Package 'monolix2rx'

Title: Converts 'Monolix' Models to 'rxode2'
Description: 'Monolix' is a tool for running mixed effects model using 'saem'. This tool allows you to convert 'Monolix' models to 'rxode2' (Wang, Hallow and James (2016) <doi:10.1002/psp4.12052>) using the form compatible with 'nlmixr2' (Fidler et al (2019) <doi:10.1002/psp4.12445>). If available, the 'rxode2' model will read in the 'Monolix' data and compare the simulation for the population model individual model and residual model to immediately show how well the translation is performing. This saves the model development time for people who are creating an 'rxode2' model manually. Additionally, this package reads in all the information to allow simulation with uncertainty (that is the number of observations, the number of subjects, and the covariance matrix) with a 'rxode2' model. This is complementary to the 'babelmixr2' package that translates 'nlmixr2' models to 'Monolix' and can convert the objects converted from 'monolix2rx' to a full 'nlmixr2' fit. While not required, you can get/install the 'lixoftConnectors' package in the 'Monolix' installation, as described at the following url <https://monolixsuite.slp-software.com/r-functions/2024R1/installation-and-initialization>. When 'lixoftConnectors' is available, 'Monolix' can be used to load its model library instead manually setting up text files (which only works with old versions of 'Monolix').
Authors: Matthew Fidler [aut, cre] , Justin Wilkins [ctb]
Maintainer: Matthew Fidler <[email protected]>
License: MIT + file LICENSE
Version: 0.0.3
Built: 2024-10-25 05:32:34 UTC
Source: CRAN

Help Index


Read and parse mlxtran lines

Description

Read and parse mlxtran lines

Usage

mlxtran(file, equation = FALSE, update = FALSE)

Arguments

file

mlxtran file to process

equation

parse the equation block to rxode2 (some models cannot be translated)

update

when true, try to update the parameter block to the final parameter estimates

Value

mlxtran object

Author(s)

Matthew L. Fidler

Examples

# First load in the model; in this case the theo model
# This is modified from the Monolix demos by saving the model
# File as a text file (hence you can access without model library)
# setup.
#
# This example is also included in the monolix2rx package, so
# you refer to the location with `system.file()`:

pkgTheo <- system.file("theo", package="monolix2rx")

mlx <- mlxtran(file.path(pkgTheo, "theophylline_project.mlxtran"))

mlx

Get equation block from a Monolix model txt file

Description

Get equation block from a Monolix model txt file

Usage

mlxTxt(file, retFile = FALSE)

Arguments

file

string representing the model text file. Can be lib:fileName.txt if library setup/available

retFile

boolean that tells mlxTxt() to return the file name instead of error if the file does not exist

Value

parsed equation or file name

Author(s)

Matthew L. Fidler

Examples

# First load in the model; in this case the theo model
# This is modified from the Monolix demos by saving the model
# File as a text file (hence you can access without model library)
# setup.
#
# This example is also included in the monolix2rx package, so
# you refer to the location with `system.file()`:

pkgTheo <- system.file("theo", package="monolix2rx")

mod <- mlxTxt(file.path(pkgTheo, "oral1_1cpt_kaVCl.txt"))

mod

Translate a monolix file to rxode2

Description

Translate a monolix file to rxode2

Usage

monolix2rx(
  mlxtran,
  update = TRUE,
  thetaMatType = c("sa", "lin"),
  sd = 1,
  cor = 1e-05,
  theta = 0.5,
  ci = 0.95,
  sigdig = 3,
  envir = parent.frame()
)

Arguments

mlxtran

file name for mlxtran to translate to rxode2

update

is a boolean that represents if the final parameter estimates should be used for the translation (when present)

thetaMatType

This lists the preferred source for thetaMat covariance matrix. By default it is sa for simulated annealing, though you could use lin for linearized covariance calculation. If only one is present, then use whatever is present

sd

Default standard deviation for between subject variability/inter-occasion variability that are missing.

cor

Default correlation for missing correlations estimate

theta

default population estimate

ci

confidence interval for validation, by default 0.95

sigdig

number of significant digits for validation, by default 3

envir

represents the environment used for evaluating the corresponding rxode2 function

Value

rxode2 model

Author(s)

Matthew L. Fidler

Examples

# First load in the model; in this case the theo model
# This is modified from the Monolix demos by saving the model
# File as a text file (hence you can access without model library)
# setup.
#
# This example is also included in the monolix2rx package, so
# you refer to the location with `system.file()`:

pkgTheo <- system.file("theo", package="monolix2rx")

rx <- monolix2rx(file.path(pkgTheo, "theophylline_project.mlxtran"))

pkgCov <- system.file("cov", package="monolix2rx")

rx <- monolix2rx(file.path(pkgCov, "warfarin_covariate3_project.mlxtran"))

rx