| Title: | Converts 'Monolix' Models to 'rxode2' |
| Version: | 0.0.5 |
| 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'). |
| License: | MIT + file LICENSE |
| URL: | https://nlmixr2.github.io/monolix2rx/, https://github.com/nlmixr2/monolix2rx/ |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.3.2 |
| LinkingTo: | dparser, rxode2, Rcpp |
| Imports: | Rcpp, checkmate, cli, dparser, withr, ggplot2, ggforce, stringi, crayon, lotri, magrittr, rxode2 (≥ 3.0.4) |
| Suggests: | devtools, testthat (≥ 3.0.0), xgxr, vdiffr |
| Config/testthat/edition: | 3 |
| Config/Needs/website: | rmarkdown |
| NeedsCompilation: | yes |
| Packaged: | 2025-07-15 20:48:32 UTC; matt |
| Author: | Matthew Fidler 
[aut, cre],
Justin Wilkins
[ctb] |
| Maintainer: | Matthew Fidler <matthew.fidler@gmail.com> |
| Repository: | CRAN |
| Date/Publication: | 2025-07-15 21:20:01 UTC |
Get the number of doses for steady state for monolix2rx
Description
Get the number of doses for steady state for monolix2rx
Usage
.getNbdoses(x)
Arguments
x |
monolix2rx object |
Value
Number of doses for monolix2rx object
Author(s)
Matthew L. Fidler
Get if the model object is stiff
Description
Get if the model object is stiff
Usage
.getStiff(x)
Arguments
x |
monolix2rx object |
Value
boolean indicating if the object is a stiff system (as indicated by monolix)
Author(s)
Matthew L. Fidler
Get the best mlxtran info or return NULL
Description
Get the best mlxtran info or return NULL
Usage
.monolixGetMlxtran(x)
Arguments
x |
item to try to extract mlxtran info |
Value
mlxtran info
Author(s)
Matthew L. Fidler
Autoplot monolix2rx object
Description
Autoplot monolix2rx object
Usage
## S3 method for class 'monolix2rx'
autoplot(
object,
...,
ncol = 3,
nrow = 3,
log = "",
xlab = "Time",
ylab = "Predictions",
page = FALSE
)
Arguments
object |
an object, whose class will determine the behaviour of autoplot |
... |
ignored parameters for |
nrow, ncol |
Number of rows and columns |
log |
Should "" (neither x nor y), "x", "y", or "xy" (or "yx") be log-scale? |
xlab, ylab |
The x and y axis labels |
page |
number of page(s) for the individual plots, by default
( |
Value
a ggplot2 object
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 |
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
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
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 |
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
Objects exported from other packages
Description
These objects are imported from other packages. Follow the links below to see their documentation.