Melinda, Tree of LifeMelinda’s artwork reflects her

journey living with HIV.

An Automation Proof of Concept of Periodic Reporting via R Shiny

Nicholas Masel (Analytics Innovation Technical Lead)Steven Haesendonckx (Senior Programmer Analyst - Statistical Programming, IDAR)Alexandra Papadopoulou (Programmer Analyst – Statistical Programming, IDAR)

September, 2019

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Disclaimer

Some of the opinions are personal and might not reflect the company’s view on things.

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AgendaR & Shiny

PSUR/DSUR as PoC

Shiny : Behind the scenes

PSUR/DSUR : The ins and outs

PSUR/DSUR : Flexibility

PSUR/DSUR: Demonstration

Fade out with Q&A

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R in Pharma• SAS: golden standard

• R: alternative to SAS

• Ongoing efforts from industry http://rinpharma.com/https://www.pharmar.org/

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Why R and shiny?

Large user baseActive community

Cutting edge statistical analysisExtensive graphical tool box

Easy to learn

R PackageBuild interactive websites

No knowledge of JS, HTML, ....requiredIdeal for interactive analysis and reporting

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Why R and shiny?

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PSUR/DSUR as a PoCPSUR/DSUR

• Periodic Safety Update Report – Development Safety Update Report

• Provided to authorities periodically

• Relatively simple safety report

• Pre-specified tables and listings generated

Automatization

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Shiny: Behind the scenes

Ø Source file needs to be created in R which defines:Ø UI(User Interface)Ø Server function

Ø UI:Ø Relevant code for layoutØ Embedded widgets

Ø Server function:Ø Translation of input to output

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Shiny: Behind the scenes

Source file in R which defines:• User Interface (UI)• Server function

UI:• Relevant code for layout• Embedded widgets

Server function:• Translation of input to output

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Shiny: Behind the sceneslibrary(shiny)

# Define UI for the applicationui <- fluidPage(

headerPanel("Hello Shiny!"))

# Define the server logicserver <- function(input, output) {}

# Run the applicationshinyApp(ui = ui, server = server)

input

output

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PSUR/DSUR: The ins and outs

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• Decreased complexity• Better readability of

source code

PSUR/DSUR: The ins and outs

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PSUR/DSUR: The ins and outs

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PSUR/DSUR: Flexibility

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PSUR/DSUR: Flexibility

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PSUR/DSUR: Flexibility

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demo

PSUR/DSUR: Demonstration

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Packages

Tidyverse• Data wrangling

Shiny• Interactive web pages• Visualization of results

Huxtable• HTML output for shiny UI• RTF output for download

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Future EnhancementsImprove on the UI/UX

Develop summary functions for complex outputs

Include interactive display mode of outputs

Include graphs

Validation• Accuracy, reproducibility, traceability • SOP of process, package selection, justification, unit testing• Docker containers and R Studio Package Manager for reproducibility

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Conclusion

R: easier to learn and cost-effective

R and Shiny: potential for interactive analysis and reporting

More key features are required for other reporting efforts

PSUR/DSUR PoC is a solid starting point for expansion

§ Thank you

Melinda, Tree of LifeMelinda’s artwork reflects her

journey living with HIV.

Thank you!

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