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      Nonlinear Mixed‐Effects Model Development and Simulation Using nlmixr and Related R Open‐Source Packages

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          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          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.

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          SymPy: symbolic computing in Python

          Aaron Meurer, Christopher Smith, Mateusz Paprocki … (2017)
          SymPy is an open source computer algebra system written in pure Python. It is built with a focus on extensibility and ease of use, through both interactive and programmatic applications. These characteristics have led SymPy to become a popular symbolic library for the scientific Python ecosystem. This paper presents the architecture of SymPy, a description of its features, and a discussion of select submodules. The supplementary material provide additional examples and further outline details of the architecture and features of SymPy.
          Article 0 comments Cited 162 times – based on 0 reviews     Review now
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            Computing normalised prediction distribution errors to evaluate nonlinear mixed-effect models: the npde add-on package for R.

            Emmanuelle Comets, Karl Brendel, France Mentré (2008)
            Pharmacokinetic/pharmacodynamic data are often analysed using nonlinear mixed-effect models, and model evaluation should be an important part of the analysis. Recently, normalised prediction distribution errors (npde) have been proposed as a model evaluation tool. In this paper, we describe an add-on package for the open source statistical package R, designed to compute npde. npde take into account the full predictive distribution of each individual observation and handle multiple observations within subjects. Under the null hypothesis that the model under scrutiny describes the validation dataset, npde should follow the standard normal distribution. Simulations need to be performed before hand, using for example the software used for model estimation. We illustrate the use of the package with two simulated datasets, one under the true model and one with different parameter values, to show how npde can be used to evaluate models. Model estimation and data simulation were performed using NONMEM version 5.1.
            Article 0 comments Cited 137 times – based on 0 reviews     Review now
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              Basic Concepts in Population Modeling, Simulation, and Model-Based Drug Development

              D Mould, R N Upton (2012)
              Modeling is an important tool in drug development; population modeling is a complex process requiring robust underlying procedures for ensuring clean data, appropriate computing platforms, adequate resources, and effective communication. Although requiring an investment in resources, it can save time and money by providing a platform for integrating all information gathered on new therapeutic agents. This article provides a brief overview of aspects of modeling and simulation as applied to many areas in drug development.
              Article 0 comments Cited 133 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Matthew Fidler: matt.fidler@novartis.com
                Journal
                Journal ID (nlm-ta): CPT Pharmacometrics Syst Pharmacol
                Journal ID (iso-abbrev): CPT Pharmacometrics Syst Pharmacol
                Journal ID (doi): 10.1002/(ISSN)2163-8306
                Journal ID (publisher-id): PSP4
                Title: CPT: Pharmacometrics & Systems Pharmacology
                Publisher: John Wiley and Sons Inc. (Hoboken )
                ISSN (Electronic): 2163-8306
                Publication date (Electronic): 16 July 2019
                Publication date (Print): September 2019
                Volume: 8
                Issue: 9 ( doiID: 10.1002/psp4.v8.9 )
                Pages: 621-633
                Affiliations
                [ 1 ] Novartis Pharmaceuticals Corporation Fort Worth Texas USA
                [ 2 ] Occams Coöperatie UA Amstelveen The Netherlands
                [ 3 ] LAP&P Consultants BV Leiden The Netherlands
                [ 4 ] Novartis Institutes for BioMedical Research Cambridge Massachusetts USA
                [ 5 ] Certara Princeton New Jersey USA
                [ 6 ] Novartis Pharmaceuticals Corporation East Hanover New Jersey USA
                Author notes
                [*] [* ]Correspondence: Matthew Fidler ( matt.fidler@ 123456novartis.com )
                Article
                Publisher ID: PSP412445
                DOI: 10.1002/psp4.12445
                PMC ID: 6765694
                PubMed ID: 31207186
                SO-VID: be0349d9-8566-4853-9505-ad32d4169221
                Copyright © © 2019 The Authors CPT: Pharmacometrics & Systems Pharmacology published by Wiley Periodicals, Inc. on behalf of the American Society for Clinical Pharmacology and Therapeutics.
                License:

                This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

                History
                Date received : 07 November 2018
                Date accepted : 29 April 2019
                Page count
                Figures: 4, Tables: 4, Pages: 10, Words: 8471
                Categories
                Subject: Tutorial
                Subject: Tutorial
                Subject: Tutorial
                Custom metadata
                source-schema-version-number 2.0
                component-id psp412445
                cover-date September 2019
                details-of-publishers-convertor Converter:WILEY_ML3GV2_TO_NLMPMC version:5.6.9 mode:remove_FC converted:29.09.2019

                Data availability:

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