# -------------------------------------------- # CITATION file created with {cffr} R package # See also: https://docs.ropensci.org/cffr/ # -------------------------------------------- cff-version: 1.2.0 message: 'To cite package "babelmixr2" in publications use:' type: software license: GPL-3.0-or-later title: 'babelmixr2: Use ''nlmixr2'' to Interact with Open Source and Commercial Software' version: 0.1.3 identifiers: - type: doi value: 10.32614/CRAN.package.babelmixr2 abstract: Run other estimation and simulation software via the 'nlmixr2' (Fidler et al (2019) ) interface including 'PKNCA', 'NONMEM' and 'Monolix'. While not required, you can get/install the 'lixoftConnectors' package in the 'Monolix' installation, as described at the following url . When 'lixoftConnectors' is available, 'Monolix' can be run directly instead of setting up command line usage. authors: - family-names: Fidler given-names: Matthew email: matthew.fidler@gmail.com orcid: https://orcid.org/0000-0001-8538-6691 - family-names: Denney given-names: Bill email: wdenney@humanpredictions.com orcid: https://orcid.org/0000-0002-5759-428X preferred-citation: type: manual title: 'nlmixr: Nonlinear Mixed Effects Models in Population Pharmacokinetics and Pharmacodynamics' authors: - family-names: Fidler given-names: Matthew email: matthew.fidler@gmail.com orcid: https://orcid.org/0000-0001-8538-6691 - family-names: Xiong given-names: Yuan email: yuan.xiong@gmail.com - family-names: Schoemaker given-names: Rik email: rik.schoemaker@occams.com orcid: https://orcid.org/0000-0002-7538-3005 - family-names: Wilkins given-names: Justin email: justin.wilkins@occams.com orcid: https://orcid.org/0000-0002-7099-9396 - family-names: Trame given-names: Mirjam email: mirjam.trame@gmail.com - family-names: Hooijmaijers given-names: Richard email: richardhooijmaijers@gmail.com - family-names: Post given-names: Teun email: t.post@lapp.nl - family-names: Wang given-names: Wenping email: wwang8198@gmail.com year: '2024' notes: R package version 0.1.3 url: https://CRAN.R-project.org/package=nlmixr repository: https://nlmixr2.r-universe.dev repository-code: https://github.com/nlmixr2/babelmixr2/ commit: 07e7f12ede17e00a3be6386b40fdd0101384250d url: https://nlmixr2.github.io/babelmixr2/ contact: - family-names: Fidler given-names: Matthew email: matthew.fidler@gmail.com orcid: https://orcid.org/0000-0001-8538-6691 references: - type: article title: Nonlinear Mixed-Effects Model Development and Simulation Using nlmixr and Related R Open-Source Packages authors: - family-names: Fidler given-names: Matthew email: matthew.fidler@gmail.com orcid: https://orcid.org/0000-0001-8538-6691 - family-names: Wilkins given-names: Justin email: justin.wilkins@occams.com orcid: https://orcid.org/0000-0002-7099-9396 - family-names: Hooijmaijers given-names: Richard email: richardhooijmaijers@gmail.com - family-names: Post given-names: Teun email: t.post@lapp.nl - family-names: Schoemaker given-names: Rik email: rik.schoemaker@occams.com orcid: https://orcid.org/0000-0002-7538-3005 - family-names: Trame given-names: Mirjam email: mirjam.trame@gmail.com - family-names: Xiong given-names: Yuan email: yuan.xiong@gmail.com - family-names: Wang given-names: Wenping email: wwang8198@gmail.com journal: 'CPT: Pharmacometrics \& Systems Pharmacology' year: '2019' volume: '8' issue: '9' month: '9' abstract: nlmixr is a free and open-source R package for fitting nonlinear pharmacokinetic (PK), pharmacodynamic (PD), joint PK-PD, and quantitative systems pharmacology mixed-effects models. Currently, nlmixr is capable of fitting both traditional compartmental PK models as well as more complex models implemented using ordinary differential equations. We believe that, over time, it will become a capable, credible alternative to commercial software tools, such as NONMEM, Monolix, and Phoenix NLME. publisher: name: John Wiley and Sons Inc. address: Hoboken url: https://doi.org/10.1002/psp4.12445 start: '621' end: '633' - type: article title: Performance of the SAEM and FOCEI Algorithms in the Open-Source, Nonlinear Mixed Effect Modeling Tool nlmixr authors: - family-names: Schoemaker given-names: Rik email: rik.schoemaker@occams.com orcid: https://orcid.org/0000-0002-7538-3005 - family-names: Fidler given-names: Matthew email: matthew.fidler@gmail.com orcid: https://orcid.org/0000-0001-8538-6691 - family-names: Laveille given-names: Christian - family-names: Wilkins given-names: Justin email: justin.wilkins@occams.com orcid: https://orcid.org/0000-0002-7099-9396 - family-names: Hooijmaijers given-names: Richard email: richardhooijmaijers@gmail.com - family-names: Post given-names: Teun email: t.post@lapp.nl - family-names: Trame given-names: Mirjam email: mirjam.trame@gmail.com - family-names: Xiong given-names: Yuan email: yuan.xiong@gmail.com - family-names: Wang given-names: Wenping email: wwang8198@gmail.com journal: 'CPT: Pharmacometrics \& Systems Pharmacology' year: '2019' volume: '8' issue: '12' month: '12' abstract: 'The free and open-source package nlmixr implements pharmacometric nonlinear mixed effects model parameter estimation in R. It provides a uniform language to define pharmacometric models using ordinary differential equations. Performances of the stochastic approximation expectation-maximization (SAEM) and first order-conditional estimation with interaction (FOCEI) algorithms in nlmixr were compared with those found in the industry standards, Monolix and NONMEM, using the following two scenarios: a simple model fit to 500 sparsely sampled data sets and a range of more complex compartmental models with linear and nonlinear clearance fit to data sets with rich sampling. Estimation results obtained from nlmixr for FOCEI and SAEM matched the corresponding output from NONMEM/FOCEI and Monolix/SAEM closely both in terms of parameter estimates and associated standard errors. These results indicate that nlmixr may provide a viable alternative to existing tools for pharmacometric parameter estimation.' url: https://doi.org/10.1002/psp4.12471 start: '923' end: '930'