NMsim (version 0.2.6)

NMwriteInits: Writes a parameter values to a control stream

Description

Edit parameter values, fix/unfix them, or edit lower/upper bounds.

Usage

NMwriteInits(
  file.mod,
  lines,
  update = TRUE,
  file.ext = NULL,
  ext,
  inits.tab,
  values,
  newfile,
  ...
)

Value

a control stream as lines in a character vector.

Arguments

file.mod

Path to control stream.

lines

Control stream as character vector. Use either `file.mod` or `lines`, not both.

update

If `TRUE` (default), the parameter values are updated based on the `.ext` file. The path to the `.ext` file can be specified with `file.ext` but that is normally not necessary.

file.ext

Optionally provide the path to an `.ext` file. If not provided, the default is to replace the file name extention on `file.mod` with `.ext`. This is only used if `update=TRUE`.

ext

An long-format parameter table as returned by `NMreadExt()`. Can contain multiple models if `file.mod` does not.

inits.tab

A wide-format parameter table, well suited for customizing initial values, limits, and for fixing parameters. For multiple custom parameter specifications, this may be the most suitable argument.

values

A list of lists. Each list specifies a parameter with named elements. Must be named by the parameter name. `lower`, `upper` and `fix` can be supplied to modify the parameter. See examples. Notice, you can use `...` instead. `values` may be easier for programming but other than that, most users will find `...` more intuitive.

newfile

If provided, the results are written to this file as a new input control stream.

...

Parameter specifications. See examples,

Details

Limitations:

• `NMwriteInits()` can only update specifications of existing parameters. It cannot insert new parameters.

• lower, init, upper, and FIX must be on same line in control stream.

• If using something like CL=(.1,4,15) in control stream, two of those cannot be on the same line.

In Nonmem an entire block is either fixed or not. `NMwriteInits()` fixes/unfixes the entire block based on the top-left element in the block. This means, if OMEGA(2,2)-OMEGA(3,3) is a block, the `FIX` status of OMEGA(2,2) determines whether the block is fixed. `FIX` of all other elements in the block has no effect.

Examples

if (FALSE) {
file.mod <- system.file("examples/nonmem/xgxr021.mod",package="NMdata")
## specify parameters using ...
NMwriteInits(file.mod,
  "theta(2)"=list(init=1.4),
  "THETA(3)"=list(FIX=1),
  "omega(2,2)"=list(init=0.1)
)
## or put them in a list in the values argument
NMwriteInits(file.mod,
values=list( "theta(2)"=list(init=1.4),
             "THETA(3)"=list(FIX=1),
             "omega(2,2)"=list(init=0.1))
)

}