Slideshow link

Co-authors

Anny Rodriguez, MPH

Roy Williams, MPH

Prasad Bhoite, MS, MPH

Ingrid Gonzalez, MPH

Catalina Canizares

Gabriel Odom, PhD, ThD

Outline

  • FIU and Stempel College of Public Health
  • Stempel Department of Biostatistics
  • Data Science
    • COVID
    • Social determinants of health
    • Mental health
    • Substance abuse
  • Questions

FIU and Stempel College of Public Health

  • Public Health, Social Work, Dietetics and Nutrition, Disaster Preparedness
  • Infectious disease, substance abuse, mental health, disparities, tobacco prevention, neurological brain behavior
  • #39 public school of public health
  • #49 public school of social work
  • #16 among most funded public schools of public health by NIH

Stempel College Department of Biostatistics

  • Science focused on study design, data collection, analysis, interpretation and communication using mathematical, statistical and computing methods in biomedicine and public health
  • Teaching, research, service, consulting department
  • 8 full time faculty and 4 masters level staff
  • 15 MPH students currently
  • 12 PhD students currently
  • Ranked 44th among public universities in US

FIU-STATCONSULT

Data Science Projects

New R Tools and Applications

  • South Florida COVID dashboard and R Shiny App
  • NHelp: Social determinants of health
  • tidyDisasters and tidyYRBS
  • CTNote; PathwayPCA and PathwayMultiomics

COVID Related Work

Back to the Future Figure

COVID Deaths in Miami Dade County

COVID Platforms

Shiny Code

NeighborhoodHELP (NHELP): Social Determinants of Health

NeighborhoodHELP

  • Provide household-centered care
    • Definition: the identification and management of the social needs within a given household
      • Employment
      • Housing
      • Healthcare Access
      • Transportation
      • Education

Impact Metrics

  • Social Stability Metric
  • Emergency Department (ED) Utilization
  • Health Stability
  • Connection to Primary Care Provider (PCP)

Data Collection

Data Collection

Portal

Health Risk Profile (HRP)

Database

Data Extraction

Data Extraction

# Import the required libraries
library(odbc)        # For Connecting to the database

# Create a Database Connection
# Note you need to set up DNS configuration before you run the code
con <- DBI::dbConnect(odbc::odbc(), "**********")


# Read the data tables from MS SQL Server
# HRP Tables

HRP_Household <- DBI::dbGetQuery(con, "select * from Household")
glimpse(HRP_Household)

HRP_Member <- DBI::dbGetQuery(con, "select * from Member")
glimpse(HRP_Member)

Data Storage

Data Analysis

Data Preparation Challenges

  • Nested data


Data Preparation Challenges

  • Identifying households that are currently active
    • Using the Window Function - lead()

::: {.panel-tabset}

Before

R Code

# Introducing the Window Function - Lead
Portal_Participating_HH <- Portal_HH_Status_History %>%
  group_by(HH_ID) %>%
  mutate(end_date = dplyr::lead(as.Date(Status_Date)-1, n = 1, default = NA)) %>% 
  mutate(end_date = ifelse(is.na(end_date), "2099-12-31", as.character(end_date))) %>%
  filter(Status %in% c('Active') & 
           (end_date >= Start_Date_Reporting_Period) & 
           (status_date < A_Day_After_End_Date_Reporting_Period)) %>%
  distinct(HH_ID, .keep_all = TRUE) %>% 
  mutate(Participating_HH = "Participating_HH")

After

Disasters and Mental Health Outcomes

tidyDisasters

tidyYRBS

Disasters

  • tidyDisasters

Disaster Datasets

  • Disaster Declaration Summaries
    • Federal Emergency Management Agency (FEMA) (United States of America)
  • Emergency Events Database (EMDAT)
    • Centre for Research on the Epidemiology of Disasters (Belgium)
  • Global Terrorism Database (GTD)
    • National Consortium for the Study of Terrorism and Responses to Terrorism (United States of America)

Data Challenges

  • FEMA
    • Cannot filter by number of people
    • ID with no information
  • EMDAT
    • States and counties joined in single cell
    • Missing locations
    • Missing end date
  • GTD
    • Minimal problems

Merge data eqivalence

  • State
  • County
  • Date or range of dates

Data Wrangling

  • Clean locations vector and dates
  • Classify disasters
  • Merge

Key contains begin year, month, state and a ticker to differentiate events with the same key

Example

Data in the tidyDisasters Package

  • allKeys_df
  • disastCasualties_df
  • disastDates_df
  • disastLocations_df
  • disastTypes_df
  • emdat_hazard_cluster_df
  • fema_hazard_cluster_df
  • hazard_report_df

Adolescent Suicidality Data

  • Youth Risk Behavioral Surveillance System (YRBSS)
    • Extracted data on suicidality and substance abuse
    • Clean up and wrangling in R

Data in the tidyYRBS Package

  • hs_district
  • hs_demographics
  • hs_suicide
  • hs_substance_use
  • clean_yrbs_2019
  • raw_yrbs_2019

Example

Acknowledgements

  • Dr. David Brown, MD
  • Dr. Rachel Clarke, PhD
  • Baptist Health South Florida
  • Dr. Mary Jo Trepka, MD, MPH
  • Dr. Emir Veledar, PhD
  • FIU Resarch Center for Minority Institutions

Thank you!