nlmixr2/rxode2 mu referencing 2.0

By Matthew Fidler in rxode2 nlmixr2

July 8, 2024

This month, I will talk about about a new iteration of mu-referencing in nlmixr2, which I call mu2.

What is mu referencing in nlmixr2

mu-referencing is combining a fixed effect, random effect and possibly a covariate in the form:

\[ \theta_\mathsf{pop}+\eta_\mathsf{individual}+\theta_\mathsf{covariate}\times \mathsf{DataCovariate} \]

Often they are placed in exponentials for these to be log-normally distributed like:

\[ \exp\left(\theta_\mathsf{pop}+\eta_\mathsf{individual}+\theta_\mathsf{covariate}\times \mathsf{DataCovariate}\right) \]

In optimization routines like saem, these are switched out with a single parameter during optimization classically called \(\phi\) in both NONMEM and Monolix.

Once the best \(\phi\) is found, then the population, individual and covariates can be found by linear regression of the individual \(\phi\) values versus the information in the optimization.

This linear model adds important stability and speed when determining these parameters in the mu-expression. (It also adds rules like they must not be time-varying for instance).

In old versions of rxode2 and nlmixr2 the \(\mathsf{DataCovariate}\) had to be in the dataset itself. This classic weight covariate adjustment:

\[ \exp\left(\theta_{Cl}+\eta_{Cl}\right)\times\left(\frac{WT}{70}\right)^{3/4} \]

would have to written:

\[ \exp\left(\theta_{Cl}+\eta_{Cl} + 3/4\times\log\left(\frac{WT}{70}\right)\right) \]

If you wanted to estimate the population parameter \(3/4\) to see if it approaches the correct value you could with:

\[ \exp\left(\theta_{Cl}+\eta_{Cl} + \theta_{Cl, \textsf{cov}}\times\mathsf{DataCovariate}\right) \]

Where

\[ \mathsf{DataCovariate} =\log\left(\frac{WT}{70}\right) \]

This is easy enough to do and adds stabilization.

However, with mu referencing 2.0 you can simply use an additive expression to setup mu-referencing:

\[ \exp\left(\theta_{Cl}+\eta_{Cl} + \frac{WT}{70}+\theta_{Cl, \textsf{cov}}\times\log\left(WT/70\right)\right) \]

This is a bit more convenient than creating a column in the dataset that does this conversion and less user-based intervention to make nlmixr2 use linear models when it can.

Checking for mu2 referencing

In rxode2 / nlmixr2 you can check to see if your version of nlmixr2 supports the mu2 referencing by evaluating the functional form:

one.compartment <- function() {
  ini({
    tka <- log(1.57); label("Ka")
    tcl <- log(2.72); label("Cl")
    tv <- log(31.5); label("V")
    wt.cl <- 0.75; label("WT on CL")
    eta.ka ~ 0.6
    eta.cl ~ 0.3
    eta.v ~ 0.1
    add.sd <- 0.7
  })
  # and a model block with the error specification and model specification
  model({
    ka <- exp(tka + eta.ka)
    cl <- exp(tcl + eta.cl + wt.cl*log(WT/70))
    v <- exp(tv + eta.v)
    d/dt(depot) <- -ka * depot
    d/dt(center) <- ka * depot - cl / v * center
    cp <- center / v
    cp ~ add(add.sd)
  })
}

one <- one.compartment()

print(one)
##  ── rxode2-based free-form 2-cmt ODE model ─────────────────────────────────────────────── 
##  ── Initalization: ──  
## Fixed Effects ($theta): 
##       tka       tcl        tv     wt.cl    add.sd 
## 0.4510756 1.0006319 3.4499875 0.7500000 0.7000000 
## 
## Omega ($omega): 
##        eta.ka eta.cl eta.v
## eta.ka    0.6    0.0   0.0
## eta.cl    0.0    0.3   0.0
## eta.v     0.0    0.0   0.1
## 
## States ($state or $stateDf): 
##   Compartment Number Compartment Name
## 1                  1            depot
## 2                  2           center
##  ── μ-referencing ($muRefTable): ──  
##   theta    eta level                         covariates
## 1   tka eta.ka    id                                   
## 2   tcl eta.cl    id log(0.0142857142857143 * WT)*wt.cl
## 3    tv  eta.v    id                                   
## 
##  ── Model (Normalized Syntax): ── 
## function() {
##     ini({
##         tka <- 0.451075619360217
##         label("Ka")
##         tcl <- 1.00063188030791
##         label("Cl")
##         tv <- 3.44998754583159
##         label("V")
##         wt.cl <- 0.75
##         label("WT on CL")
##         add.sd <- c(0, 0.7)
##         eta.ka ~ 0.6
##         eta.cl ~ 0.3
##         eta.v ~ 0.1
##     })
##     model({
##         ka <- exp(tka + eta.ka)
##         cl <- exp(tcl + eta.cl + wt.cl * log(WT/70))
##         v <- exp(tv + eta.v)
##         d/dt(depot) <- -ka * depot
##         d/dt(center) <- ka * depot - cl/v * center
##         cp <- center/v
##         cp ~ add(add.sd)
##     })
## }

If the mu2 referencing is supported it will show the following mu reference table:

── μ-referencing ($muRefTable): ──
  theta    eta level                         covariates
1   tka eta.ka    id
2   tcl eta.cl    id log(0.0142857142857143 * WT)*wt.cl
3    tv  eta.v    id

Here it shows the transformation that is used when creating the transformed data used for mu-based covariate modeling. In this case, we have log(0.0142857142857143 * WT). It is a bit different than what is written because it is prepossessed by symengine and looks at the derivative with respect to the covariate parameter wt.cl.

In general, I am excited by this new feature in nlmixr2 because it adds a new level of simplicity to user-based models and more often detects mu-referenced code when it may not have been detected in the past.

Why the Pokemon icon?

Why the icon for mu2 referencing? Every time I hear mu2 I think of the ultimate genetically modified Pokemon mewtwo (which is a link to where the image comes from).

Posted on:
July 8, 2024
Length:
4 minute read, 755 words
Categories:
rxode2 nlmixr2
Tags:
mu
See Also: