Reproducible Pharmacometrics 2.0: Generation of submission-ready Word reports based on open source tools

PAGE 2019 Meeting, June 10 Monday, 13:00-17:00
Mindset Konferens, Room: Ettan, Mäster Samuelsgatan 60, Stockholm [View Map]

Workshop Description

Pharmacometric reports typically contain a large number of figures, tables, text files, in-line text, and numerical values that have been generated during the conduct of analyses. While these results are often generated in a script-based manner, reporting of these results is complicated by corporate requirements to use Microsoft Word and a specific in house-style guide, requiring scientists to copy, paste, and format results manually in a time-consuming and error-prone process.

Wilkins and Jonsson [Reproducible pharmacometrics, PAGE Meeting, Glasgow, Scotland, 2013] presented an approach to Reproducible Pharmacometrics that allowed a full end-to-end scripting of the analysis and the creation of publication-ready reports. Their solution was based on LaTeX, knitr, and R. While this approach is very powerful, LaTeX can be perceived as a cumbersome language. More importantly, the output is a PDF rather than a Word document, which often does not comply with corporate publication policy. In recent years, R Markdown has been developed, allowing to use the more lightweight language Markdown, and RStudio supporting the conversion to Word. However, no R Markdown support is available for critical Word features, such as cross-references, figure and table captions, and choice of more complex Word styles, impeding the generation of submission-ready Word documents.

In this workshop, participants will first get familiar with R Markdown and its limitations to produce submission-ready Word reports. We will then introduce Extended Markdown language and present the framework on how one would leverage open-source tools to overcome those shortcomings. Using IntiQuan IQReport, a standalone software that implements the presented approach, participants will engage in the hands-on experience of creating Word reports using any desired/template Word style and automatically integrating analysis results without the need of manual copy & paste. Free license for IQReport with the duration of 12 months will be provided on request to all interested participants.

The workshop is designed as a hands-on tutorial, allowing participants to work through all examples under guidance of the presenters. All material (slides, example reports, R code, required R libraries, and additional software) will be shared with the participants at least 2 weeks before the workshop. In case a participant would like to have hands-on experience during the workshop, a laptop (preferably Windows) with an R installation should be brought to the workshop.

Workshop location:

Mindset Konferens
Mäster Samuelsgatan 60
[View Map]


The regular workshop fee is 250 EUR for industry, 150 EUR for academia/government/non-profit, and 100 EUR for students. This includes workshop material and coffee break. Payment can be done conveniently and securely via PayPal, here below:

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June 10th Monday
Time Topic Presenter
12:00-13:00 Lunch will be provided for participants that take part in both the QSP modeling and the reporting workshop
13:00-13:15 Welcome and Introduction Henning Schmidt 
  • General approach to automatic reporting and underlying tools used
  • Report elements that are critical for typical pharmacometric reports
  • Advantages and disadvantages of alternative approaches (Rmarkdown, knitr, LaTeX)
  • Markdown and Extended Markdown
Henning Schmidt 
  • Generation of a simple example Word report
  • Import of text files (e.g. NONMEM control/output files) into Word
  • Import of figures in different formats into Word
  • Import of R / MATLAB / etc. data frames and matrices as tables into Word
Henning Schmidt 
15:00-15:15 Coffee break
  • Advanced formatting of figures and tables through Extended Markdown
  • Cross references
  • Introduction of Value Tables, allowing in-line adding of analysis results
  • Annotating imported WORD tables, figures, and text files with trace-ability information
  • Generation of a full popPK example report
Henning Schmidt 
  • Adjusting the report Word style to a specific corporate style
  • Script based generation of a full report from R
Henning Schmidt 
16:45-17:00 Concluding remarks Henning Schmidt