PharmTeX: a LaTeX-Based Open-Source Platform for Automated Reporting Workflow

Abstract

Every year, the pharmaceutical industry generates a large number of scientific reports related to drug research, development, and regulatory submissions. Many of these reports are created using text processing tools such as Microsoft Word. Given the large number of figures, tables, references, and other elements, this is often a tedious task involving hours of copying and pasting and substantial efforts in quality control (QC). In the present article, we present the LaTeX-based open-source reporting platform, PharmTeX, a community-based effort to make reporting simple, reproducible, and user-friendly. The PharmTeX creators put a substantial effort into simplifying the sometimes complex elements of LaTeX into user-friendly functions that rely on advanced LaTeX and Perl code running in the background. Using this setup makes LaTeX much more accessible for users with no prior LaTeX experience. A software collection was compiled for users not wanting to manually install the required software components. The PharmTeX templates allow for inclusion of tables directly from mathematical software output as well and figures from several formats. Code listings can be included directly from source. No previous experience and only a few hours of training are required to start writing reports using PharmTeX. PharmTeX significantly reduces the time required for creating a scientific report fully compliant with regulatory and industry expectations. QC is made much simpler, since there is a direct link between analysis output and report input. PharmTeX makes available to report authors the strengths of LaTeX document processing without the need for extensive training. Graphical Abstract ᅟ.

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

“…Reproducibility of scientific research findings is increasingly coming under the spotlight, and although there are a number of approaches available for facilitating reproducible research in pharmacometrics, none of the NLMEM tools mentioned previously by themselves are well suited to use in scripted, literate‐programming workflows of the kind flourishing in the R ecosystem by means of packages such as “knitr” and “rmarkdown.” Add‐on packages for each of these tools have been added because of this need . nlmixr allows the integration without the need of an additional tool.…”

LaTeX tutorial for the standardization and automation of population analysis reports

“…Standardization and elements of automation should thus be used for recurring steps as much as possible. Typically, a project‐centric model development workflow is applied, where analyses are roughly divided into data, analysis, and report subsections through an appropriate directory and file structure 5,6 . However, the need to make this workflow more automated and reproducible is often interrupted by the fact that the actual report generation is performed separately from the analysis using a standard word processor.…”

“…Admittedly, for authors who are used to creating reports with word processors, switching to a markup language like LaTeX can be quite a hurdle. In order to lower the entry threshold for new LaTeX users, efforts have recently been made to provide templates and scripts specifically adapted for authors in the field of pharmacometrics 5 . What is still missing, however, is an example of how to automatize getting from the initial data via the analysis to the submission ready report.…”

“…Typically, a project‐centric model development workflow is applied, where analyses are roughly divided into data, analysis, and report subsections through an appropriate directory and file structure. 5 , 6 However, the need to make this workflow more automated and reproducible is often interrupted by the fact that the actual report generation is performed separately from the analysis using a standard word processor. Additional problems encountered are copy‐pasting errors across documents, manual checking of acronym introductions, or proper cross‐referencing.…”

“…In order to lower the entry threshold for new LaTeX users, efforts have recently been made to provide templates and scripts specifically adapted for authors in the field of pharmacometrics. 5 What is still missing, however, is an example of how to automatize getting from the initial data via the analysis to the submission ready report. This tutorial attempts to fill this gap by providing concrete examples of code through a step‐by‐step description using a typical pharmacometric example taken from the literature.…”