ACoP9-Workshop: Reproducible Pharmacometrics 2.0: Generation of submission-ready Word reports based on open source tools

ACoP9 Meeting, October 11th Thursday, Loews Coronado Bay Resort near San Diego, CA, US

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.

Program

October 11th Thursday
Time Topic Presenter
13:00-13:15 Welcome and Introduction Henning Schmidt & Andrijana Radivojevic
13:15-14:00
  • 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
14:00-15:00
  • 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
15:15-16:00
  • 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
16:00-16:45
  • 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 & Andrijana Radivojevic

Presenters

  Andrijana Radivojevic, PhD, IntiQuan GmbH (external)

Andrijana has years of international experience in biotech and big pharma. She has contributed to programs in all phases of drug development, spanning various therapeutic areas and pharmacometric activities. She is currently leading an industry-wide effort for Data Standards in Pharmacometrics, sponsored by ISoP’s Best Practices and Standards Committee and aiming towards an improved quality and efficiency for data preparation. She is working as an independent consultant, focusing on the business development for companies and personal & professional growth for great scientists. 
  Henning Schmidt, PhD, IntiQuan GmbH

Engineer by training with a long background in modeling of a wide range of general linear and non-linear systems (automotive & process industry, biological, physiological, and pharmacological systems), using both modeling and simulation results as a basis for impactful quantitative support of decision making in large and small, early and late phase drug development projects. Developer of several open source tools for modeling and simulation across Pharmacometrics, Systems Pharmacology, and Systems Biology.

Registration

Workshop location: The workshop will be held at the Loews Coronado Bay Resort near San Diego, CA, US, which is the venue for the ACoP9 meeting.

Workshop fee: Regular fee 300 USD. This includes workshop material, and coffee break. Students/Academia/Government/Non-profit employees may enroll at a fee of 150 USD.

Registration: This is a post-meeting workshop that requires registering for the ACoP 2018 meeting. Please register ASAP in view of the limited course capacity.

Contact: Henning Schmidt, IntiQuan GmbH, Spalenring 150, 4055 Basel, Switzerland; Phone: +41 76 603 28 06; Email: henning.schmidt@intiquan.com.