Spatial Epidemiology – Spring 2014
GEOG/PATH 560 Will Be Updated for Spring 2016
Tuesdays: 3:4:50 Lectures & Discussions Room 2506 VMBSB
Thursdays: 3:-4:50 Lab exercises Room 2281 VMBSB
This is the published class meeting time. We MAY adjust to accommodate conflicts.
TBD on first day of class
Instructor
Marilyn O’Hara Ruiz, PhD
Office: 2639 VMBSB
Office Hours: Tu 1:30-3:00, Fri 2:30-4 or by appointment
Phone: 217-265-5115
moruiz@illinois.edu
In this course, we will examine
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patterns of health and disease in place and time, and what we can learn from
those patterns
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application of geospatial technologies and methods for epidemiology
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analysis of time-space relations
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clusters and diffusion of disease
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geographical epidemiology of selected infectious and chronic diseases and
conditions.
Lectures, Discussions and Labs
Class time is divided between lectures, discussions and lab sessions. Usually,
lectures and discussions are on Tuesday and labs are on Thursday. The lectures will
take about one hour and the discussions about one hour.
Readings will be assigned each week for the following week. For each reading, one
student will provide a 3-5 minute overview summarizing the main points and
general nature of the reading and will develop several discussion questions. Try to
provide questions that generate discussion, rather than questions of fact. It is
understood that this can be difficult, but it is a good skill to work on.
Students will each lead paper discussions 3-4 times during the semester, depending
on the number of students. Readings will be distributed through links on the course
website. The discussion of readings is an essential part of this course and all
students are expected to participate.
Lab assignments are designed to provide students hands-on experience with a
variety of methods and software useful for the spatial analysis of disease and
environmental data. Most of the labs can be completed during the two-hour lab
sessions, but in some cases, additional time may be required to complete the
assignments. Labs are graded based on completion and participation. We will
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summarize and discuss each lab during a subsequent period after a lab is assigned.
The data and instructions for each lab will be available through the course web site.
Software is an essential part of the toolbox for spatial epidemiology, and you can
expect to spend time learning how to use tools that are new to you.
The primary software needed to perform the labs is available in the public computer
lab, Room 2281, in the VMBSB. That room is open 24 hours a day, 7 days a week,
except when other classes are in session. You may request after hours access to the
building if needed.
ArcGIS is a geographic information system from ESRI for general mapping and
manipulation of digital map data. In addition, the ArcGIS Spatial Analyst and
Geostatistical Analyst extensions will be introduced in lab assignments. The ESRI
software is available free to students and staff through a University of Illinois site
license. If you want to run this software on a computer other than in the lab,
licensing information is available at the UIUC Webstore. Search under ESRI. .
PATH 560 does not include class time for general training on how to use ArcGIS. For
the labs, we try to provide adequate instructions for the novice user, but we
recognize that some people will need more help. As needed, we will pair up people
who have more GIS background with those who have less.
If you want additional individual training on the ArcGIS software, check with the
instructor.
A number of other freely available tools will be used. These will be made available in
room 2281 VMBSB and links to the software will be provided as they are introduced
during the semester.
Grading
Your grade will be based on your participation in discussions and labs (40%) and
the term project (60%). For the project, you will be expected to pose a substantive
question related to spatial epidemiology, develop appropriate methods and data,
perform an analysis, and report your results in a paper and as an oral presentation.
Further details will be provided in class.
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General Schedule for the Semester
This outline provides a general picture of the semester. A more detailed listing with
details on the lab exercises and readings is provided on the Compass Website.
Week 1 Tues, 21 Jan & Thu, 23 Jan
Topic: What is spatial epidemiology. What will we do in this course?
Overview of the course, introduction to the labs, readings and term project
Lab 1: Confidential health data and mapping
Week 2 Tues, 28 Jan & Thu, 30 Jan
Topic: Vital records and demography. Awais Vaid, guest speaker. Epidemiologist
from the CU Public Health District
Lab 2: Birth and death records in Champaign County
Week 3 Tues, 4 Feb & Thu, 6 Feb
Topic: Spatial autocorrelation and clustering
Lab 3: Measuring spatial clusters and autocorrelation GeoDa
Week 4 Tues, 11 Feb & Thu, 13 Feb
Topic: Causality: health and place
Lab 4: Space-time clusters - SaTScan
Week 5 Tues, 18 Feb & Thu, 20 Feb
Topic: Vector-borne diseases
Lab 5: Spatial sampling, error and scale, geostatistical tools
Week 6 Tues, 25 Feb & Thu, 27 Feb
Topic: Climate and health
Lab 6: Ecological niche models - MAXENT
Week 7 Tues, 4 Mar & Thu, 6 Mar
Topic: Models to predict health risk
Lab 7: Disease transmission models - Netlogo
Week 8 Tues, 11 Mar & Thu, 13 Mar
Topic: Urban health and landscape ecology
Lab 8: Measures of landscape – FRAGSTATS
Week 9 Tues, 18 Mar & Thu, 20 Mar
Topic: Molecular epidemiology and phylogeography
Lab 9: Challenge lab – Midterm
SPRING BREAK
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April class will mostly be in a studio style. The topics of discussion will be
based on the term project initiated by students. Students will work in groups
of 2 or more to complete the projects. Each group will lead a readings
discussion and give an overview of the data and methods needed for their
project.
Week 10 Tues, 1 Apr & Thu, 3 Apr
Topic: Guest speaker Mei-Po Kwan
Lab 10: Term project
Week 11 Tues, 8 Apr & Thu, 10 Apr
Topic: Readings discussion based on project topics
Lab 11: Collect data on the IGotU sensor
Week 12 Tues, 15 Apr at Vet Med & Thu, 17 Apr
Topic: Finish discussions of readings based on project topics
Lab 12: Meet with instructor by appointment
Week 13 Tues, 22 Apr in Davenport & Thu, 24 Apr
Topic: Final project methods presentations to class 5 min each student
Final overview of course.
Meet with instructor by appointment
Lab 13: Meet with instructor by appointment
Week 14 Tues, 29 Apr & Thu, 1 May
Topic: Meet with instructor by appointment
Lab 14: Term project
Week 15 Tues 6 May
Topic: Presentation by student to class
Final paper due 14 May 2014 by midnight
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