Syllabus

Key Points on Syllabus

• Instructor Information and Office Hours
   
• Course Content
   
• Attendance
   
• Homework
   
• Course Project
  -  Proposal
  -  Final report

Instructor Information and Office Hours

• Hui Hu, PhD
   
• Office: CTRB 4224
   
• Email: huihu@ufl.edu
   
• Phone: 352-294-5944
   
• Office hours: By appointment

Tell us

• your name
   
• what program you are in
   
• any experience working on spatial data
   
• what skills you want to learn from this course

Course Content

• Course Overview
  - VM setup, R crash course
• Spatial Data Engineering
  - Basic SQL
  - PostGIS
  - Geocoding
  - Spatial data linkage
• Spatial Data Visualization
  - QGIS
  - R and Carto
• Spatial Data Analysis
  - Disease mapping: smoothing and interpolation
  - Disease clustering: densities and spatial autocorrelation
  - Ecological analysis: mixed-effects models
  - Geographically weighted regression
  - Bayesian models: JAGS and R-INLA

Optional Textbook

Lawson AB, Banerjee S, Haining RP, Ugarte MD, editors. Handbook of spatial epidemiology. CRC Press; 2016 Apr 6.

Attendance

• Attendance is mandatory
   
• UF policy for excused absences applies (must notify instructor in writing before class when possible)
   
• Each unexcused absence results in a 1.5% deduction from the final grade
   
• >3 unexcused absences results in failure

Homework

• 6 homework assignments
  -  10% each
  -  the highest 5 grades will count towards the final grade
   
• Often simple exercises
   
• Requirements:
  -  turn in assignment no later than 11:59 pm on the day it is due
  -  late assignment will NOT be accepted
  -  no handwritten assignment
  -  DO NOT copy others' work

Course Project

• Requirements:
  -  must include spatial data engineering, analysis, and visualization
   

• You can work individually or work as a team

  If choose to work as a team:
  -  each team can have up to 2 members
  -  clearly delineate roles and responsibilities of each team member

   

• Project Due:
  -  January 30, 2019: form a project team
  -  March 20, 2019: midterm presentation and project proposal
  -  Apr 17, 2019: final presentation
  -  Apr 24, 2019: final project report

Midterm

• Project proposal:
  -  Abstract: up to 1 page
  -  Project description: up to 5 pages
      ~ Specific Aims/Objectives
      ~ Background and Significance
      ~ Approach/Research Design
      ~ Timeline
  -  Citations: no page limit, use the Vancouver style
  -  Single column, single spacing; Arial or Times New Roman font; font size no smaller than 11 point; tables and figure labels can be in 10 points; minimum 0.5 inch margins
   
• Proposal presentations:
  -  up to 15 slides
  -  up to 15 minutes presentation with 5 minutes Q&A
  -  send the slides to instructor at least 3 days in advance

Final

• Final Report: up to ten pages (including references)
  -  Abstract: no more than 250 words summarizing the project
  -  Introduction: a short background and objective(s) of the study
  -  Methods: design, setting, dataset, approaches, and main outcome measurements
  -  Results: key findings and visualizations
  -  Discussion: key conclusions with direct reference to the implications of the methods and/or results
  -  References: please follow the Vancouver style
   
• Final presentations:
  -  up to 15 slides
  -  up to 15 minutes presentation with 5 minutes Q&A
  -  send the slides to instructor at least 3 days in advance

Grading

• Attendance: 5%
   
• Homework: 50%
   
• Midterm (project proposal and presentation): 15%
   
• Final (project report and presentation): 30%

Introduction to Spatial Epidemiology

What is Epidemiology

Epidemiology is the study of the distribution and determinants of health-related states or events in specified populations, time, and place, and the application of this study to the control of health problems

Last JM, Abramson JH, Freidman GD, editors. A dictionary of epidemiology. New York: Oxford university press; 2001.

Why Place Matters?

What is Spatial Epidemiology

• The description of spatial patterns of disease incidence and mortality -- English 1992
   
• Concerns the analysis of the spatial/geographical distribution of the incidence of disease -- Lawson 2013
   
• Encompasses research that incorporates the spatial perspective into the design and analysis of the distribution, determinants, and outcomes of all aspects of health and well-being across the continuum from prevention to treatment -- Kirby et al. 2017

Spatial Epidemiology vs. Health/Medical Geography

• Not synonymous
   
• Spatial Epidemiology refers to inquiries that use epidemiological study designs that involve spatial data or spatially derived information about study subjects, health facilities, or sources of exposure, with primary focus on populations
   
• Health/medical geography encompasses research applying geographic analytical methods to health, disease, or health care issues, with primary focus on spatial patterns and context

History of Spatial Epidemiology

• Hippocrates (460 BC – 377 BC), father of medicine and ancient Greek physician, understood the the effect of location on one’s health:
  -  people living high elevation or in drier, less humid area were less likely to have a disease than those living at low elevation near waterway
   
• John Snow (1813 – 1858), father of modern epidemiology, conducted an outbreak investigation in London, which is regarded as the beginning of Epidemiology as well as spatial epidemiology.

Original map by John Snow showing the clusters of cholera cases in the London epidemic of 1854

Concepts of Place and Neighborhood

• Some examples:
  -  women living in rural areas may have to travel longer distances to reach mammography facilities, potentially leading to a decrease of breast cancer screening or a delay in their diagnosis
  -  children living in a pedestrian friendly environment where parks and playground are readily accessible are more likely to engage in physical activity, reducing the odds of obesity
   
• Documenting the role of the geographic environment where individuals live and interact will improve the understanding of health outcomes, and have deep policy implications for local interventions and resource allocation

Definition of Neighborhood

• Many ways to define a neighborhood
   
• The neighborhood definition chosen for use in a research project is usually the result of a compromise between data availability, the conceptual relevance for the outcome being studied and confidentiality concerns

Role of GIS in Spatial Epidemiology

• Geographic information systems (GIS):
  -  computer-based systems for the integration and analysis of geographic data
   
• GIS has been used in many epidemiological applications:

• disease mapping
   
• rate smoothing
   
• cluster or hot spot analysis
   
• spatial modeling

Role of GIS in Spatial Epidemiology (cont'd)

• To create spatially explicit variables
  -  availability and accessibility (food access)
  -  built environment measures (land use)
  -  environmental exposures (air pollution)
  -  demographic indicators (poverty)
   
• To measure and describe the extent of spaital relationships
  -  calculate distance between two points
  -  quantify spatial dependencies in analytic models
  -  identify locally varying predictors

Methodologies in Spatial Epidemiology

• Geocoding and uncertainty
   
• Distance estimation
   
• Residential mobility
   
• Data linkages
   
• Disease mapping
   
• Spatial and spatio-temporal clustering
   
• Small area estimation
   
• Spatial regression models

Virtual Machine Setup

https://ufl.instructure.com/courses/367489/pages/virtual-machine-setup?module_item_id=7229041

R Crash Course

What is R?

• An object-oriented programming language focused on manipulating and analyzing data
  -  everything in R is an object: e.g. datasets, functions, models, etc.
   
• An open-source language
  -  anyone can contribute to the R project, and develop and distribute code to run in R
   
• One of the most popular languages used by statisticians and data sicentists

https://ufl.instructure.com/courses/367489/pages/introduction-to-linux-terminal-and-git?module_item_id=7229040

CARTO Account

CARTO for students accounts