Monolix Controller for nlmixr2

Usage

monolixControl(
  nbSSDoses = 7,
  useLinearization = FALSE,
  stiff = FALSE,
  addProp = c("combined2", "combined1"),
  exploratoryAutoStop = FALSE,
  smoothingAutoStop = FALSE,
  burnInIterations = 5,
  smoothingIterations = 200,
  exploratoryIterations = 250,
  simulatedAnnealingIterations = 250,
  exploratoryInterval = 200,
  exploratoryAlpha = 0,
  omegaTau = 0.95,
  errorModelTau = 0.95,
  variability = c("none", "firstStage", "decreasing"),
  runCommand = getOption("babelmixr2.monolix", ""),
  rxControl = NULL,
  sumProd = FALSE,
  optExpression = TRUE,
  calcTables = TRUE,
  compress = TRUE,
  ci = 0.95,
  sigdigTable = NULL,
  absolutePath = FALSE,
  modelName = NULL,
  muRefCovAlg = TRUE,
  run = TRUE,
  ...
)

Arguments

nbSSDoses: Number of steady state doses (default 7)
useLinearization: Use linearization for log likelihood and fim.
stiff: boolean for using the stiff ODE solver
addProp: Type of additive-plus-proportional error: `"combined1"`, where standard deviations add: $$y = f + (a + b\times f^c) \times \varepsilon$$; or `"combined2"`, where variances add: $$y = f + \sqrt{a^2 + b^2\times f^{2\times c}} \times \varepsilon$$. Here y = observed, f = predicted, a = additive sd, b = proportional/power sd, c = power exponent (1 in the proportional case).
exploratoryAutoStop: logical to turn on or off exploratory phase auto-stop of SAEM (default 250)
smoothingAutoStop: Boolean indicating if the smoothing should automatically stop (default FALSE)
burnInIterations: Number of burn in iterations
smoothingIterations: Number of smoothing iterations
exploratoryIterations: Number of iterations for exploratory phase (default 250)
simulatedAnnealingIterations: Number of simulating annealing iterations
exploratoryInterval: Minimum number of iterations in the exploratory phase (default 200)
exploratoryAlpha: Convergence memory in the exploratory phase (only used when exploratoryAutoStop is TRUE)
omegaTau: Proportional rate on variance for simulated annealing
errorModelTau: Proportional rate on error model for simulated annealing
variability: This describes the methodology for parameters without variability. It could be: - Fixed throughout (none) - Variability in the first stage (firstStage) - Decreasing until it reaches the fixed value (decreasing)
runCommand: is a shell command or function to run monolix; You can specify the default by options("babelmixr2.monolix"="runMonolix"). If it is empty and 'lixoftConnectors' is available, use lixoftConnectors to run monolix. See details for function usage.
rxControl: `rxode2` ODE solving options during fitting, created with `rxControl()`
sumProd: Is a boolean indicating if the model should change multiplication to high precision multiplication and sums to high precision sums using the PreciseSums package. By default this is FALSE.
optExpression: Optimize the rxode2 expression to speed up calculation. By default this is turned on.
calcTables: This boolean is to determine if the foceiFit will calculate tables. By default this is TRUE
compress: Should the object have compressed items
ci: Confidence level for some tables. By default this is 0.95 or 95% confidence.
sigdigTable: Significant digits in the final output table. If not specified, then it matches the significant digits in the `sigdig` optimization algorithm. If `sigdig` is NULL, use 3.
absolutePath: Boolean indicating if the absolute path should be used for the monolix runs
modelName: Model name used to generate the NONMEM output. If NULL try to infer from the model name (could be x if not clear). Otherwise use this character for outputs.
muRefCovAlg: When `TRUE` (default), algebraic expressions that can be mu-referenced are internally rewritten as mu-referenced covariates and restored after optimization. Mirrors saemControl(muRefCovAlg=)/nlmeControl(muRefCovAlg=); for foceiControl() only takes effect when muModel != "none".
run: Should monolix be run and the results be imported to nlmixr2? (Default is TRUE)
...: Ignored parameters

Value

A monolix control object

Details

If runCommand is given as a string, it will be called with the system() command like:

runCommand mlxtran.

For example, if runCommand="'/path/to/monolix/mlxbsub2021' -p " then the command line used would look like the following:

'/path/to/monolix/mlxbsub2021' monolix.mlxtran

If runCommand is given as a function, it will be called as FUN(mlxtran, directory, ui) to run Monolix. This allows you to run Monolix in any way that you may need, as long as you can write it in R. babelmixr2 will wait for the function to return before proceeding.

If runCommand is NA, nlmixr() will stop after writing the model files and without starting Monolix.

Note that you can get the translated monolix components from a parsed/compiled rxode2 ui object with ui$monolixModel and ui$mlxtran

Author

Matthew Fidler