Using R-shiny as a data reviewing and validation tool in clinical trials, 9/22/2018 Page 1

Using R-shiny as a data

reviewing and validation tool

in clinical trialsMarkus Niederstrasser, Novartis Pharma K.K.

Using R-shiny as a data reviewing and validation tool in clinical trials, 9/22/2018 Page 2

Disclaimer

The opinions expressed in this presentation

and on the following slides are solely those

of the presenter and not necessarily those of Novartis.

Novartis does not guarantee the accuracy or reliability

of the information provided herein.

Using R-shiny as a data reviewing and validation tool in clinical trials, 9/22/2018 Page 3

• Introduction

• Goals

• Requirements

• Software / Libraries

• Server / Client Setup

• Prototype demonstration

• Summary

• Questions

Agenda

Using R-shiny as a data reviewing and validation tool in clinical trials, 9/22/2018 Page 4

• Traditionally SAS has been widely used for statistical analysis

and reporting during the entire clinical drug development

cycle in the industry.

• Especially during the trial execution phase reviewing,

validating and reporting of "work in progress data“ is often

needed (for example DMCs, SMRs)

• Such time consuming tasks consists mainly of examining data

within the table viewer, and running short code parts in SAS

to select, group or summarize data for further investigations

and reporting.

Introduction

Using R-shiny as a data reviewing and validation tool in clinical trials, 9/22/2018 Page 5

• Relieve the burden of repetitive programming for such

set of deliverables

• Interactive data exploration

• Increase speed

• Have an easier access in terms of creation, usage and

sharing of data/results

Goals

Using R-shiny as a data reviewing and validation tool in clinical trials, 9/22/2018 Page 6

• Able to deal with "work in progress data”

• Reproducibility of results

• User friendly interface (point and click, self explaining)

• Provide multi user access

• Web based (Easy to install)

• Fast response time

• Export functionality (Results, Code)

Requirements

Using R-shiny as a data reviewing and validation tool in clinical trials, 9/22/2018 Page 7

Software/Libraries

• R - is an open source programming language and software

environment for statistical computing and graphics. The R

language is widely used among statisticians and data miners for

developing statistical software and data analysis.

https://en.wikipedia.org/wiki/R_(programming_language)

• Shiny library - is an open source R package that provides an

elegant and powerful web framework for building web

applications using R. Shiny helps to turn analyses into interactive

web applications without requiring HTML, CSS, or JavaScript

knowledge. https://www.rstudio.com/products/shiny

Using R-shiny as a data reviewing and validation tool in clinical trials, 9/22/2018 Page 8

Software/Libraries

• Haven Library - is an R package to facilitate the transfer of data

between R and SAS, SPSS, and Stata

• data.table - is an R package that provides an enhanced version of

data frames (for improved speed and code syntax)

Using R-shiny as a data reviewing and validation tool in clinical trials, 9/22/2018 Page 9

Server/Client Setup

Web client

R/Shiny Server

Unix file server

selection logic an data

Tables/Reports

Provides SAS DatasetsSettings

SAS code

Imports

Exports

Exports

UserInteracts

R/Shiny

reporting

programs

Insta

lls

Developer

Using R-shiny as a data reviewing and validation tool in clinical trials, 9/22/2018 Page 10

Prototype demonstration

Example of general review tool (R code 700 lines)

ADaM: ADAE

Using R-shiny as a data reviewing and validation tool in clinical trials, 9/22/2018 Page 11

Using R-shiny as a data reviewing and validation tool in clinical trials, 9/22/2018 Page 12

Prototype demonstration

Example of general review tool (R code 700 lines)

ADaM: ADLB

Using R-shiny as a data reviewing and validation tool in clinical trials, 9/22/2018 Page 13

Using R-shiny as a data reviewing and validation tool in clinical trials, 9/22/2018 Page 14

Prototype demonstration

Example of an enhanced AE report (R code 250 lines)

Using R-shiny as a data reviewing and validation tool in clinical trials, 9/22/2018 Page 15

Prototype demonstrationExample of an enhanced AE report (R code 250 lines)

Using R-shiny as a data reviewing and validation tool in clinical trials, 9/22/2018 Page 16

Prototype demonstration

Example of an enhance LB report (R code 250 lines)

Using R-shiny as a data reviewing and validation tool in clinical trials, 9/22/2018 Page 17

Prototype demonstrationExample of an enhance LB report (R code 250 lines)

Using R-shiny as a data reviewing and validation tool in clinical trials, 9/22/2018 Page 18

Summary

• R/shiny for presentation/exploration of SAS

data could be a useful additional tool during

the trial execution Phase! (DMCs, self

validation, acceptance checks)

• Development for the local/server based R

shiny server is quite fast and straightforward .

Applications in R can be small and very

flexible

• Could be a easy to use counterpart for the

validation of standardized outputs

• Could be used as generator for prototype SAS

code / Macro calls of a reporting system

Using R-shiny as a data reviewing and validation tool in clinical trials, 9/22/2018 Page 19

Questions

Using R-shiny as a data reviewing and validation tool in clinical trials, 9/22/2018 Page 20