ruminate (version 0.3.1)

rx2other: Converts an rxode2 Object Into Specified Model Format

Description

If you have an rxode2 or nlmixr2 model object you can use this function to translate that object into other formats. See output_type below for the allowed formats.

In order to do this you need at least one between-subject variability term and one endpoint. If these are missing then dummy values will be added. The dummy values for between-subject variablitiy are IIV will be POP_RUMINATE, TV_RUMINATE, and ETA.RUMINATE. The dummy terms for endpoints are OUT_RUMINATE and add.OUT_RUMINATE.

Usage

rx2other(
  object,
  out_type = "nonmem",
  dataset = NULL,
  export_name = "my_model",
  export_path = tempfile(pattern = "dir")
)

Value

List with the following elements:

• isgood: Return status of the function.

• msgs: Error or warning messages if any issues were encountered.

• files: If succesful this will contain a list with an entry for each file generated to support the requested format. the current file format. For example if "nonmem" was selected this will include elements for "ctl" and "csv". Each of these are lists with the following format:

  • fn: Exported file name

  • fn_full: Exported file name with the full path.

  • contents: Contents of the file.

Arguments

object

rxode2 model object

out_type

Output type (either "nonmem", "monolix")

dataset

Optional dataset

export_name

Basename for models used

export_path

Location to place output files (default tempdir())

Details

Known issues: If you have specified bioavailability in the model, it will fail on the Monolix conversion.

Examples

library(ruminate)
if( Sys.getenv("ruminate_rxfamily_found") == "TRUE"){
 # First create an rxode2 model:
 library(rxode2)
 one.compartment <- function() {
   rxode2::ini({
     tka <- log(1.57); label("Ka")
     tcl <- log(2.72); label("Cl")
     tv <- log(31.5); label("V")
     eta.ka ~ 0.6
     eta.cl ~ 0.3
     eta.v ~ 0.1
     add.sd <- 0.7
   })
   # and a model block with the error specification and model specification
   rxode2::model({
     ka <- exp(tka + eta.ka)
     cl <- exp(tcl + eta.cl)
     v <- exp(tv + eta.v)
     d/dt(depot) <- -ka * depot
     d/dt(center) <- ka * depot - cl / v * center
     cp <- center / v
     cp ~ add(add.sd)
   })
 }

 nmout = rx2other(one.compartment, out_type="nonmem")

}