Optimizing Subject Management of a Large Multi-site Randomized Controlled Trial: Implementation of R Shiny Dashboard with Real-time Data

Yongqi Zhong y.zhong@wustl.edu

Feb 21, 2018 Washington University Department of Psychiatry | healthymind.wustl.edu

Overview

▪ Introduction of R Shiny ▪ Redcap Reports & API ▪ Optimum Dashboard ▪ Demonstration of Sample Shiny App ▪ Implications

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Introduction of R Shiny Shiny & Shiny Dashboard

“ Shiny is an R package that makes it easy to build interactive web apps straight from R.

- R Studio

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Basic Structure of Shiny

▪ library(Shiny) ▪ ui <- fluidPage() ▪ server <- function (input, output){} ▪ shinyApp(ui = ui, server = server)

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Server

▪ Input (defined in either server or UI) ▫ Dropdown Menu ▫ Radio Button ▫ Text, Slider, etc.

▪ Output ▫ Data Table ▫ Plot ▫ Text, Image, etc.

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Server Cont.

▪ server <- function (input, output){ ▫ output$plot <- renderPlot({

▫ hist(iris$Petal.Length) ▫ })

}

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UI

▪ HTML ▪ CSS ▪ JS ▪ Layouts ▪ Shiny Dashboard

8 *Extracted from Shiny Cheat Sheet

Shiny Dashboard ▪ ui <- dashboardPage(

▫ dashboardHeader(title="test"), ▫ dashboardSidebar(sidebarMenu(

▫ menuItem( ▫ "Welcome", ▫ tabName = "welcome", ▫ icon = icon("gift")))),

▫ dashboardBody( ▫ tabItems(

▫ tabItem( ▫ tabName = "welcome", ▫ h3("Welcome"), ▫ box("Iris Petal Length Histogram",

▫ plotOutput("plot")) ▪ ))))

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Other Dashboard Layout Option ▪ flexdashboard (R Markdown)

▫ https://rmarkdown.rstudio.com/flexdashboard/

10 Source: https://beta.rstudioconnect.com/jjallaire/shiny-eruptions/

Redcap Reports & API Viewing Data from Redcap

Traditional Redcap Reports

▪ Pros ▫ Easy to use

▪ Cons ▫ Limited options

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Place your screenshot here

Redcap API ▪ library(RCurl) ▪ result <- postForm(

▫ uri=‘XXXXXXX’, ▫ token=‘XXXXXXXXXXX', ▫ content='report', ▫ format=‘csv', ▫ report_id='‘XXXX”, ▫ rawOrLabel='raw', ▫ rawOrLabelHeaders='raw', ▫ exportCheckboxLabel='false', ▫ returnFormat=‘csv'

▪ ) ▪ result_df <-read.csv(textConnection(result), sep = ",", fill = T, stringsAsFactors = F, na.strings =

"", header = T) 13

Place your screenshot here

Redcap API Cont.

Export Options ▪ Record ID ▪ Reports ▪ Instruments

Other Packages ▪ redcapAPI

▫ https://github.com/nutterb/redcapAPI

▪ REDCapR ▫ https://github.com/OuhscBbmc/RE

DCapR

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Optimum Dashboard WashU’s first Shiny web application using Shiny Server Pro.

Optimizing Outcomes of Treatment-Resistant Depression in Older Adults

▪ Principal Investigator: Dr. Eric Lenze

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Washington University Department of Psychiatry

https://www.optimumstudy.org/

Step 1 (for 10 weeks): Patient is prescribed augmentation with aripiprazole or bupropion, or switched to bupropion

OPTIMUM study design

What are we measuring?

We look at symptomatic remission, well-being, safety, falls, cognitive function,

& mobility.

4-month acute phase(above)

• Age 60+

• Major depression

• Non-responder to two or more antidepressant trials

N=500

N=500

N=500

N=1,500

STUDY POPULATION

N=400

Augmentationwith aripiprazole

Augmentationwith bupropion

Switch tobupropion

Remission

Switch to nortriptyline

Augmentationwith lithium

N=400

(N estimated)

Those who complete acute phase will be followed in a one-year continuation.

1 Step 2 (for 10 weeks): Those who do not improve in Step 1 receive lithium augmentation or switched to nortriptyline

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Community clinicians are at the center

The OPTIMUM study team partners with community clinicians to treat older adults with depression. •Patients stay with their own provider. •Provider prescribes medication. • Study team guides treatment steps.

Enrollment at 5 sites

▪ Washington University serves as the Central Coordinating Site

ColumbiaUniversity

New

York

WashingtonHeights

Harlem

NEW

YORK

Toronto

ONTARIO

CANADA

U.S.

Buffalo

Algonquin

Provincial

Park

Universityof Toronto

WestHollywood

HolmbyHills

LaderaHeights

ElSegundo

SantaMonica

Los Angeles

UCLA

Pittsburgh

AlleghenyCounty

University ofPittsburgh

St.Louis

Ferguson

Wellston

Pine Lawn

Soulard

MISSOURIILLINOIS

WashingtonUniversity

$ 13,500,000 Grant awarded from PCORI

50+ staff for 5 years Need reports

1,500 subjects at 5 sites We aimed to enroll

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What we need? ▪ Tables for weekly internal subject review ▪ Study participant’s characteristics & enrollment ▪ Data & safety monitoring ▪ Real-time report ▪ Easy to access and use ▪ …

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Optimum Dashboard

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Dashboard Structure ▪ Welcome (Landing Page) ▪ Patient Tracking ▪ Patient Information ▪ Aggregated Charts ▪ To-do List

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Welcome (Landing Page)

Better user experience

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Patient Tracking

Date: PHQ9: Continue/Increase/Decrease Med X mg (multiple rows of data in one cell)

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Patient Information

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Patient Information Cont.

Active Medications

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Aggregated Charts

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Aggregated Charts Cont.

Place your screenshot here

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To-do List

User Authentication & Privileges Dashboard Deployment on Shiny Server Pro 🔑 ▪ User authentication is only available when the app is deployed on

the server (https://www.rstudio.com/products/shiny-server-pro/) ▫ Protected Health Information (PHI) ▫ Access outside WashU ▫ Version control using Git on GitLab

▪ Collaboration with the Institute for Informatics (I2) (http://informatics.wustl.edu/)

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Data Flow & User Privileges

Redcap

All Sites’ Data

Eligibility Database

(Cross-sectional)

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Main Database (Longitudinal)

Site Subsetted

Data

All Data

Individual-level Data

Aggregated Data

Tables & Charts

Admin

Site Users

No Individual

Data Shown

All Users

Demonstration of Sample Shiny App • https://shiny.rstudio.com/gallery/personalized-ui.html • https://yqzhong7.shinyapps.io/Multiple-selectors/

Implications Explore new possibilities

Implications Needs and workflow of the study Thinking like a product manager as well as data analyst

Real-time data management Consider the efficiency of the codes for data wrangling & cleaning

Opportunities Publishing Shiny apps in academic journals (e.g. Bowman RL, Wang Q, Carro A, Verhaak RG, Squatrito M. GlioVis data portal for visualization and analysis of brain tumor expression datasets. Neuro-oncology. 2016 Nov 9;19(1):139-41.) 35

References ▪ Optimum Study:

▫ https://www.optimumstudy.org/ ▪ Shiny Cheat Sheet:

▫ https://github.com/rstudio/cheatsheets/raw/master/shiny.pdf ▪ http://shiny.rstudio.com/ ▪ https://rstudio.github.io/shinydashboard/index.html ▪ https://rstudio.github.io/DT/

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THANKS! Any questions? You can find me at: y.zhong@wustl.edu

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Washington University Department of Psychiatry | healthymind.wustl.edu