monolixControl: Monolix Controller for nlmixr2

In nlmixr2/babelmixr: Use 'nlmixr2' to Interact with Open Source and Commercial Software

Monolix Controller for nlmixr2

Description

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	specifies the type of additive plus proportional errors, the one where standard deviations add (combined1) or the type where the variances add (combined2). The combined1 error type can be described by the following equation: y = f + (a + b\times f^c) \times \varepsilon The combined2 error model can be described by the following equation: y = f + \sqrt{a^2 + b^2\times f^{2\times c}} \times \varepsilon Where: - y represents the observed value - f represents the predicted value - a is the additive standard deviation - b is the proportional/power standard deviation - c is the power exponent (in the proportional case c=1)
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	This controls if algebraic expressions that can be mu-referenced are treated as mu-referenced covariates by: 1. Creating a internal data-variable 'nlmixrMuDerCov#' for each algebraic mu-referenced expression 2. Change the algebraic expression to 'nlmixrMuDerCov# * mu_cov_theta' 3. Use the internal mu-referenced covariate for saem 4. After optimization is completed, replace 'model()' with old 'model()' expression 5. Remove 'nlmixrMuDerCov#' from nlmix2 output In general, these covariates should be more accurate since it changes the system to a linear compartment model. Therefore, by default this is 'TRUE'.
run	Should monolix be run and the results be imported to nlmixr2? (Default is TRUE)
...	Ignored parameters

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

Value

A monolix control object

Author(s)

Matthew Fidler

nlmixr2/babelmixr documentation built on Nov. 21, 2024, 3:16 a.m.