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January 12, 2020

ClinBAY's partnership with a Major Pharma, to develop an open-source R package (ggPMX)

We are pleased that Novartis chose to partner with ClinBAY for the development of the ggPMX R package

ggPMX is an open-source R package freely available on CRAN since April 2019. It generates standard diagnostic plots for mixed effect models used in pharmacometric activities

The package builds on the R-package ggplot2 and aims at providing a workflow that is consistent, reproducible and efficient, resulting in high quality graphics ready-to-use in submission documents and publications. Intuitive functions and options allow for optimal figure customization and graphics stratification. ggPMX enables straightforward generation of PDF, Word or PNG output files that contain all diagnostic plots for keeping track of modeling results. The package is currently compatible with Monolix versions 2016 and later, and nlmixr outputs as well.

Using simple function calls, the toolbox can produce different model diagnostic plots (e.g. residual and EBE-based plots assessing possible trends and the shape of the distributions such as IWRES vs IPRED, VPCs, observations vs predictions, etc.).

In addition, shrinkage and summary parameters tables can be also produced. By default, the PDF- or Word-format diagnostic report contains essential goodness-of-fit plots. However, these can be adapted to produce different sets of diagnostics as desired by the user, and any of the plots may be customized individually. The types of supported customizations include modifications of the graphical parameters, labels, and various stratifications by covariates.

ClinBAY provides a strong expertise in development and validation of software for the pharmaceutical industry. Some of the software that we have developed and that you can download for free are:

  • Datasly is a lightweight and user-friendly application to easily browse and visualize data (including viewing, filtering, grouping features). Some additional modules enable advanced functionalities, as exporting data, performing SQL queries, data analytics, etc.  It reads a number of data files, including SAS®, XPT, CSV, and Excel formats.
  • ClinLogViewer is a syntax-colored viewer for SAS® log files, including other features, such as extracting a SAS program from a SAS log.
  • ClinMacroDoc is a simple, free to download tool to generate documentation for a SAS® macro library.


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