In nlmixrdevelopment/nlmixrtargets: Targets for 'nlmixr2' Pipelines

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(nlmixr2targets)

Introduction to `nlmixr2targets`

The nlmixr2targets improves reproducibility by ensuring that your model is up-to-date with your data, and it speeds your workflow using the targets package to only run models when the model or data have changed.

There are two main functions that are used within the package:

tar_nlmixr() which runs a single model, and
tar_nlmixr_multimodel() which runs multiple models for a single dataset.

Using nlmixr2targets requires the use of the targets package. To learn about the targets package, see (https://docs.ropensci.org/targets/)[the targets website].

Running one model with one dataset (`tar_nlmixr()`)

The tar_nlmixr() function allows you to estimate one model with one dataset. It will generate three targets: a simplified version of the model, a minimal version of the dataset, and the estimation step.

The simplified version of the model removes parts that are less reproducible but changes none of the model intent. (Advanced information: The parts that are removed are that the source references and the model name. Also, the model is modified at this step for setting initial values as described in the previous section of this vignette.)

library(targets)
library(tarchetypes)
library(nlmixr2targets)

pheno <- function() {
  ini({
    lcl <- log(0.008); label("Typical value of clearance")
    lvc <-  log(0.6); label("Typical value of volume of distribution")
    etalcl + etalvc ~ c(1,
                        0.01, 1)
    cpaddSd <- 0.1; label("residual variability")
  })
  model({
    cl <- exp(lcl + etalcl)
    vc <- exp(lvc + etalvc)
    kel <- cl/vc
    d/dt(central) <- -kel*central
    cp <- central/vc
    cp ~ add(cpaddSd)
  })
}

plan_model <-
  tar_plan(
    myData = nlmixr2data::pheno_sd,
    tar_nlmixr(
      model_pheno,
      object = pheno,
      data = myData,
      est = "saem"
    )
  )

list(
  plan_model
)

Running multiple models with one dataset (`tar_nlmixr_multimodel()`)

A common use case is to generate multiple models using a single dataset and estimation method. tar_nlmixr_multimodel() allows the generation of a named list of models to allow subsequent analysis of all models.

Internally, tar_nlmixr_multimodel() passes all the models to tar_nlmixr() so that the data set simplification and equivalent steps run once per model, and not model is run more often than required for dataset or model changes.

library(targets)
library(tarchetypes)
library(nlmixr2targets)

pheno <- function() {
  ini({
    lcl <- log(0.008); label("Typical value of clearance")
    lvc <-  log(0.6); label("Typical value of volume of distribution")
    etalcl + etalvc ~ c(1,
                        0.01, 1)
    cpaddSd <- 0.1; label("residual variability")
  })
  model({
    cl <- exp(lcl + etalcl)
    vc <- exp(lvc + etalvc)
    kel <- cl/vc
    d/dt(central) <- -kel*central
    cp <- central/vc
    cp ~ add(cpaddSd)
  })
}

pheno2 <- function() {
  ini({
    lcl <- log(0.008); label("Typical value of clearance")
    lvc <-  log(0.6); label("Typical value of volume of distribution")
    etalcl + etalvc ~ c(2,
                        0.01, 2)
    cpaddSd <- 3.0; label("residual variability")
  })
  model({
    cl <- exp(lcl + etalcl)
    vc <- exp(lvc + etalvc)
    kel <- cl/vc
    d/dt(central) <- -kel*central
    cp <- central/vc
    cp ~ add(cpaddSd)
  })
}

plan_model <-
  tar_nlmixr_multimodel(
    all_models,
    data = nlmixr2data::pheno_sd,
    est = "saem",
    "Base model; additive residual error = 1" = pheno,
    "Base model; additive residual error = 3" = pheno2
  )

plan_report <-
  tar_plan(
    # Determine the AIC for all tested models
    aic_list = sapply(X = all_models, FUN = AIC)
  )

list(
  plan_model,
  plan_report
)

Model piping for multiple models estimated with one dataset

Model piping for nlmixr2 models (see vignette("modelPiping", package = "nlmixr2")) is possible within the multiple models being estimated with tar_nlmixr_multimodel(). It simplifies examples like the one above so that you can focus on the model content and avoid rewriting models, as with all nlmixr2 model piping.

To use model piping, simply refer to the model by its name like a named list. Behind the scenes, nlmixr2targets will work out the dependencies between the models and only rerun the dependent model if it or the dependent model changes.

library(targets)
library(tarchetypes)
library(nlmixr2targets)
library(nlmixr2)

pheno <- function() {
  ini({
    lcl <- log(0.008); label("Typical value of clearance")
    lvc <-  log(0.6); label("Typical value of volume of distribution")
    etalcl + etalvc ~ c(1,
                        0.01, 1)
    cpaddSd <- 0.1; label("residual variability")
  })
  model({
    cl <- exp(lcl + etalcl)
    vc <- exp(lvc + etalvc)
    kel <- cl/vc
    d/dt(central) <- -kel*central
    cp <- central/vc
    cp ~ add(cpaddSd)
  })
}

plan_model <-
  tar_nlmixr_multimodel(
    all_models,
    data = nlmixr2data::pheno_sd,
    est = "saem",
    "Base model; additive residual error = 1" = pheno,
    "Base model; additive residual error = 3" =
      all_models[["Base model; additive residual error = 1"]] |>
      ini(cpaddSd = 3)
  )

list(
  plan_model
)