ode_nonmem: DeSolve pharmacometrics model creator

In Peccary-PMX/Peccary: PD and PK results

DeSolve pharmacometrics model creator

Description

Create a NONMEM code with a deSolve model.

Usage

ode_nonmem(func = Lorenz, parms = parameters, y = state,
  output = "", add_param = "", mu_referencig = T, BLQ = F,
  datafile = "", outputcat = T, ...)

Arguments

func	Function (same as deSolve in functions)
parms	Parameters (same as deSolve in functions)
y	same as the ode
output	vector of the output names. In case of several outputs, use the format c("name1 = X", "name2 = Y",...), with X/Y being the YTYPE number.
add_param	vector of parameter names to add, mostly usefull for adding baseline parameters. If it has the format "X1_0", with X1 being the name of a cmt, add it as a baseline for the concerned cmt. If the format is "Z = 21", add a new parameter with the name Z and initial value 21.
mu_referencig	booléen, declaration of parameters with/without mu referencing.
datafile	Either a .tab or an other cfl

Author(s)

Thibaud Derippe

Examples

## Not run: 
ODE<-function(t,y,p){

#parameters
V   <- p[1]
k   <- p[2]
k12 <- p[3]
k21 <- p[4]
k13 <- p[5]
k31 <- p[6]
ku  <- p[7]


#--- ODE system - start ---#
A1 <- y[1]
A2 <- y[2]
A3 <- y[3]
A4 <- y[4]

yd1 <- k21 * A2 + k31 * A3 - k12 * A1 - k13 * A1 - k * A1 - ku * A1
yd2 <- k12 * A1 - k21 * A2
yd3 <- k13 * A1 - k31 * A3
yd4 <- ku * A1

Cc <- A1/V

#Output: list(c(initial conditions), c(output variable))
list(c(yd1, yd2, yd3, yd4),
    c(Cc = A1/V, A_urine = y[4]))
}

params <- c(V = 3,
           k = 0.281,
           k12 = 0.467,
           k21 = 6.23e-05,
           k13 = 0.00666,
           k31 = 0.116,
           ku = 0.6)

dose <- 1.5 * 70 * 1000



init <- c(231, 0, 0, 0)

time <- seq(0, 24, 0.1)
out <- lsoda(y = eval(init), times = time, func = ODE, parms = params)

ode_nonmem( BLQ = T, add_param = "X1_0", output = c("A(1)/V = 1", "A(4) = 2") , y = init, times = time, func = ODE, parms = params, mu_referencig = T)

## End(Not run)

Peccary-PMX/Peccary documentation built on Jan. 17, 2024, 9:27 p.m.