rxode2 additional model types

As suggested in the name, rxode2 is often concerned with solutions to ordinary differential equations. The syntax of the ODE models is covered in the rxode2 syntax vignette

You can create other types of models with rxode2:

Prediction only models without ODE systems in them ($PRED models in NONMEM).
1, 2 and 3 solved compartment models (ADVAN/TRANS in NONMEM).
Mixing any of these items with ODE systems.

Prediction only models

Prediction only models are simple to create. You use the rxode2 syntax without any ODE systems in them. A very simple example is a one-compartment model.

library(rxode2)

## rxode2 3.0.3 using 2 threads (see ?getRxThreads)
##   no cache: create with `rxCreateCache()`

mod <- function(){
  model({
    ipre <- 10 * exp(-ke * t)
  })
}

Solving the rxode2 models are the same as saving the simple ODE system, but faster of course.

et  <- et(seq(0,24,length.out=50))
cmt1 <- rxSolve(mod,et,params=c(ke=0.5))

## i parameter labels from comments are typically ignored in non-interactive mode

## i Need to run with the source intact to parse comments

## using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’

cmt1

## -- Solved rxode2 object --
## -- Parameters (x$params): --
##  ke 
## 0.5 
## -- Initial Conditions (x$inits): --
## named numeric(0)
## -- First part of data (object): --
## # A tibble: 50 x 2
##    time  ipre
##   <dbl> <dbl>
## 1 0     10   
## 2 0.490  7.83
## 3 0.980  6.13
## 4 1.47   4.80
## 5 1.96   3.75
## 6 2.45   2.94
## # i 44 more rows

Solved compartment models

Solved models are also simple to create. You simply place the linCmt() psuedo-function into your code. The linCmt() function figures out the type of model to use based on the parameter names specified.

Most often, pharmacometric models are parameterized in terms of volume and clearances. Clearances are specified by NONMEM-style names of CL, Q, Q1, Q2, etc. or distributional clearances CLD, CLD2. Volumes are specified by Central (VC or V), Peripheral/Tissue (VP, VT). While more translations are available, some example translations are below:

Another popular parameterization is in terms of micro-constants. rxode2 assumes compartment 1 is the central compartment. The elimination constant would be specified by K, Ke or Kel. Some example translations are below:

The last parameterization possible is using alpha and V and/or A/B/C. Some example translations are below:

Once the linCmt() sleuthing is complete, the 1, 2 or 3 compartment model solution is used as the value of linCmt().

The compartments where you can dose in a linear solved system are depot and central when there is an linear absorption constant in the model ka. Without any additional ODEs, these compartments are numbered depot=1 and central=2.

When the absorption constant ka is missing, you may only dose to the central compartment. Without any additional ODEs the compartment number is central=1.

These compartments take the same sort of events that a ODE model can take, and are discussed in the rxode2 events vignette.

mod <- function() {
  ini({
    kel <- 0.5
    V <- 1
  })
  model({
    ipre <- linCmt(V, kel)
  })
}

This then acts as an ODE model; You specify a dose to the depot compartment and then solve the system:

et  <- et(amt=10,time=0,cmt=depot) %>%
  et(seq(0,24,length.out=50))
cmt1 <- rxSolve(mod,et)

## i parameter labels from comments are typically ignored in non-interactive mode

## i Need to run with the source intact to parse comments

## using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’

cmt1

## -- Solved rxode2 object --
## -- Parameters (x$params): --
## kel   V 
## 0.5 1.0 
## -- Initial Conditions (x$inits): --
## named numeric(0)
## -- First part of data (object): --
## # A tibble: 50 x 2
##    time  ipre
##   <dbl> <dbl>
## 1 0     10   
## 2 0.490  7.83
## 3 0.980  6.13
## 4 1.47   4.80
## 5 1.96   3.75
## 6 2.45   2.94
## # i 44 more rows

Mixing Solved Systems and ODEs

In addition to pure ODEs, you may mix solved systems and ODEs. The prior 2-compartment indirect response model can be simplified with a linCmt() function:

library(rxode2)
## Setup example model
mod1 <-function() {
  model({
    C2 = centr/V2
    C3 = peri/V3
    d/dt(depot) =-KA*depot
    d/dt(centr) = KA*depot - CL*C2 - Q*C2 + Q*C3
    d/dt(peri)  =                    Q*C2 - Q*C3
    d/dt(eff)  = Kin - Kout*(1-C2/(EC50+C2))*eff
  })
}

## Seup parameters and initial conditions

theta <-
    c(KA=2.94E-01, CL=1.86E+01, V2=4.02E+01, # central
      Q=1.05E+01,  V3=2.97E+02,              # peripheral
      Kin=1, Kout=1, EC50=200)               # effects

inits <- c(eff=1)

## Setup dosing event information
ev <- et(amountUnits="mg", timeUnits="hours") %>%
    et(amt=10000, addl=9, ii=12) %>%
    et(amt=20000, addl=4, time=120, ii=24) %>%
    add.sampling(0:240)

## Setup a mixed solved/ode system:
mod2 <- function() {
  model({
    ## the order of variables do not matter, the type of compartmental
    ## model is determined by the parameters specified.
    C2   = linCmt(KA, CL, V2, Q, V3);
    eff(0) = 1  ## This specifies that the effect compartment starts at 1.
    d/dt(eff) =  Kin - Kout*(1-C2/(EC50+C2))*eff;
  })
}

This allows the indirect response model above to assign the 2-compartment model to the C2 variable and the used in the indirect response model.

When mixing the solved systems and the ODEs, the solved system’s compartment is always the last compartment. This is because the solved system technically isn’t a compartment to be solved. Adding the dosing compartment to the end will not interfere with the actual ODE to be solved.

Therefore,in the two-compartment indirect response model, the effect compartment is compartment #1 while the PK dosing compartment for the depot is compartment #2.

This compartment model requires a new event table since the compartment number changed:

ev <- et(amountUnits='mg', timeUnits='hours') %>%
  et(amt=10000, addl=9, ii=12, cmt=2) %>%
  et(amt=20000, addl=4, time=120, ii=24, cmt=2) %>%
  et(0:240)

This can be solved with the following command:

x <- mod2 %>%  solve(theta, ev)

## i parameter labels from comments are typically ignored in non-interactive mode

## i Need to run with the source intact to parse comments

## using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’

print(x)

## -- Solved rxode2 object --
## -- Parameters ($params): --
##      KA      CL      V2       Q      V3     Kin    Kout    EC50 
##   0.294  18.600  40.200  10.500 297.000   1.000   1.000 200.000 
## -- Initial Conditions ($inits): --
## eff 
##   1 
## -- First part of data (object): --
## # A tibble: 241 x 3
##   time    C2   eff
##    [h] <dbl> <dbl>
## 1    0 249.   1   
## 2    1 121.   1.35
## 3    2  60.3  1.38
## 4    3  31.0  1.28
## 5    4  17.0  1.18
## 6    5  10.2  1.11
## # i 235 more rows

Note this solving did not require specifying the effect compartment initial condition to be 1. Rather, this is already pre-specified by eff(0)=1.

This can be solved for different initial conditions easily:

x <- mod2 %>%  solve(theta, ev,c(eff=2))

## i parameter labels from comments are typically ignored in non-interactive mode

## i Need to run with the source intact to parse comments

print(x)

## -- Solved rxode2 object --
## -- Parameters ($params): --
##      KA      CL      V2       Q      V3     Kin    Kout    EC50 
##   0.294  18.600  40.200  10.500 297.000   1.000   1.000 200.000 
## -- Initial Conditions ($inits): --
## eff 
##   2 
## -- First part of data (object): --
## # A tibble: 241 x 3
##   time    C2   eff
##    [h] <dbl> <dbl>
## 1    0 249.   2   
## 2    1 121.   1.93
## 3    2  60.3  1.67
## 4    3  31.0  1.41
## 5    4  17.0  1.23
## 6    5  10.2  1.13
## # i 235 more rows

The rxode2 detective also does not require you to specify the variables in the linCmt() function if they are already defined in the block. Therefore, the following function will also work to solve the same system.

mod3 <- function() {
  ini({
    KA <- 2.94E-01
    CL <- 1.86E+01
    V2 <- 4.02E+01
    Q <- 1.05E+01
    V3 <- 2.97E+02
    Kin <- 1
    Kout <- 1
    EC50 <- 200
  })
  model({
    # Since the parameters are in the ini block, put them in linCmt so
    # that the model is detected correctly
    C2   <- linCmt(KA, CL, V2, Q, V3)
    eff(0) <- 1  ## This specifies that the effect compartment starts at 1.
    d/dt(eff) <-  Kin - Kout*(1-C2/(EC50+C2))*eff;
  })
}

x <- mod3 %>%  solve(ev)

## i parameter labels from comments are typically ignored in non-interactive mode

## i Need to run with the source intact to parse comments

print(x)

## -- Solved rxode2 object --
## -- Parameters ($params): --
##      KA      CL      V2       Q      V3     Kin    Kout    EC50 
##   0.294  18.600  40.200  10.500 297.000   1.000   1.000 200.000 
## -- Initial Conditions ($inits): --
## eff 
##   1 
## -- First part of data (object): --
## # A tibble: 241 x 3
##   time    C2   eff
##    [h] <dbl> <dbl>
## 1    0 249.   1   
## 2    1 121.   1.35
## 3    2  60.3  1.38
## 4    3  31.0  1.28
## 5    4  17.0  1.18
## 6    5  10.2  1.11
## # i 235 more rows

Note that you do not specify the parameters when solving the system since they are built into the model, but you can override the parameters:

x <- mod3 %>%  solve(c(KA=10),ev)

## i parameter labels from comments are typically ignored in non-interactive mode

## i Need to run with the source intact to parse comments

print(x)

## -- Solved rxode2 object --
## -- Parameters ($params): --
##    KA    CL    V2     Q    V3   Kin  Kout  EC50 
##  10.0  18.6  40.2  10.5 297.0   1.0   1.0 200.0 
## -- Initial Conditions ($inits): --
## eff 
##   1 
## -- First part of data (object): --
## # A tibble: 241 x 3
##   time    C2   eff
##    [h] <dbl> <dbl>
## 1    0 249.   1   
## 2    1 121.   1.35
## 3    2  60.3  1.38
## 4    3  31.0  1.28
## 5    4  17.0  1.18
## 6    5  10.2  1.11
## # i 235 more rows

2024-12-17

Prediction only models

Solved compartment models

Mixing Solved Systems and ODEs