R crashes with dur in the model

[lirui0321]

Hi Matt,

I am trying to set the infusion duration within the model. However, R always crashes when I run the model. When you get time, could you tell me if I code my model correctly? Thank you!

# Load RxODE
library(RxODE)

# Define and Compile model

mod1 <- RxODE({
  CLH_int = THETA[1];
  CLD = THETA[2];
  V_centr = THETA[3];
  V_peri = THETA[4];
  fup = 0.28; #
  RBP = 1;
  CLR = 0 ;
  ka = 10;
  FQ_LV = 1.26
  BW = 70; # kg
  Qh = FQ_LV *BW;
  CLH =  Qh*CLH_int*fup/(Qh+CLH_int*fup/RBP)
  Fh = 1 - CLH/RBP/Qh
  FaFg = 0.82
  C_centr = A_centr/V_centr ;#           venous (VE) total  venous blood
  C_peri = A_peri/V_peri ;#  			arterial (AR) total  arterial blood
  d/dt(A_centr)= - C_centr*(CLR+CLH) + C_peri*CLD - C_centr*CLD + ka * A_absorption ; #	central
  d/dt(A_peri) = - C_peri*CLD + C_centr*CLD ; # peripheral
  d/dt(A_absorption) = - ka * A_absorption ;
  f(A_absorption) = Fh * FaFg;
  dur(A_absorption) = THETA[5]
  DV = DV; # copying data columns from data set for fitting 
  MDV = MDV;
  PRED = C_centr;
});

# data
NM_data <- read.csv("data.csv", header=TRUE, sep=",", na.strings=".", stringsAsFactors=FALSE) # read NONMEM data set
NM_data[is.na(NM_data)] = 0 # replace NA with 0

# simulation 
THETA <- c(10   ,2.619, 10, 22.14, 5)
x <- solve(mod1, NM_data , params=setNames(THETA, paste0("THETA[",1:5,"]")))

Here is data file
data.zip

[mattfidler]

I have reproduced the issue and put this in the issues #399. I will see if there is a work-around for now.

[lirui0321]

Thank you for the bug-report; It helps the package get better 😄

Matt, thank you! RxODE is the exact modeling tool I have been looking for over years. Almost everything I want has been included in this package. In addition, as an R package, I can also easily combine this package with tons of other package available in R. I wish that I could know this package earlier.

[mattfidler]

I got an error message when installed RxODE through github, although it worked before. Do you have any idea what is the problem?

Yes. You need the new dparser; You can install from CRAN or github:

install.packages("dparser", type="source")
# or
remotes::install_github("nlmixredevlopment/dparser-R")

The new dparser binaries haven't hit cran yet (though the source package has).

[mattfidler]

Matt, thank you! RxODE is the exact modeling tool I have been looking for over years. Almost everything I want has been included in this package. In addition, as an R package, I can also easily combine this package with tons of other package available in R. I wish that I could know this package earlier.

Thank you!

[lirui0321]

I got an error message when installed RxODE through github, although it worked before. Do you have any idea what is the problem?

Yes. You need the new dparser; You can install from CRAN or github:

install.packages("dparser", type="source")
# or
remotes::install_github("nlmixredevlopment/dparser-R")

The new dparser binaries haven't hit cran yet (though the source package has).

Thanks, Matt! Now it works.

[mattfidler]

Great!