Pharmaceutical Reporting Automation with officer and flextable

Introduction

About this Workshop

This workshop focuses on creating sophisticated clinical reports in Word format using R with a reproducible approach. You will learn how to leverage the powerful combination of the officer and flextable packages to go from clinical data all the way through to complete pharmaceutical report generation.

The pharmaceutical industry requires high-quality, standardized documentation that meets rigorous regulatory standards. This workshop demonstrates how R can be used to automate the creation of such reports while maintaining full reproducibility and compliance with industry best practices.

What You Will Learn

This workshop is divided into two main parts:

Part 1: Fundamentals of Table and Document Creation

Introduction to flextable

Learn how to create and format sophisticated tables that meet pharmaceutical standards:

• Creating tables from data frames and other R objects
• Formatting content (numbers, dates, text)
• Customizing visual properties (colors, fonts, borders)
• Managing column widths and table layouts
• Working with headers and footers
• Building real-world pharmaceutical tables:
  • Cancer statistics tables with complex layouts
  • Adverse event tables following industry standards

Converting data structures to flextable

Master the as_flextable() function to quickly transform common R objects:

• Creating demographic tables with summarizor() and as_flextable()
• Building frequency tables from table() objects

Introduction to officer

Discover how to programmatically create and manipulate Word documents:

• Creating custom paragraph styles for consistent formatting
• Adding paragraphs, headings, and tables of contents
• Integrating flextables into Word documents
• Incorporating ggplot2 visualizations
• Managing page breaks and document structure

Part 2: Advanced Clinical Reporting Techniques

Patient profile reports

Build complete, individualized patient reports:

• Structuring clinical trial data (CDISC/ADaM datasets) for report generation
• Creating patient-specific reports with demographics, vital signs, and visualizations
• Implementing automatic numbering for tables and figures
• Adding table of tables (ToT) and table of figures (ToF)

Managing sections in Word documents

Control document layout with advanced section management:

• Understanding Word section properties
• Creating sections with custom page orientations (portrait/landscape)
• Implementing custom headers and footers per section
• Using even and odd page layouts for professional reports
• Applying section properties programmatically with prop_section()

Table pagination

Ensure professional table presentation across pages:

• Understanding row solidarity to prevent awkward page breaks
• Using paginate() to control table flow across pages
• Keeping headers with data rows
• Maintaining group cohesion in long tables
• Choosing between single paginated tables and split tables per section

Prerequisites

This workshop assumes you are familiar with:

• Basic R programming
• The tidyverse approach (we will use |> pipes)
• Basic knowledge of ‘Microsoft Word’

By the end of this workshop, you will be able to create complete, reproducible pharmaceutical reports that meet industry standards and can be easily maintained and updated as data changes.