return(q)
}
#====================================================================================================
getLifecourseAdiposePerfusionFemale <- function(age)
#====================================================================================================
{
m = getLifecourseAdiposeVolumeFemaleSciV(age)
m35 = getLifecourseAdiposeVolumeFemaleSciV(35)
q = m*30.1/m35
return(q)
}
#====================================================================================================
getLifecourseBonePerfusion <- function(age, gender, source = "sciv")
#====================================================================================================
{
if(is.na(age)) return(NA)
if(source == "bosgra"){
if(gender == "M") {
return(getLifecourseBonePerfusionMale(age))
}
else if(gender == "F") {
return(getLifecourseBonePerfusionFemale(age))
}
}else if(source == "sciv"){
if(gender == "M") {
return(getLifecourseBonePerfusionMaleSciV(age))
}
else if(gender == "F") {
return(getLifecourseBonePerfusionFemaleSciV(age))
}
}
}
getLifecourseBonePerfusionMaleSciV<- function(age){
qbone25c <- 0.03
qc <- getLifecourseCardiacOutput(age,"M")
bw25 <- getLifecourseBodyWeightMale(25)
bw <- getLifecourseBodyWeightMale(age)
vbonec25 <- getLifecourseBoneVolumeMaleSciV(25)/bw25
vbonec <- getLifecourseBoneVolumeMaleSciV(age)/bw
qbone <- qc*(vbonec/vbonec25)*qbone25c
return(qbone)
}
getLifecourseBonePerfusionFemaleSciV<- function(age){
qbone25c <- 0.03
qc <- getLifecourseCardiacOutput(age,"F")
bw25 <- getLifecourseBodyWeightFemale(25)
bw <- getLifecourseBodyWeightFemale(age)
vbonec25 <- getLifecourseBoneVolumeFemaleSciV(25)/bw25
vbonec <- getLifecourseBoneVolumeFemaleSciV(age)/bw
qbone <- qc*(vbonec/vbonec25)*qbone25c
return(qbone)
}
#====================================================================================================
getLifecourseBonePerfusionMale <- function(age)
#====================================================================================================
{
m = getLifecourseBoneVolumeMale(age)
m35 = getLifecourseBoneVolumeMale(35)
q = m*7.8/m35
return(q)
}
#====================================================================================================
getLifecourseBonePerfusionFemale <- function(age)
#====================================================================================================
{
m = getLifecourseBoneVolumeFemale(age)
m35 = getLifecourseBoneVolumeFemale(35)
q = m*7.1/m35
return(q)
}
#====================================================================================================
getLifecourseBrainPerfusion <- function(age, gender,source = "sciv")
#====================================================================================================
{
if(is.na(age)) return(NA)
if(source == "bosgra"){
if(gender == "M") {
return(getLifecourseBrainPerfusionMale(age))
}
else if(gender == "F") {
return(getLifecourseBrainPerfusionFemale(age))
}
}else if (source == "sciv"){
if(gender == "M") {
return(getLifecourseBrainPerfusionMaleSciV(age))
}
else if(gender == "F") {
return(getLifecourseBrainPerfusionFemaleSciV(age))
}
}
}
#====================================================================================================
getLifecourseBrainPerfusionMale <- function(age)
#====================================================================================================
{
m = getLifecourseBrainVolumeMale(age)
m35 = getLifecourseBrainVolumeMale(35)
q = m*46.8/m35
return(q)
}
#====================================================================================================
getLifecourseBrainPerfusionFemale <- function(age)
#====================================================================================================
{
m = getLifecourseBrainVolumeFemale(age)
m35 = getLifecourseBrainVolumeFemale(35)
q = m*42.5/m35
return(q)
}
getLifecourseBrainPerfusionMaleSciV<- function(age){
qc <- getLifecourseCardiacOutput(age,"M")
qbrnc <- (3/age)*exp(-0.5*(log(age/41.92)/1.876)^2)
qbrn <- qbrnc*qc
return(qbrn)
}
getLifecourseBrainPerfusionFemaleSciV<- function(age){
qc <- getLifecourseCardiacOutput(age,"F")
qbrnc <- (3.064/age)*exp(-0.5*(log(age/47.57)/1.94)^2)
qbrn <- qbrnc*qc
return(qbrn)
}
#====================================================================================================
getLifecourseGonadPerfusion <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseGonadPerfusionMale(age))
}
else if(gender == "F") {
return(getLifecourseGonadPerfusionFemale(age))
}
}
#====================================================================================================
getLifecourseGonadPerfusionMale <- function(age)
#====================================================================================================
{
m = getLifecourseGonadVolumeMale(age)
m35 = getLifecourseGonadVolumeMale(35)
q = m*0.195/m35
return(q)
}
#====================================================================================================
getLifecourseGonadPerfusionFemale <- function(age)
#====================================================================================================
{
m = getLifecourseGonadVolumeFemale(age)
m35 = getLifecourseGonadVolumeFemale(35)
q = m*0.071/m35
return(q)
}
#====================================================================================================
getLifecourseHeartPerfusion <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseHeartPerfusionMale(age))
}
else if(gender == "F") {
return(getLifecourseHeartPerfusionFemale(age))
}
}
#====================================================================================================
getLifecourseHeartPerfusionMale <- function(age)
#====================================================================================================
{
m = getLifecourseHeartVolumeMale(age)
m35 = getLifecourseHeartVolumeMale(35)
q = m*15.6/m35
return(q)
}
#====================================================================================================
getLifecourseHeartPerfusionFemale <- function(age)
#====================================================================================================
{
m = getLifecourseHeartVolumeFemale(age)
m35 = getLifecourseHeartVolumeFemale(35)
q = m*17.7/m35
return(q)
}
#====================================================================================================
getLifecourseIntestinePerfusion <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseIntestinePerfusionMale(age))
}
else if(gender == "F") {
return(getLifecourseIntestinePerfusionFemale(age))
}
}
#====================================================================================================
getLifecourseIntestinePerfusionMale <- function(age)
#====================================================================================================
{
m = getLifecourseIntestineVolumeMale(age)
m35 = getLifecourseIntestineVolumeMale(35)
q = m*54.6/m35
return(q)
}
#====================================================================================================
getLifecourseIntestinePerfusionFemale <- function(age)
#====================================================================================================
{
m = getLifecourseIntestineVolumeFemale(age)
m35 = getLifecourseIntestineVolumeFemale(35)
q = m*56.6/m35
return(q)
}
#====================================================================================================
getLifecourseKidneyPerfusion <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseKidneyPerfusionMale(age))
}
else if(gender == "F") {
return(getLifecourseKidneyPerfusionFemale(age))
}
}
#====================================================================================================
getLifecourseKidneyPerfusionMale <- function(age)
#====================================================================================================
{
m = getLifecourseKidneyVolumeMale(age)
m35 = getLifecourseKidneyVolumeMale(35)
q = m*74.1/m35
return(q)
}
#====================================================================================================
getLifecourseKidneyPerfusionFemale <- function(age)
#====================================================================================================
{
m = getLifecourseKidneyVolumeFemale(age)
m35 = getLifecourseKidneyVolumeFemale(35)
q = m*60.2/m35
return(q)
}
#====================================================================================================
getLifecourseLiverArterialPerfusion <- function(age, gender, source = "sciv")
#====================================================================================================
{
if(is.na(age)) return(NA)
if(source == "bosgra"){
if(gender == "M") {
return(getLifecourseLiverArterialPerfusionMale(age))
}
else if(gender == "F") {
return(getLifecourseLiverArterialPerfusionFemale(age))
}
}else if (source == "sciv"){
if(gender == "M") {
return(getLifecourseLiverArterialPerfusionMaleSciV(age))
}
else if(gender == "F") {
return(getLifecourseLiverArterialPerfusionFemaleSciV(age))
}
}
}
#====================================================================================================
getLifecourseLiverArterialPerfusionMale <- function(age)
#====================================================================================================
{
m = getLifecourseLiverVolumeMale(age)
m35 = getLifecourseLiverVolumeMale(35)
q = m*25.35/m35
return(q)
}
#====================================================================================================
getLifecourseLiverArterialPerfusionFemale <- function(age)
#====================================================================================================
{
m = getLifecourseLiverVolumeFemale(age)
m35 = getLifecourseLiverVolumeFemale(35)
q = m*23.0/m35
return(q)
}
getLifecourseLiverArterialPerfusionMaleSciV<- function(age){
vliv <- getLifecourseLiverVolumeMaleSciV(age)
bw <- getLifecourseBodyWeightMale(age)
qc <- getLifecourseCardiacOutput(age,"M")
vlivc <- vliv/bw
qlivartc <- (vlivc/0.0199)*0.065
qlivart <- qlivartc*qc
return(qlivart)
}
getLifecourseLiverArterialPerfusionFemaleSciV<- function(age){
vliv <- getLifecourseLiverVolumeFemaleSciV(age)
bw <- getLifecourseBodyWeightFemale(age)
qc <- getLifecourseCardiacOutput(age,"F")
vlivc <- vliv/bw
qlivartc <- (vlivc/0.0199)*0.065
qlivart <- qlivartc*qc
return(qlivart)
}
getLifecourseGutPerfusion<- function(age,gender){
if(is.na(age)) return(NA)
if(gender == "M"){
return(getLifecourseGutPerfusionMale(age))
}else if(gender == "F"){
return(getLifecourseGutPerfusionFemale(age))
}
}
getLifecourseGutPerfusionMale<- function(age){
vgutc25 <- 0.016
qgutc25 <- 0.15
vgut <- getLifecourseGutVolumeMale(age)
bw <- getLifecourseBodyWeightMale(age)
qc <- getLifecourseCardiacOutput(age,"M")
vgutc <- vgut/bw
qgutc <- (vgutc/vgutc25)*qgutc25
qgut <- qgutc *qc
return(qgut)
}
getLifecourseGutPerfusionFemale<- function(age){
vgutc25 <- 0.0170660419467526
qgutc25 <- 0.17
vgut <- getLifecourseGutVolumeFemale(age)
bw <- getLifecourseBodyWeightFemale(age)
qc <- getLifecourseCardiacOutput(age,"F")
vgutc <- vgut/bw
qgutc <- (vgutc/vgutc25)*qgutc25
qgut <- qgutc *qc
return(qgut)
}
#====================================================================================================
getLifecourseLiverSplancnicPerfusion <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseLiverSplancnicPerfusionMale(age))
}
else if(gender == "F") {
return(getLifecourseLiverSplancnicPerfusionFemale(age))
}
}
#====================================================================================================
getLifecourseLiverSplancnicPerfusionMale <- function(age)
#====================================================================================================
{
q = getLifecoursePancreasPerfusionMale(age) +
getLifecourseSpleenPerfusionMale(age) +
getLifecourseStomachPerfusionMale(age) +
getLifecourseIntestinePerfusionMale(age)
return(q)
}
#====================================================================================================
getLifecourseLiverSplancnicPerfusionFemale <- function(age)
#====================================================================================================
{
q = getLifecoursePancreasPerfusionFemale(age) +
getLifecourseSpleenPerfusionFemale(age) +
getLifecourseStomachPerfusionFemale(age) +
getLifecourseIntestinePerfusionFemale(age)
return(q)
}
#====================================================================================================
getLifecourseLiverTotalPerfusion <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseLiverTotalPerfusionMale(age))
}
else if(gender == "F") {
return(getLifecourseLiverTotalPerfusionFemale(age))
}
}
#====================================================================================================
getLifecourseLiverTotalPerfusionMale <- function(age)
#====================================================================================================
{
q = getLifecourseLiverArterialPerfusionMale(age) +
getLifecourseLiverSplancnicPerfusionMale(age)
return(q)
}
#====================================================================================================
getLifecourseLiverTotalPerfusionFemale <- function(age)
#====================================================================================================
{
q = getLifecourseLiverArterialPerfusionFemale(age) +
getLifecourseLiverSplancnicPerfusionFemale(age)
return(q)
}
#====================================================================================================
getLifecourseMusclePerfusion <- function(age, gender, source = "sciv")
#====================================================================================================
{
if(is.na(age)) return(NA)
if(source == "sciv"){
if(gender == "M") {
return(getLifecourseMusclePerfusionMaleSciV(age))
}
else if(gender == "F") {
return(getLifecourseMusclePerfusionFemaleSciV(age))
}
}else if(source == "bosgra"){
if(gender == "M") {
return(getLifecourseMusclePerfusionMale(age))
}
else if(gender == "F") {
return(getLifecourseMusclePerfusionFemale(age))
}
}
}
getLifecourseMusclePerfusionMaleSciV <- function(age){
vmuscc25 <- getLifecourseMuscleVolumeMaleSciV(25)/getLifecourseBodyWeightMale(25)
qmuscc25 <- 0.17
vmusc <- getLifecourseMuscleVolumeMaleSciV(age)
bw <- getLifecourseBodyWeightMale(age)
qc <- getLifecourseCardiacOutput(age,"M")
vmuscc <- vmusc/bw
qmuscc <- (vmuscc/vmuscc25)*qmuscc25
qmusc <- qmuscc *qc
return(qmusc)
}
getLifecourseMusclePerfusionFemaleSciV <- function(age){
vmuscc25 <- getLifecourseMuscleVolumeFemaleSciV(25)/getLifecourseBodyWeightFemale(25)
qmuscc25 <- 0.12
vmusc <- getLifecourseMuscleVolumeFemaleSciV(age)
bw <- getLifecourseBodyWeightFemale(age)
qc <- getLifecourseCardiacOutput(age,"F")
vmuscc <- vmusc/bw
qmuscc <- (vmuscc/vmuscc25)*qmuscc25
qmusc <- qmuscc *qc
return(qmusc)
}
#====================================================================================================
getLifecourseMusclePerfusionMale <- function(age)
#====================================================================================================
{
m = getLifecourseMuscleVolumeMaleSciV(age)
m35 = getLifecourseMuscleVolumeMaleSciV(35)
q = m*66.3/m35
return(q)
}
#====================================================================================================
getLifecourseMusclePerfusionFemale <- function(age)
#====================================================================================================
{
m = getLifecourseMuscleVolumeFemaleSciV(age)
m35 = getLifecourseMuscleVolumeFemaleSciV(35)
q = m*42.5/m35
return(q)
}
#====================================================================================================
getLifecoursePancreasPerfusion <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecoursePancreasPerfusionMale(age))
}
else if(gender == "F") {
return(getLifecoursePancreasPerfusionFemale(age))
}
}
#====================================================================================================
getLifecoursePancreasPerfusionMale <- function(age)
#====================================================================================================
{
m = getLifecoursePancreasVolumeMale(age)
m35 = getLifecoursePancreasVolumeMale(35)
q = m*3.9/m35
return(q)
}
#====================================================================================================
getLifecoursePancreasPerfusionFemale <- function(age)
#====================================================================================================
{
m = getLifecoursePancreasVolumeFemale(age)
m35 = getLifecoursePancreasVolumeFemale(35)
q = m*3.54/m35
return(q)
}
#====================================================================================================
getLifecourseSkinPerfusion <- function(age, gender, source = "sciv")
#====================================================================================================
{
if(is.na(age)) return(NA)
if (source == "bosgra"){
if(gender == "M") {
return(getLifecourseSkinPerfusionMale(age))
}
else if(gender == "F") {
return(getLifecourseSkinPerfusionFemale(age))
}
}else if(source == "sciv"){
if(gender == "M") {
return(getLifecourseSkinPerfusionMaleSciV(age))
}
else if(gender == "F") {
return(getLifecourseSkinPerfusionFemaleSciV(age))
}
}
}
#====================================================================================================
getLifecourseSkinPerfusionMale <- function(age)
#====================================================================================================
{
m = getLifecourseSkinVolumeMale(age)
m35 = getLifecourseSkinVolumeMale(35)
q = m*19.5/m35
return(q)
}
getLifecourseSkinPerfusionMaleSciV<- function(age){
vsknc25 <- getLifecourseSkinVolumeMaleSciV(25)/getLifecourseBodyWeightMale(25)
qsknc25 <- 0.058
vskn <- getLifecourseSkinVolumeMaleSciV(age)
bw <- getLifecourseBodyWeightMale(age)
qc <- getLifecourseCardiacOutput(age,"M")
vsknc <- vskn/bw
qsknc <- (vsknc/vsknc25)*qsknc25
qskn <- qsknc *qc
return(qskn)
}
getLifecourseSkinPerfusionFemaleSciV<- function(age){
vsknc25 <- getLifecourseSkinVolumeFemaleSciV(25)/getLifecourseBodyWeightFemale(25)
qsknc25 <- 0.058
vskn <- getLifecourseSkinVolumeFemaleSciV(age)
bw <- getLifecourseBodyWeightFemale(age)
qc <- getLifecourseCardiacOutput(age,"F")
vsknc <- vskn/bw
qsknc <- (vsknc/vsknc25)*qsknc25
qskn <- qsknc *qc
return(qskn)
}
#====================================================================================================
getLifecourseSkinPerfusionFemale <- function(age)
#====================================================================================================
{
m = getLifecourseSkinVolumeFemale(age)
m35 = getLifecourseSkinVolumeFemale(35)
q = m*17.7/m35
return(q)
}
#====================================================================================================
getLifecourseSpleenPerfusion <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseSpleenPerfusionMale(age))
}
else if(gender == "F") {
return(getLifecourseSpleenPerfusionFemale(age))
}
}
#====================================================================================================
getLifecourseSpleenPerfusionMale <- function(age)
#====================================================================================================
{
m = getLifecourseSpleenVolumeMale(age)
m35 = getLifecourseSpleenVolumeMale(35)
q = m*11.7/m35
return(q)
}
#====================================================================================================
getLifecourseSpleenPerfusionFemale <- function(age)
#====================================================================================================
{
m = getLifecourseSpleenVolumeFemale(age)
m35 = getLifecourseSpleenVolumeFemale(35)
q = m*10.6/m35
return(q)
}
#====================================================================================================
getLifecourseStomachPerfusion <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseStomachPerfusionMale(age))
}
else if(gender == "F") {
return(getLifecourseStomachPerfusionFemale(age))
}
}
#====================================================================================================
getLifecourseStomachPerfusionMale <- function(age)
#====================================================================================================
{
m = getLifecourseStomachVolumeMale(age)
m35 = getLifecourseStomachVolumeMale(35)
q = m*3.9/m35
return(q)
}
#====================================================================================================
getLifecourseStomachPerfusionFemale <- function(age)
#====================================================================================================
{
m = getLifecourseStomachVolumeFemale(age)
m35 = getLifecourseStomachVolumeFemale(35)
q = m*3.54/m35
return(q)
}
#====================================================================================================
getLifecourseThymusPerfusion <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseThymusPerfusionMale(age))
}
else if(gender == "F") {
return(getLifecourseThymusPerfusionFemale(age))
}
}
#====================================================================================================
getLifecourseThymusPerfusionMale <- function(age)
#====================================================================================================
{
m = getLifecourseThymusVolumeMale(age)
m35 = getLifecourseThymusVolumeMale(35)
q = m*0.39/m35
return(q)
}
#====================================================================================================
getLifecourseThymusPerfusionFemale <- function(age)
#====================================================================================================
{
m = getLifecourseThymusVolumeFemale(age)
m35 = getLifecourseThymusVolumeFemale(35)
q = m*0.37/m35
return(q)
}
#====================================================================================================
getLifecourseRemainingPerfusion <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseRemainingPerfusionMale(age))
}
else if(gender == "F") {
return(getLifecourseRemainingPerfusionFemale(age))
}
}
#====================================================================================================
getLifecourseRemainingPerfusionMale <- function(age)
#====================================================================================================
{
m = getLifecourseRemainingVolumeMale(age)
m35 = getLifecourseRemainingVolumeMale(35)
q = m*21.8/m35
return(q)
}
#====================================================================================================
getLifecourseRemainingPerfusionFemale <- function(age)
#====================================================================================================
{
m = getLifecourseRemainingVolumeFemale(age)
m35 = getLifecourseRemainingVolumeFemale(35)
q = m*20.5/m35
return(q)
}
#====================================================================================================
getLifecourseLungPerfusion <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseLungPerfusionMale(age))
}
else if(gender == "F") {
return(getLifecourseLungPerfusionFemale(age))
}
}
#====================================================================================================
getLifecourseLungPerfusionMale <- function(age)
#====================================================================================================
{
# Using data from Jongeneelen...
# Their reported lung perfusion is not cardiac output,
# but a small arterial flow (fraction of their reported CO)
q0 = 390*0.03 # They report CO as 390 L/h, their perfusion fraction if 0.03
m = getLifecourseRemainingVolumeMale(age)
m35 = getLifecourseRemainingVolumeMale(35)
q = m*q0/m35
return(q)
}
#====================================================================================================
getLifecourseLungPerfusionFemale <- function(age)
#====================================================================================================
{
# Using data from Joneneelen...
# Their reported lung perfusion is not cardiac output,
# but a small arterial flow (fraction of their reported CO)
q0 = 390*0.03 # They report CO as 390 L/h, their perfusion fraction if 0.03
m = getLifecourseRemainingVolumeFemale(age)
m35 = getLifecourseRemainingVolumeFemale(35)
q = m*q0/m35
return(q)
}
#===========
getLifecourseRichlyPerfusedTissuePerfusion<- function(age,gender){
if (is.na(age)) return(NA)
if(gender == "M"){
getLifecourseRichlyPerfusedTissuePerfusionMale(age)
}else if(gender == "F"){
getLifecourseRichlyPerfusedTissuePerfusionFemale(age)
}
}
getLifecourseRichlyPerfusedTissuePerfusionMale <- function(age){
vrpfc25 <- 0.042
qrpfc25 <- 0.215
vrpf <- getLifecourseRapidlyPerfusedVolumeMaleSciV(age)
bw <- getLifecourseBodyWeightMale(age)
qc <- getLifecourseCardiacOutput(age,"M")
vrpfc <- vrpf/bw
qrpfc <- (vrpfc/vrpfc25)*qrpfc25
qrpf <- qrpfc *qc
return(qrpf)
}
getLifecourseRichlyPerfusedTissuePerfusionFemale <- function(age){
vrpfc25 <- 0.042
qrpfc25 <- 0.215
vrpf <- getLifecourseRapidlyPerfusedVolumeFemaleSciV(age)
bw <- getLifecourseBodyWeightFemale(age)
qc <- getLifecourseCardiacOutput(age,"F")
vrpfc <- vrpf/bw
qrpfc <- (vrpfc/vrpfc25)*qrpfc25
qrpf <- qrpfc *qc
return(qrpf)
}
#===========
getLifecourseSlowlyPerfusedTissuePerfusion<- function(age,gender){
if (is.na(age)) return(NA)
if(gender == "M"){
getLifecourseSlowlyPerfusedTissuePerfusionMale(age)
}else if(gender == "F"){
getLifecourseSlowlyPerfusedTissuePerfusionFemale(age)
}
}
getLifecourseSlowlyPerfusedTissuePerfusionMale <- function(age){
vspfc25 <- getLifecourseSlowlyPerfusedVolumeMale(25)/getLifecourseBodyWeightMale(25)
qspfc25 <- 0.190 - 0.058 # 0.058 was fractional skin perfion
vspf <- getLifecourseSlowlyPerfusedVolumeMale(age)
bw <- getLifecourseBodyWeightMale(age)
qc <- getLifecourseCardiacOutput(age,"M")
vspfc <- vspf/bw
qspfc <- (vspfc/vspfc25)*qspfc25
qspf <- qspfc *qc
return(qspf)
}
getLifecourseSlowlyPerfusedTissuePerfusionFemale <- function(age){
vspfc25 <- getLifecourseSlowlyPerfusedVolumeFemale(25)/getLifecourseBodyWeightFemale(25)
qspfc25 <- 0.190 - 0.058 # 0.058 was fractional skin perfion
vspf <- getLifecourseSlowlyPerfusedVolumeFemale(age)
bw <- getLifecourseBodyWeightFemale(age)
qc <- getLifecourseCardiacOutput(age,"F")
vspfc <- vspf/bw
qspfc <- (vspfc/vspfc25)*qspfc25
qspf <- qspfc *qc
return(qspf)
}
#' Get the cardiac output based on the life course equations
#' @description Get the cardiac output for a specific age and gender. Uses either Bosgra or ScitoVation equations
#' @param age Age in years
#' @param gender Gender can be either "M" for male or "F" for female
#' @param source Source of the equations. Either from Bosgra et al. "bosgra" or from ScitoVation publications as "sciv"
#' @param qc_var variability for cardiac output. Used to account for exercise level. Can only be used when source = "sciv"
#' @export
#'
getLifecourseCardiacOutput <- function(age, gender, source = "sciv",qc_var= 0)
#====================================================================================================
{
if(is.na(age)) return(NA)
if (source == "bosgra"){
if(gender == "M") {
return(getLifecourseCardiacOutputMale(age))
}
else if(gender == "F") {
return(getLifecourseCardiacOutputFemale(age))
}
}else if(source == "sciv"){
if(gender == "M") {
return(getLifecourseCardiacOutputMaleSciV(age,qc_var))
}
else if(gender == "F") {
return(getLifecourseCardiacOutputFemaleSciV(age,qc_var))
}
}
}
#============================
getLifecourseCardiacOutputMaleSciV<- function(age,qc_var){
mbsa <- getLifecourseBodySurfaceAreaMale(age)
# scaling factor for body surface area to cardiac output
bsa_qc_scaling <- 3.5
# QC min is variability factor for inter individual variation in QC,
# can be also used to adjust cardiac output based on activity level
qc <- mbsa*bsa_qc_scaling*(1+qc_var)*60
}
#============================
getLifecourseCardiacOutputFemaleSciV<- function(age,qc_var){
mbsa <- getLifecourseBodySurfaceAreaFemale(age)
# scaling factor for body surface area to cardiac output
bsa_qc_scaling <- 3.5
# QC min is variability factor for inter individual variation in QC,
# can be also used to adjust cardiac output based on activity level
qc <- mbsa*bsa_qc_scaling*(1+qc_var)*60
}
#====================================================================================================
getLifecourseCardiacOutputMale <- function(age)
#====================================================================================================
{
q = getLifecourseAdiposePerfusionMale(age) +
getLifecourseBonePerfusionMale(age) +
getLifecourseBrainPerfusionMale(age) +
getLifecourseGonadPerfusionMale(age) +
getLifecourseHeartPerfusionMale(age) +
getLifecourseKidneyPerfusionMale(age) +
getLifecourseLiverArterialPerfusionMale(age) +
getLifecourseMusclePerfusionMale(age) +
getLifecourseRemainingPerfusionMale(age) +
getLifecourseSkinPerfusionMale(age) +
getLifecourseThymusPerfusionMale(age) +
getLifecourseIntestinePerfusionMale(age) +
getLifecoursePancreasPerfusionMale(age) +
getLifecourseSpleenPerfusionMale(age) +
getLifecourseStomachPerfusionMale(age)
return(q)
}
#====================================================================================================
getLifecourseCardiacOutputFemale <- function(age)
#====================================================================================================
{
q = getLifecourseAdiposePerfusionFemale(age) +
getLifecourseBonePerfusionFemale(age) +
getLifecourseBrainPerfusionFemale(age) +
getLifecourseGonadPerfusionFemale(age)+
getLifecourseHeartPerfusionFemale(age) +
getLifecourseKidneyPerfusionFemale(age) +
getLifecourseLiverArterialPerfusionFemale(age) +
getLifecourseMusclePerfusionFemale(age) +
getLifecourseRemainingPerfusionFemale(age) +
getLifecourseSkinPerfusionFemale(age) +
getLifecourseThymusPerfusionFemale(age) +
getLifecourseIntestinePerfusionFemale(age) +
getLifecoursePancreasPerfusionFemale(age) +
getLifecourseSpleenPerfusionFemale(age) +
getLifecourseStomachPerfusionFemale(age)
return(q)
}
#' Get the ventilation rate for a given age and gender
#' @description Uses life course equation to calculate a ventilation rate for a specific age and gender
#' @param age Age in years
#' @param gender Either "M" for Male for "F" for Female
#' @param activity Activity level. Can be "rest" or "light exercise"
#' @param source source of equations either "sciv" or "bosgra"
#' @export
getLifecourseVentilationRate <- function(age, gender,activity="rest",source="sciv")
#====================================================================================================
{
if(is.na(age)) return(NA)
if (source == "bosgra"){
if (activity != "rest"){
warning(sprintf(
"The source does not have valid equations for activity type '%s'.
Using the default 'rest' activity instead",activity)
)
}
if(gender == "M") {
return(getLifecourseVentilationRateMale(age))
}
else if(gender == "F") {
return(getLifecourseVentilationRateFemale(age))
}
} else if(source == "sciv") {
if(gender == "M"){
return(getLifecourseVentilationRateMaleSCIV(age,activity))
}else if(gender == "F"){
return(getLifecourseVentilationRateFemaleSCIV(age,activity))
}
}
}
#=====
getLifecourseVentilationRateMaleSCIV <- function(age,activity){
if (activity == "rest"){
return(0.4493*exp(log(0.09919/0.4493)*exp(-0.175*age))*1000)
}
}
#=======
getLifecourseVentilationRateFemaleSCIV<- function(age,activity){
if (activity == "rest"){
return(0.3255*exp(log(0.08771/0.3255)*exp(-0.3731*age))*1000)
}
}
#====================================================================================================
getLifecourseVentilationRateMale <- function(age)
#====================================================================================================
{
co = getLifecourseCardiacOutputMale(age)
qp = 0.96*co + 58
return(qp)
}
#====================================================================================================
getLifecourseVentilationRateFemale <- function(age)
#====================================================================================================
{
co = getLifecourseCardiacOutputFemale(age)
qp = 0.62*co + 82
return(qp)
}
#'Get the Lung Dead Space for a given age and gender
#' @description Uses life course equation to calculate the lung dead space for a specific age and gender
#' @param age Age in years
#' @param gender Either "M" for Male for "F" for Female
#' @export
getLifecourseLungDeadSpace<- function(age,gender){
if(is.na(age)) return(NA)
if(gender == "M"){
return(getLifecourseLungDeadSpaceMale(age))
}else if(gender == "F"){
return(getLifecourseLungDeadSpaceFemale(age))
}
}
#=========
getLifecourseLungDeadSpaceMale <- function(age){
return(0.17*exp(log(0.01371/0.17)*exp(-0.13*age)))
}
#=========
getLifecourseLungDeadSpaceFemale <- function(age){
return(0.1274*exp(log(0.01345/0.1274)*exp(-0.1609*age)))
}
#' Get the tidal volume for a given age and gender
#' @description Uses life course equation to calculate the tidal volume for a specific age and gender
#' @param age Age in years
#' @param gender Either "M" for Male for "F" for Female
#' @param activity Activity level. Can be "rest" or "light activity"
#' @export
getLifecourseTidalVolume <- function(age,gender,activity ="rest"){
if(is.na(age)) return(NA)
if (gender=="M"){
return(getLifecourseTidalVolumeMale(age,activity))
}else if(gender=="F"){
return(getLifecourseTidalVolumeFemale(age,activity))
}
}
#======
getLifecourseTidalVolumeMale<- function(age,activity){
if (activity == "rest"){
return(0.6842*exp(log(0.04306/0.6842)*exp(-0.1357*age)))
}else if(activity == "light exercise"){
if(age <= 1){
return(1.661*exp(log(0.07428/1.661)*exp(-0.1095*age)))
}else{
return(0.1041+(age^2.727)*(1.478-0.1041)/(age^2.727+12.23^2.727))
}
}
}
#=======
getLifecourseTidalVolumeFemale<- function(age,activity){
if (activity == "rest"){
return(0.02712+(age^0.9173)*(0.9599-0.02712)/(age^0.9173+27.01^0.9173))
}else if(activity == "light exercise"){
if (age <= 1){
return(1.159*exp(log(0.07248/1.159)*exp(-0.1362*age)))
}else{
return(0.1036+(age^3.064)*(1.055-0.1036)/(age^3.064+9.58^3.064))
}
}
}
#' Get the urine production rate for a given age and gender
#' @description Uses life course equation to calculate a urine production rate for a specific age and gender
#' @param age Age in years
#' @param gender Either "M" for Male for "F" for Female
#' @export
getLifecourseUrineProductionRate <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseUrineProductionRateMale(age))
}
else if(gender == "F") {
return(getLifecourseUrineProductionRateFemale(age))
}
}
#====================================================================================================
getLifecourseUrineProductionRateMale <- function(age)
#====================================================================================================
{
ur = -2.96538E-06*age^4 + 7.71852E-04*age^3 - 7.54327E-02*age^2 + 3.04687E+00*age + 1.26931E+01
return(ur)
}
#====================================================================================================
getLifecourseUrineProductionRateFemale <- function(age)
#====================================================================================================
{
ur = 1.59275E-04*age^3 - 3.09917E-02*age^2 + 1.70013E+00*age + 2.07921E+01
return(ur)
}
#' Get the Glomerular Filteration Rate for a given age and gender
#' @description Uses life course equation to calculate a GFR for a specific age and gender
#' @param age Age in years
#' @param gender Either "M" for Male for "F" for Female
#' @export
getLifecourseGlomerularFiltrationRate <- function(age, gender)
#====================================================================================================
{
if(is.na(age)) return(NA)
if(gender == "M") {
return(getLifecourseGlomerularFiltrationRateMale(age))
}
else if(gender == "F") {
return(getLifecourseGlomerularFiltrationRateFemale(age))
}
}
#====================================================================================================
getLifecourseGlomerularFiltrationRateMale <- function(age)
#====================================================================================================
{
gfr = NA
bw = getLifecourseBodyWeightMale(age)
mbw10d = getLifecourseBodyWeightMale(1/365)
mbw1 = getLifecourseBodyWeightMale(1)
bsa = getLifecourseBodySurfaceAreaMale(age)
bsa1 = getLifecourseBodySurfaceAreaMale(1)
bsa30 = getLifecourseBodySurfaceAreaMale(30)
gfr_bsa = 7.62
days = age/365
if(age >= 0 && age <= 1/365) # 1 day
{
gfr = 0.12 * (1.0 + 1.0) * (-0.0013 * mbw10d**2.0 + 0.2025 * mbw10d - 0.1363) * (gfr_bsa * bsa1 / 1.73) / ((-0.0013 * mbw1**2.0 + 0.2025 * mbw1 - 0.1363) * (0.48 + (0.0571 * (10.0 - 3.0))))
}
else if (age > 1/365 && age <= 3/365) # 3 days
{
gfr = 0.12 * (1.0 + days) * (-0.0013 * mbw10d**2.0 + 0.2025 * mbw10d - 0.1363) * (gfr_bsa * bsa1 / 1.73) / ((-0.0013 * mbw1**2.0 + 0.2025 * mbw1 - 0.1363) * (0.48 + (0.0571 * (10.0 - 3.0))))
}
else if (age > 3/365 && age <= 10/365) # 10 days
{
gfr = (0.48 + (0.0571 * (days - 3))) * (-0.0013 * mbw10d**2.0 + 0.2025 * mbw10d - 0.1363) * (gfr_bsa * bsa1 / 1.73) / ((-0.0013 * mbw1**2.0 + 0.2025 * mbw1 - 0.1363) * (0.48 + (0.0571 * (10.0 - 3.0))))
}
else if (age > 10/365 && age <= 1)
{
gfr = (-0.0013 * bw**2.0 + 0.2025 * bw - 0.1363) * (gfr_bsa * bsa1 / 1.73) / (-0.0013 * mbw1**2.0 + 0.2025 * mbw1 - 0.1363)
}
else if (age > 1 && age <= 30)
{
gfr = gfr_bsa * bsa / 1.73
}
else if (age > 30)
{
gfr = gfr_bsa * bsa30 / 1.73 - (0.0066 * (7.62 * bsa30 / 1.73) * (age - 30))
}
return(gfr)
}
#====================================================================================================
getLifecourseGlomerularFiltrationRateFemale <- function(age)
#====================================================================================================
{
gfr = NA
bw = getLifecourseBodyWeightFemale(age)
mbw10d = getLifecourseBodyWeightFemale(1/365)
mbw1 = getLifecourseBodyWeightFemale(1)
bsa = getLifecourseBodySurfaceAreaFemale(age)
bsa1 = getLifecourseBodySurfaceAreaFemale(1)
bsa30 = getLifecourseBodySurfaceAreaFemale(30)
gfr_bsa = 7.62
days = age/365
if(age >= 0 && age <= 1/365) # 1 day
{
gfr = 0.12 * (1.0 + 1.0) * (-0.0013 * mbw10d**2.0 + 0.2025 * mbw10d - 0.1363) * (gfr_bsa * bsa1 / 1.73) / ((-0.0013 * mbw1**2.0 + 0.2025 * mbw1 - 0.1363) * (0.48 + (0.0571 * (10.0 - 3.0))))
}
else if (age > 1/365 && age <= 3/365) # 3 days
{
gfr = 0.12 * (1.0 + days) * (-0.0013 * mbw10d**2.0 + 0.2025 * mbw10d - 0.1363) * (gfr_bsa * bsa1 / 1.73) / ((-0.0013 * mbw1**2.0 + 0.2025 * mbw1 - 0.1363) * (0.48 + (0.0571 * (10.0 - 3.0))))
}
else if (age > 3/365 && age <= 10/365) # 10 days
{
gfr = (0.48 + (0.0571 * (days - 3))) * (-0.0013 * mbw10d**2.0 + 0.2025 * mbw10d - 0.1363) * (gfr_bsa * bsa1 / 1.73) / ((-0.0013 * mbw1**2.0 + 0.2025 * mbw1 - 0.1363) * (0.48 + (0.0571 * (10.0 - 3.0))))
}
else if (age > 10/365 && age <= 1)
{
gfr = (-0.0013 * bw**2.0 + 0.2025 * bw - 0.1363) * (gfr_bsa * bsa1 / 1.73) / (-0.0013 * mbw1**2.0 + 0.2025 * mbw1 - 0.1363)
}
else if (age > 1 && age <= 30)
{
gfr = gfr_bsa * bsa / 1.73
}
else if (age > 30)
{
gfr = gfr_bsa * bsa30 / 1.73 - (0.0062 * (7.62 * bsa30 / 1.73) * (age - 30))
}
return(gfr)
}
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.