nonmemControl: NONMEM estimation control

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

NONMEM estimation control

Description

NONMEM estimation control

Usage

nonmemControl(
  est = c("focei", "imp", "its", "posthoc"),
  advanOde = c("advan13", "advan8", "advan6"),
  cov = c("r,s", "r", "s", ""),
  maxeval = 1e+05,
  tol = 6,
  atol = 12,
  sstol = 6,
  ssatol = 12,
  sigl = 12,
  sigdig = 3,
  print = 1,
  extension = getOption("babelmixr2.nmModelExtension", ".nmctl"),
  outputExtension = getOption("babelmixr2.nmOutputExtension", ".lst"),
  runCommand = getOption("babelmixr2.nonmem", ""),
  iniSigDig = 5,
  protectZeros = FALSE,
  muRef = TRUE,
  addProp = c("combined2", "combined1"),
  rxControl = NULL,
  sumProd = FALSE,
  optExpression = TRUE,
  calcTables = TRUE,
  compress = TRUE,
  ci = 0.95,
  sigdigTable = NULL,
  readRounding = FALSE,
  readBadOpt = FALSE,
  niter = 100L,
  isample = 1000L,
  iaccept = 0.4,
  iscaleMin = 0.1,
  iscaleMax = 10,
  df = 4,
  seed = 14456,
  mapiter = 1,
  mapinter = 0,
  noabort = TRUE,
  modelName = NULL,
  muRefCovAlg = TRUE,
  run = TRUE,
  ...
)

Arguments

est	NONMEM estimation method
advanOde	The ODE solving method for NONMEM
cov	The NONMEM covariance method
maxeval	NONMEM's maxeval (for non posthoc methods)
tol	NONMEM tolerance for ODE solving advan
atol	NONMEM absolute tolerance for ODE solving
sstol	NONMEM tolerance for steady state ODE solving
ssatol	NONMEM absolute tolerance for steady state ODE solving
sigl	NONMEM sigl estimation option
sigdig	the significant digits for NONMEM
print	The print number for NONMEM
extension	NONMEM file extensions
outputExtension	Extension to use for the NONMEM output listing
runCommand	Command to run NONMEM (typically the path to "nmfe75") or a function. See the details for more information.
iniSigDig	How many significant digits are printed in $THETA and $OMEGA when the estimate is zero. Also controls the zero protection numbers
protectZeros	Add methods to protect divide by zero
muRef	Automatically mu-reference the control stream
addProp, sumProd, optExpression, calcTables, compress, ci, sigdigTable	Passed to nlmixr2est::foceiControl
rxControl	Options to pass to rxode2::rxControl for simulations
readRounding	Try to read NONMEM output when NONMEM terminated due to rounding errors
readBadOpt	Try to read NONMEM output when NONMEM terminated due to an apparent failed optimization
niter	number of iterations in NONMEM estimation methods
isample	Isample argument for NONMEM ITS estimation method
iaccept	Iaccept for NONMEM ITS estimation methods
iscaleMin	parameter for IMP NONMEM method (ISCALE_MIN)
iscaleMax	parameter for IMP NONMEM method (ISCALE_MAX)
df	degrees of freedom for IMP method
seed	is the seed for NONMEM methods
mapiter	the number of map iterations for IMP method
mapinter	is the MAPINTER parameter for the IMP method
noabort	Add the NOABORT option for ⁠$EST⁠
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 NONMEM be run (and the files imported to nlmixr2); default is TRUE, but FALSE will simply create the NONMEM control stream and data file.
...	optional genRxControl argument controlling automatic rxControl generation.

Details

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

runCommand controlFile outputFile.

For example, if runCommand="'/path/to/nmfe75'" then the command line used would look like the following:

'/path/to/nmfe75' one.cmt.nmctl one.cmt.lst

If runCommand is given as a function, it will be called as FUN(ctl, directory, ui) to run NONMEM. This allows you to run NONMEM 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 NONMEM.

Value

babelmixr2 control option for generating NONMEM control stream and reading it back into babelmixr2/nlmixr2

Author(s)

Matthew L. Fidler

Examples

nonmemControl()

nlmixr2/babelmixr documentation built on Jan. 21, 2025, 7:38 p.m.