PFIM

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Evaluate or optimize designs for nonlinear mixed effects models using the Fisher Information Matrix.

Methods used in the package refer to Mentré F, Mallet A, Baccar D (1997) doi:10.1093/biomet/84.2.429, Retout S, Comets E, Samson A, Mentré F (2007) doi:10.1002/sim.2910, Bazzoli C, Retout S, Mentré F (2009) doi:10.1002/sim.3573, Le Nagard H, Chao L, Tenaillon O (2011) doi:10.1186/1471-2148-11-326, Combes FP, Retout S, Frey N, Mentré F (2013) doi:10.1007/s11095-013-1079-3 and Seurat J, Tang Y, Mentré F, Nguyen TT (2021) doi:10.1016/j.cmpb.2021.106126

Version: 6.1

This version 6.1 of PFIM is optimized for computational efficiency, delivering enhanced performance and faster processing times.

Depends: R (≥ 4.0.0)

Imports: methods, rmarkdown, stats, scales, deSolve, kableExtra, gtable, Deriv, grid, knitr, markdown, Matrix, ggplot2, ggbreak, pracma, Rcpp, filesstrings

Suggests: testthat, inline, utils, devtools, htmltools

Published: 2024-10-23

Author: France Mentré ORCID https://orcid.org/0000-0002-7045-1275 [aut]

Author and creator: Romain Leroux [aut, cre]

Contributors: Jérémy Seurat [ctb], Lucie Fayette [ctb]

Maintainer: Romain Leroux <romain.leroux at inserm.fr>

License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]

Vignettes

The folder vignettes/ contains the two exemples that are given as vignettes on the CRAN.

Examples

Several examples have been implemented in PFIM 6 and the full list and reports are given in Examples_reports.md. Source scripts are available in the folder Examples/, whose sub folders are organized as follows:

• Examples/
  • evaluation/
    • analytic/
    • analytic_infusion/
    • ode/
    • ode_infusion/
  • optimization/
    • AlgoMutiplicatif/
    • FedorovWynn/
    • PGBO/
    • PSO/
    • Simplex/

To execute all those scripts successively, one can run the script run_Examples.R. The reports will be created in the folder Outputs/Examples/.

Evaluation tests

Several tests are available for design evaluation with PFIM; they are located in the folder tests_evaluation/, whose sub-folders are organized as follows:

• tests_evaluation/ :
  • library_of_models/ : contains scripts that test the building of models with the library
  • models_library_of_model/ : contains scripts that perform evaluation on models built with the library of models
  • models_user_defined/ : contains scripts that perform evaluation on models built manually by the user

To execute one scripts from models_library_of_model/ or models_user_defined/, one has to define the variable fimType to either population, individual or Bayesian.

To execute all those scripts successively, one can run the script run_tests_evaluation.R. The outputs will be displayed in the folder Outputs/tests_evaluation/.

Optimization tests

Several tests are available for design optimization with PFIM; they are located in the folder tests_optimization/, whose sub-folders are organized by algorithm.

• tests_optimization/ :
  • FedorovWynn/
  • MultiplicativeAlgorithm/
  • PGBO/
  • PSO/
  • Simplex/

To execute all those scripts successively, one can run the script run_tests_optimization.R. The outputs will be displayed in the folder Outputs/tests_evaluation/.

Getting help

If you encounter a clear bug, please file the issue with a minimal reproducible example on GitHub:

https://github.com/iame-researchCenter/PFIM/issues

For questions and other discussion, please use the PFIM group mailing list:

thepfimgroup@googlegroups.com