calculate_AUC {gammaFuncModel}R Documentation

Function that produces Area Under the Curve(AUC) property for a single individual in a particular group, for a specific metabolite

Description

Function that produces Area Under the Curve(AUC) property for a single individual in a particular group, for a specific metabolite

Usage

calculate_AUC(f, upperbound)

Arguments

f

function that returns the prediction of a metabolite concentration, for a single individual in a particular group

upperbound

Numeric value that serves as the upperbound of integration

Value

AUC for this metabolite, in a particular group for a single individual

References

Wickham, H. (2022). dplyr: A Grammar of Data Manipulation. R package version 1.0.10. Available at: https://CRAN.R-project.org/package=dplyr

Pinheiro, J. C., & Bates, D. M. (2022). nlme: Linear and Nonlinear Mixed Effects Models. R package version 3.1-153. Available at: https://CRAN.R-project.org/package=nlme

Examples


require(gammaFuncModel)
require(cubature)
require(dplyr)
require(nlme)
modify.df <- data.frame(
  ID = rep(sprintf("%02d", 1:10), each = 9 * 3),
  Time = rep(rep(1:9, each = 3), 10),
  Diet = as.factor(rep(1:3, times = 9 * 10)),
  Age = rep(sample(20:70, 10, replace = TRUE), each = 9 * 3),
  BMI = round(rep(runif(10, 18.5, 35), each = 9 * 3), 1),
  Concentration = NA
)
for (i in 1:10) {
 for (d in 1:3) {
   C0 <- runif(1, 10, 15)    # initial concentration
   k <- runif(1, 0.1, 0.3)   # decay rate constant
   modify.df$Concentration[modify.df$ID == sprintf("%02d", i) & modify.df$Diet == d] <- 
     C0 * exp(-k * modify.df$Time[modify.df$ID == sprintf("%02d", i) & modify.df$Diet == d])
 }
}
covariates <- c("ID", "Diet", "Age", "BMI")
model <- gammaFunction(
  modify.df, 
  covariates, 
  time_grp_inter = FALSE, 
return_ml_model = FALSE, include_grp = TRUE
)[[1]]
test_data <- modify.df %>% 
  filter(Diet == 1 & ID == "04") %>% 
  select(-c("Concentration", "ID", "Diet")) 
f_dat = modify.df %>% 
  filter(Diet == 1 & ID == "04") %>% 
  select(-Concentration)
f <- generate_f_function(
  data = f_dat, 
  model = model,  
  grp_var = 1, 
  grp_name = "Diet", 
  ID = "04", 
  ref = 1
)
AUC <- calculate_AUC(f, 9)
AUCInf <- calculate_AUC(f, Inf)


[Package gammaFuncModel version 5.0 Index]