Package: pmxNODE 0.1.0

pmxNODE: Application of NODEs in 'Monolix', 'NONMEM', and 'nlmixr2'

An easy-to-use tool for implementing Neural Ordinary Differential Equations (NODEs) in pharmacometric software such as 'Monolix', 'NONMEM', and 'nlmixr2', see Bräm et al. (2024) <doi:10.1007/s10928-023-09886-4> and Bräm et al. (2025) <doi:10.1002/psp4.13265>. The main functionality is to automatically generate structural model code describing computations within a neural network. Additionally, parameters and software settings can be initialized automatically. For using these additional functionalities with 'Monolix', 'pmxNODE' interfaces with 'MonolixSuite' via the 'lixoftConnectors' package. The 'lixoftConnectors' package is distributed with 'MonolixSuite' (<https://monolixsuite.slp-software.com/r-functions/2024R1/package-lixoftconnectors>) and is not available from public repositories.

Authors:Dominic Bräm [aut, cre], Bernhard Steiert [ctb], Gilbert Koch [ctb], Matthew Fidler [ctb]

pmxNODE_0.1.0.tar.gz
pmxNODE_0.1.0.zip(r-4.7)pmxNODE_0.1.0.zip(r-4.6)pmxNODE_0.1.0.zip(r-4.5)
pmxNODE_0.1.0.tgz(r-4.6-any)pmxNODE_0.1.0.tgz(r-4.5-any)
pmxNODE_0.1.0.tar.gz(r-4.7-any)pmxNODE_0.1.0.tar.gz(r-4.6-any)
pmxNODE_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
pmxNODE/json (API)

# Install 'pmxNODE' in R:
install.packages('pmxNODE', repos = c('https://braemd.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/braemd/pmxnode/issues

On CRAN:

Conda:

4.08 score 4 stars 9 scripts 140 downloads 28 exports 31 dependencies

Last updated from:a0bcd70191. Checks:4 OK, 5 WARNING. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK204
source / vignettesOK269
linux-release-x86_64OK177
macos-release-arm64WARNING182
macos-oldrel-arm64WARNING250
windows-develWARNING141
windows-releaseWARNING150
windows-oldrelWARNING122
wasm-releaseOK191

Exports:copy_examplesder_state_plot_mlxder_state_plot_nlmixrder_state_plot_nmfind_nmfeget_example_listind_der_state_plot_mlxind_der_state_plot_nlmixrind_der_state_plot_nmind_rhs_plot_mlxind_rhs_plot_nlmixrind_rhs_plot_nmindparm_extractor_mlxindparm_extractor_nlmixrindparm_extractor_nmNNnn_converter_mlxnn_converter_nlmixrnn_converter_nmNNbsvpre_fixef_extractor_mlxpre_fixef_extractor_nmrhs_plot_mlxrhs_plot_nlmixrrhs_plot_nmrun_mlxrun_nmsoftware_initializer

Dependencies:backportscheckmateclicpp11dplyrfarvergenericsggplot2gluegtableisobandlabelinglifecyclemagrittrpillarpkgconfigpurrrR6RColorBrewerrlangS7scalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
Copy examples to your foldercopy_examples
Generate Derivative versus State Plot (Monolix)der_state_plot_mlx
Generate Derivative versus State Plot (nlmixr2)der_state_plot_nlmixr
Generate Derivative versus State Plot (NONMEM)der_state_plot_nm
Finde path to NONMEM nmfe filefind_nmfe
List of examples availableget_example_list
Generate Derivative versus State Plot for individual parameter estimates (Monolix)ind_der_state_plot_mlx
Generate Derivative versus State Plot for individual parameter estimates (nlmixr2)ind_der_state_plot_nlmixr
Generate Derivative versus State Plot for individual parameter estimates (NONMEM)ind_der_state_plot_nm
Generate individual Right-hand side data plot (Monolix)ind_rhs_plot_mlx
Generate individual Right-hand side data plot (nlmixr2)ind_rhs_plot_nlmixr
Generate individual Right-hand side data plot (NONMEM)ind_rhs_plot_nm
Monolix individual estimations extractorindparm_extractor_mlx
nlmixr individual estimations extractorindparm_extractor_nlmixr
NONMEM individual estimations extractorindparm_extractor_nm
Neural Network ODE language in nlmixr2 langauageNN
NN converter for Monolixnn_converter_mlx
NN converter for nlmixrnn_converter_nlmixr
NN converter for NONMEMnn_converter_nm
Change a population Neural Network model to a model with between subject variabilityNNbsv
Monolix estimations extractorpre_fixef_extractor_mlx
THETA extraction from results filepre_fixef_extractor_nm
Generate Right-hand side data plot (Monolix)rhs_plot_mlx
Generate Right-hand side data plot (nlmixr2)rhs_plot_nlmixr
Generate Right-hand side data plot (NONMEM)rhs_plot_nm
Run Monolix from Rrun_mlx
Run NONMEM from Rrun_nm
Initialize software (Suspended)software_initializer