GEOG 591
GIS for Analysis of Health

Geography 591 Syllabus

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This syllabus is divided into several sections. You can read it sequentially by scrolling down the length of the document or by clicking on any of the links below to “jump” to a specific section. That being said, it is essential that you read the entire document as well as material covered in the Course Orientation. Together these serve the role of our course "contract."

Instructor

Justine Blanford

Dutton e-Education Institute and the Department of Geography
The Pennsylvania State University
Earth and Engineering Sciences Building
University Park, PA 16802 USA

E-MAIL: Please use the course e-mail system in Canvas. If the matter is urgent, and the course e-mail is not working correctly, you can try my personal e-mail at jib18@psu.edu

Course Overview

GEOG 591: GIS for Analysis of Health. Choosing and applying analytical methods for mapping, modeling and analyzing health and disease, including point pattern analysis, surface analysis, overlay analysis, network analysis, cluster and regression analysis.

Prerequisite: GEOG 484 or permission of the instructor

Geography 591 is an elective course in the Penn State Professional Masters in Geographic Information Systems. This section is being offered to students around the globe through Penn State's World Campus. It is a "paced" course, which means that there is an established start and end date and that you will interact with other students throughout the course. The course is 10 weeks in length (plus a required "Orientation Week"), at a rate of 1 lesson per week. The course is organized around six weekly projects (due in weeks 1, 4, 5, 6, 7 and 8) and a more substantial project pursued through all ten weeks of the course. Weekly projects include associated readings, quizzes, and discussions about the analysis and mapping of different health and disease topics. In addition, I have included a regular reading assignment that requires you to read Spillover, a book about different diseases and outbreaks which I hope you will find interesting and useful. Since this will be a busy term I don't expect you to read the entire book but have provided specific readings for weeks 4 and 8. I do hope you find it interesting and encourage you to contribute to the discussions.

This is a course about the process and application of statistical and spatial methods used to map, model and analyze health and disease. The techniques introduced are often mathematically complex, but while these aspects are covered in the course, the emphasis is on the choice and application of appropriate methods for the analysis of the spatial data often encountered in applied geography as well as developing a framework in which to approach the analysis. Weekly projects are hands-on, using geographic information systems or other appropriate computational tools, so that students appreciate the practical complexities involved, but also develop an understanding of the limitations of these methods.

Through the weekly projects, students acquire familiarity with use of a single method or family of methods in standard desktop tools, so that they can focus on aspects of that method and develop a thorough understanding of its potential and of its limitations and how the method(s) can be used for tackling a specific health or disease problem. Topics range across data surveillance and infrastructure planning, modeling vector-borne diseases, planning for recovery through an evaluation of healthcare accessibility, cluster analysis, predicting health outcomes, and responding to outbreaks and epidemics. The term project is intended to allow students to formulate a research problem in a topic area of their own choosing, to gather and organize appropriate available datasets, and to understand how a variety of methods among those covered in the course can be applied in combination to thoroughly explore real questions. Students will be asked to engage with their peers' work during the project planning stage.

Like other courses in the program, this is a 10 week course. Throughout this course, there is a strong emphasis on the theory behind the methods you will be applying to help you understand which methods are appropriate and when as well as how to interpret the results. This is particularly important when deciding on the method to use since this may actually determine which GIS package you will use to tackle a given problem (because not all methods are supported by all GIS programs).

All of the material you need for the course is covered in the course texts highlighted earlier, supported by supplementary notes and commentary in the weekly lessons. It's worth noting that all of the texts cover considerably more material than we could ever get through in the 10 weeks of this course—so don't be too alarmed! Each week, you will be given clear instructions about exactly what you need to read and skim, including guidance on which aspects are particularly important that you understand.

The general format for each week is:

  1. First, I will provide you with an overview of the lesson, which typically includes an introduction, lesson learning objectives, textbook reading assignments, and an outline of the deliverables for the lesson (i.e., things you need to submit by the end of that week).
  2. Next, I will provide lecture notes for the lesson which will summarize the key concepts for the lesson. I will clarify any information you might find troublesome, link to additional information and highlight relevant readings. You may find that it helps to read these notes and then read the relevant pages—so that you have an idea of what to focus on.
  3. Once you have completed the lecture, you will complete a quiz (some weeks there are two) designed to help you assess your comprehension of the material. You have an unlimited number of attempts on each quiz and must score 90% or more.
  4. Finally, I will wrap up each lesson with a "Weekly Assignment"—specific instructions for the lesson project activities and/or how to submit the lesson deliverables.

In addition to these activities, a term project is required for you to complete the course. This is a more substantial piece of work, where you are expected to apply ideas and methods learned in the course. By prior agreement with me, ideas and methods not explicitly covered in the course, but which are related to health and disease, may also be used. Each week, there are deadlines in the term project to keep you on track, so that you work consistently on the project throughout the term rather than leaving it all to the last minute. More details of the term project are provided on the Project Overview page.

Using the Lessons link in the menu bar above, you can navigate to any lesson in the course. From there, you can also access each page within the lesson. Each is clearly titled.

Given this overall structure, I would strongly advise that you do the reading and quiz part of the course work early each week. Since course weeks run from Wednesday to the following Tuesday, you should therefore aim to complete the reading and quiz (or quizzes) by Friday of each week. This will leave you plenty of time to tackle the weekly project so that you can submit it by the Tuesday night deadline.

This course requires a minimum of 8-12 hours of student activity each week, depending on the speed at which you work. Included in the 8-12 hours each week is time to complete projects and related activities. Some weeks, you may spend less time than that, so keep this in mind in the tougher weeks (when you'll be making up the difference!). You'll be glad to know that you don't have to show up for class at a certain time! All you need to do is complete each project and a quiz before the published deadline at the end of the course week.

You will need to check out the course discussion forums regularly. That's where students and the instructor share comments, pose questions, and suggest answers. I strongly encourage you to get in the habit of logging in to the course website every day to check in on the class. With only occasional exceptions, I check discussion forums six (and usually seven) days a week. You can be sure that I will read, but not necessarily respond to, every single message. If I anticipate not logging in for more than a day, I will let you know and also clearly state when you can next expect to hear from me.

My colleagues and I have worked hard to make this the most effective and convenient educational experience possible. How much and how well you learn is ultimately up to you. You will succeed if you are diligent about keeping up with the class schedule and if you take advantage of opportunities to communicate with me, as well as with your fellow students.

Finally, I would reiterate the importance of contributing to discussions on the course Discussion Forums. In an online course, this is particularly important to give everyone a sense of involvement with the course. It is also worth 7% of the final credit!

... And what you can expect from me (the course instructor)

I have to be organized in much the same way that you are in order to teach the course!

I aim to answer any specific queries about the readings and commentary within 24 hours, unless otherwise indicated in course announcements, particularly relating to times when I am travelling during the term (which I do).

My answers may not always be direct - if it seems to me that you are relying too heavily on answers from me and others rather than on careful reading and your own efforts. I also hope that you will all chip in with responses to the puzzlement of your colleagues. Any such contributions will be noted when it comes to final grading. Of course, I will add to any comments from students, especially when they are inaccurate (i.e., wrong!) or incomplete.

Whenever possible, I will respond more quickly to problems with the projects, as I know how frustrating it can be if things seem not to be working. Again, please feel free to help one another out here. While I will treat questions about the projects as urgent, practical considerations mean that I can't commit to a more rapid response time than 24 hours. Note that this means it is imperative that you be well underway with the project work each week by Sunday, so that any problems can be resolved in good time for you to continue working and still submit on Tuesday night.

Required Course Materials

The course materials consist of textbooks; Esri ArcGIS with Spatial Analyst extensions; R a free statistical analysis package available online; GeoDa a free exploratory spatial data analysis software available from the GeoDa Center for geospatial analysis and computation at Arizona State University; and a required course website that contains the online lessons and communications tools, such as message boards and an e-mail system.

In order to access the online materials, you need to have an active Penn State Access Account user ID and password (used to access the online course resources). If you have any questions about obtaining or activating your Penn State Access Account, please contact the Outreach Helpdesk.

You will need to purchase course materials from MBS Direct (the bookstore used by Penn State's World Campus) or another bookstore, such as Amazon. For MBS pricing and ordering information, please see MBS Direct. MBS Direct can also be contacted at 1-800-325-3252. Materials will be available at MBS Direct approximately three weeks before the course begins. Be sure to order early enough to allow for shipping and installation prior to the course start date

The required material you need to purchase or obtain:

Required Texts
Book cover - GIS and Public health
Cromley, E.K. & McLafferty, S.L. (2012) GIS and Public health. 2nd Edition. Guilford Press. New York. pp 503. ISBN 978-1-60918-750-7. Available from the vendor of your choice or from Amazon.com - GIS and Public Health.
Book cover - Spillover: Animal Infections and the Next Human Pandemic
Quammen, D. (2012) Spillover: Animal Infections and the Next Human Pandemic. 1st Edition. ISBN-13: 978-0393346619. Available from the vendor of your choice or from Amazon.com - Spillover: Animal Infections and the Next Human Pandemic.
Book cover - Basic epidemiology
Bonita, R., Beaglehole, R., Kjellstrom, T. (2006) Basic epidemiology, 2nd Ed. World Health Organization (WHO), Geneva, Switzerland. Pp 219

Free

Book cover - Principles of Epidemiology in Public Health Practice
CDC (2012) Principles of Epidemiology in Public Health Practice, 3rd Ed. U.S. Department of Health and Human Services, Centers for Disease Control and Prevention, Atlanta, USA. Pp 500

Free

Note: As soon as you obtain Spillover start reading! Throughout the lessons, I will highlight sections that are relevant to what you will be learning.

Additional recommended texts:

  • O'Sullivan, D. and Unwin, D. J., 2010, Geographic Information Analysis, 2nd edition (Wiley, Hoboken, NJ). ISBN-10: 0470288574.
    Or, perhaps a copy of the e-book from the Penn State Library. You can find the book through LionSearch by typing in the title
  • Burt, J.E., Barber, G. M. and Rigby, D.L., 2009, Elemtary Statistics for Geographers. 3rd edition (Guilford Press, NY). pp652.
  • Koch, T., 2011, Disease Maps. Epidemics on the ground. University of Chicago Press. Chicago. Pp344.
    ISBN: 9780226449401.
  • If you do not know much about mosquitoes then this book is an interesting read. You will learn fun things about mosquitoes as well as about the diseases that they transmit and the history of their discovery. It is a light read.
    Spielman, A. Sc.D. & D'Antonio, M. Mosquito: The Story of Man's Deadliest Foe.
    ISBN-13: 978-0786886678
  • Quammen, D. (2014) Ebola: The natural and human history of a deadly virus. 1st Edition. ISBN-13: 088-4479281517

Journals

Throughout this course we will also be reading various journal articles. I have highlighted a few journals of interest some of which are open-access. For those that are not please use web of science through the Penn State Library to obtain a journal article of interest. This is a short list and mainly highlights geography journals.

Software

You will also need to have access to the following software:

  • R, the free statistical analysis software package;
  • GeoDa, free exploratory spatial data analysis software available from Arizona State University GeoDA Center for Geospatial Analysis and Computation
  • Esri's ArcGIS that includes the Spatial Analyst extension
  • Skype, free software for communicating in group discussions or zoom through Penn State.
  • ArcGIS online

During the term, we will have a group discussion and will use Skype. Details to follow once the term has started.

IMPORTANT: In addition to these free materials, you will be using Esri's ArcGIS software including the Spatial Analyst extension in this course. The best option for this if you do not have access to a copy is to obtain a free one-year student licensed copy, which you are entitled to do as a student in the class.

The best way to request access to the software is through our order form.

Thru the order form we ask you to confirm that the email address(es) we have on file are current accounts that you check frequently before submitting your order. This helps us make sure that we have your current contact information. In the future, please use this form.

As a registered student in GEOG 591, you will also be able to use this software through the University system that delivers Arc/Info to students. It's called Web Apps. Specific instructions and points of contact for using this solution will be provided. NOTE: The point of contact for support on this is Marty Gutowski at mjg8@psu.edu. However, most students find it more convenient to work with a personal copy of the software, so this is the preferred option if you can organize it.

NOTE: ArcGIS is a commercial software package that is restricted to personal use by the student. It is unlawful for anyone to use this software package without the appropriate commercial license from Esri Inc. to generate personal or corporate profit or revenue.

Assignments and Grading

Your course grade will be based on four components:
 

Weekly Quizzes - 20% of course grade.
This means that each quiz is worth about 2% of the final course credit. Note that the primary purpose of the quizzes is to encourage you to do the reading, rather than to test your knowledge - you get as many goes as you need to score 100% on the quizzes, so this is intended for you to review the reading, not as a 'test'. Weekly quizzes will attract full points provided they are completed by the stated deadline and you were able to score 90% or more for each one. Any quiz that you fail to complete by scoring 90% or more by the stated deadline will count for 0, with each quiz treated as equal value. Deadlines will be rigidly applied: Canvas will not allow you to submit results after the deadline.

6 Weekly Project activities - 48% of course grade (8% each):

  • Week 1: Analyzing John Snow's Cholera outbreak of 1854 using modern tools.
  • Week 4: Mapping the risk of Malaria across Africa.
  • Week 5: Planning for recovery through the mapping and evaluation of healthcare accessibility.
  • Week 6: Assess health variables across enumeration units to learn which cluster together and at what strength.
  • Week 7: Predicting health outcomes and analyzing the strength of those predictions.
  • Week 8: Ebola dealing with a crisis. Interactive maps, analysis and communication during an outbreak.

1 Term Project - 25% of course grade:
Throughout this course, a major ongoing activity is a personal GIS project that you will develop and research on your own (with lots of input from everyone else taking the course!). This is a more substantial piece of work than the weekly projects, where you are expected to apply concepts learned in the course. By prior agreement with me, ideas and methods not explicitly covered in the course, but which fall under the description 'spatial analysis' may also be used. Many students enrolled in the MGIS program find this project to be a great opportunity to explore an idea for their capstone project. You should expect to work on different activities in the term-long project each week. This is designed to keep you on track, so that you work consistently on the project throughout the term rather than leaving it all to the last minute. Waiting until the last minute is never a good practice in spatial statistics.

The 25% credit available will be divided as follows:

  • 1 point for posting topic ideas (week 1)
  • 1 point for a more detailed posting of a topic idea (week 2)
  • 2 points for on-time submission of satisfactory brief project proposal (week 4)
  • 3 points for feedback for project proposal (week 5)
  • 5 points final project proposal (week 6)
  • 2 points for on-time submission of final project (week 9)
  • 8 points for quality of the project content and report (week 10)
  • 3 points for your involvement in discussions of the final project (week 10)

Items in the term-long project will have drop-boxes and deadlines will be rigidly enforced by the Canvas course management system.

Participation - 7% of course grade:
Class participation is expected throughout the course on discussion forums and in feedback to other students. While posting questions is considered participation, you should also try to help others out with their questions. Consistently constructive input will be the most valued and beneficial.

Participation includes comments you provide to the Spillover discussions forum about what you learn from the readings and how it might relate to the weekly lesson. 

Notes about Assignments and Grades:

  • Weekly projects must be submitted by the stated deadline.
  • Late Submission - Each late submission is subject to a late penalty.
  • As a general guide, you can expect the following letter grades to apply:
    • F / D for non-completion.
    • C / C+ / B- for submission of unsatisfactory work that fails to answer all questions or supply all the requested items. Exactly where you fall on this scale will depend on how bad the submission is!
    • B for work that answers all questions asked and includes all requested items, and shows some insight into the lesson materials.
    • B+ for work that covers all requested items, and shows a firm grasp of all the material.
    • A- for work at least as good as the previous category, but where answers show evidence of thinking carefully through issues and problems related to the material.
    • A for exceptional work that in places goes beyond what is asked. This could include gathering outside data or reference sources, or providing truly outstanding analysis and graphics.
  • When submitting each project, you should use the drop box supplied in that week's lesson materials. You may submit in either PDF or Word doc formats.

Letter grades will be based on the following percentages:

Grading scale
A 90-100%
A- 87.5-89.9%
B+ 85-87.4%
B 80-84.9%
B- 77.5-79.9%
C+ 75-77.4%
C 70-74.9%
D 60-69.9%
F <60%
X Unsatisfactory (student did not participate)

Percentages refer to the proportion of all possible points earned by the student.

Final overall grades may be determined based on relative performance of all students, and not on a fixed points basis, especially if overall percentages are too high or too low.

GEOG 591 Course Schedule

imagePrintable Schedule

Below you will find a summary of the lesson objectives for this course and the associated time frames. For additional details scroll down to the detailed outline. Assignment information will be located on each lesson's checklist. This course is 10 weeks in length, with an orientation week preceding the official start of the course. Each lesson is one week long and opens on Wednesday.

 
Course Assignment Schedule
Week Topic Weekly Assignment
Deliverables
Term Project
Deliverables

1

Mapping Disease and health: Past to present

  • Weekly Assignment:

    • Analyzing John Snow’s Cholera outbreak of 1854 using modern tools

  • Quiz

  • Post a Topic Idea for your Term Project.

2

Data, data,data

  • Weekly Assignment:

    • NONE

    • Post comments to Discussion

  • Quiz

  • Provide an abstract of the Term Project topic Idea (250-500 words)

  • Obtain and explore data

3

Statistics and data visualizations

  • Weekly Assignment:
    • NONE
  • Quiz
  • Develop Term Project Proposal and Post to Discussion

  • Obtain and Explore data

4

Vector- borne disease and ecology

  • Weekly Assignment:
    • Mapping the risk of malaria across Africa

  • Quiz
None

5

Access to healthcare and healthy environments

  • Weekly Assignment:
    • Planning for recovery through the mapping and evaluation of healthcare accessibility
  • Quiz
  • Review Term Project Proposals. Provide comments to Discussion Forum

6

Clustering analysis

  • Weekly Assignment:
    • Analyzing health variables across enumeration units to learn which cluster together and at what strength. 
  • Quiz
  • Sumbit Final Term Project Proposal

7

Multiple regression analysis

  • Weekly Assignment:
    • Predicting health outcomes and analyzing the strength of those predictions. 
  • Quiz
  • Work on Term Project

8

Responding to disease outbreaks and epidemics.
 

  • Weekly Assignment:
    • Ebola dealing with a crisis. Interactive maps, analysis and communication during an outbreak.

  • Quiz
  • Work on Term Project
9 Putting it all together
  • Weekly Assignment:
    • NONE
  • Complete Term Project
10 DONE
  • Weekly Assignment:
    • NONE
  • Review Final Term Projects
Course Schedule
Week COurse Objectives Assignment and Activities
Week 0 After completing Week 0 you should be able to:
  1. Describe the expectations we have of you as a student in GEOG 591
  2. Locate key information about the course, including assignments, due dates, technical information, places to get help, and course policies
  3. Navigate the library and materials available to you as a Penn State Student.
  4. Recall the rules and regulations regarding Academic Integrity and plagiarism at Penn State
  5. Communicate in this course environment
Introduce yourself. Post a brief personal introduction to the Personal Introducations Discussion board and then review those your peers have posted to learn more about them.

Week 1

Mapping Disease and health: From Past to present

READ:

Quammen, D (SPILLOVER)

After completing Week 1 you should be able to:
  1. Define what epidemiology is
  2. Explain the chain of infection
  3. Describe the different modes of transmission
  4. List the three components of the epidemiologic triad
  5. List factors important in the occurrence of infectious diseases and non-communicable diseases
  6. Describe the public health response ready cycle and how it can be used for managing and planning public health
  7. List how maps have been used in health and disease
  8. Define GIS and spatial analysis
  9. Describe the five classes of spatial analysis functions
  10. Describe how modern tools and technologies are useful for mapping and analyzing disease

Quiz: Complete the quiz satisfactorily (you have an unlimited number of attempts and must score 90% or more).

Weekly Project Assignment: Complete analyzing John Snow’s Cholera Outbreak of 1854 using modern tools.

Term-project: Think about your term project and provide one or more suggested topics to the message board.

Spillover Discussion: Post comments to the message board

Week 2

Data, Data, Data

READ:

Quammen, D (SPILLOVER)

After completing Week 2 you should be able to:
  1. List different data types
  2. Identify data sources useful for exploring health and disease outcomes
  3. Explain why spatial data is special and limitations associated with spatial data (MAUP, boundary effects, patterns)
  4. Distinguish and critique between authoritative vs. non-authoritiative data sources
  5. Explain privacy concerns associated with mapping and using health and disease data
  6. Explore new technologies and assess how these can be used for collecting health and disease data
  7. List and explain the critical components important in conceptualizing a data framework for monitoring public health

Quiz: Complete the quiz satisfactorily (you have an unlimited number of attempts and must score 90% or more).

Weekly Project Assignment: None

Term-project: Provide a brief project abstract of your term project. Identify and obtain data that is relevant for your project.

Spillover Discussion: Post comments to the message board

Week 3

Statistics and data visualizations

READ:

Quammen, D (SPILLOVER)

After completing Week 3 you should be able to:
  1. Describe the research process used to investigate patterns associated with health and disease 
  2. Calculate summary statistics (central tendency, variability)
  3. Calculate the three centers of spatial data distributions
  4. Explain and calculate measures of risk that are used to characterize overall health of populations (ratio, proportion, incidence proportion, incidence rate, prevalence, mortality rate)
  5. Describe the concepts of basic biostatistics and how these can be applied to summarize and analyze health and disease data
  6. Assess how visualizations can be useful for examining disease

Quiz:Complete the quiz satisfactorily (you have an unlimited number of attempts and must score 90% or more).

Weekly Project Assignment: None

Term-project: Submit a term project proposal.  Obtain and explore the data that is relevant for your project

Spillover Discussion: Post comments to the message board

Week 4

Vector- borne disease and ecology

READ:

Quammen, D (SPILLOVER)

After completing Week 4 you should be able to:
  1. List factors important in understanding the ecology of vector-borne diseases
  2. Examine the epidemiologic triad for different vector-borne diseases
  3. Examine different methods of complexity used to map and model vector-borne diseases
  4. Explain data-driven approaches 
  5. Explain theoretical approaches and how overlay methods and raster-based modeling approaches can be used
  6. Describe the epidemiologic triad for malaria
  7. Apply complex map algebra operations to model risk of vector-borne disease - malaria
  8. Describe how these outputs are useful for recovery and response planning

Quiz: Complete the quiz satisfactorily (you have an unlimited number of attempts and must score 90% or more).

Weekly Project Assignment: Complete mapping risk of malaria across Africa project. Include any comments from Spillover into the write-up

Term-project: Post term final project proposal for peer-review

Spillover Discussion: Post comments to the message board

Week 5

Access to healthcare and healthy environments

After completing Week 5 you should be able to:
  1. List factors important in determining accessibility to health care
  2. Review different approaches used to model accessibility to healthcare
  3. Describe approaches useful for examining access to healthcare based on distance, time and cost.
  4. Explain the map algebra concept and describe focal operations, local operations and between-map operations
  5. Evaluate disparities of accessibility to health care
  6. Propose solutions to improving access to health care

Quiz: Complete the quiz satisfactorily (you have an unlimited number of attempts and must score 90% or more).

Weekly Project Assignment: Complete planning for recovery through the mapping and evaluation of healthcare accessibility

Term-project: Peer-review of course proposals in an online forum.

Week 6

Clustering analysis

READ:

Quammen, D (SPILLOVER)

After completing Week 6 you should be able to:
  1. Explain what cluster analysis is
  2. Explain how cluster analysis can be used in health studies
  3. List different clustering methods
  4. Differentiate between field based and object-based approaches
  5. List different tools that can be used for clustering analysis
  6. Identify the reasons for and advantages of cluster analysis.
  7. Interpret graphical output (dendograms) and their functions in cluster analysis.
  8. Describe the different measures that cluster analysis provides.
  9. Perform statistical analysis on the resulting clusters.
  10. Map clusters to see the spatial patterns in the data.

Quiz: Complete the quiz satisfactorily (you have an unlimited number of attempts and must score 90% or more).

Weekly Project Assignment: Complete analyzing health variables across enumeration units to learn which cluster together and at what strength project

Term-project: Submit a revised (final) project proposal.

Spillover Discussion: Post comments to the message board

Week 7

Multiple Regression Analysis

After completing Week 7 you should be able to:
  1. Explain how our environment can influence our health.
  2. List methods useful for understanding why a disease is occurring
  3. Perform descriptive statistics on environmental factors related to health
  4. Understand how correlation analysis can help understand relationships between factors and health
  5. Create scatterplots to view correlations between environmental factors and health
  6. Describes the relationships of factors to a disease using regression analysis and predict how these factors contribute to health outcomes
  7. Map the regression residuals to determine patterns in environmental factors

Quiz: Complete the quiz satisfactorily (you have an unlimited number of attempts and must score 90% or more).

Weekly Project Assignment: Complete predicting health outcomes and analyzing the strength of those predictions project.

Term-project: Continue the term-long project.

Week 8

outbreaks and epidemics.

READ:

Quammen, D (SPILLOVER)

After completing Week 8 you should be able to:
  1. Explain Epidemic theory
  2. Identify what surveillance data are important
  3. List the steps important in an outbreak investigation
  4. Describe the spatial tools that are useful at each of these steps
  5. Identify data limitations during a crisis-response situation
  6. Analyze the Ebola case data for 2014 and describe the spread and distribution of human cases in West Africa
  7. Critique analytical outputs and data visualizations and evaluate their usefulness in assessing and communicating risk
  8. Create an interactive outbreak map that would be useful for communicating risk
  9. Evaluate the usefulness of web maps in communicating risk during an on-going outbreak

Complete the quiz satisfactorily (you have an unlimited number of attempts and must score 90% or more).

Weekly Project Assignment: Complete the Ebola dealing with a crisis. Interactive maps, analysis and communication during an outbreak project. Include comments from the Spillover readings into the write-up

Term-project: Continue the term-long project.

Week 9 Note that there are no other course activities at all this week, to give you plenty of time to work on completion of the project. This week, you should complete your term-long project work and post a report with links to data, maps, charts etc., summarizing project activities and results. This should be suitable for anyone involved with the course to read and understand.
WEEK 10 Submit/present your term-long project and get involved in the discussions around all the submitted projects!

Project Overview: Breakdown of Week by Week Activities

Below is an outline of the weekly project activities for the term-long projects. You should refer back to this page periodically as a handy guide to the project 'milestones'. NOTE: I highly recommend keeping a regular diary of your activities on the term-long project. If you do this carefully enough, then the final report for the project should almost write itself!

Project Weekly Activities
Week Detailed Description of weekly activity on term project

Week 1

Read this overview! Identify and briefly describe a possible project topic (or topics). Post this information to the 'Term Project Discussion - Project Ideas (Wk 1)' as a new message.

Week 2

There is no weekly assignment this week to give you time to develop your project proposal and obtain the data you will be using in your project.

Submit a brief project proposal (250-500 words) to the assessment box as well as to the 'Term Project Discussion - Project Ideas (Wk 1)' board as a plain text. Since we talked about data this week, you should start to obtain the data you will need for your project. The proposal must identify at least two (preferably more) likely data sources for the project work, since this will be critical to success in the final project.  Over the next few weeks you will be developing your proposal which will be reviewed by other students and by me, and revised to a more complete form due in Week 6.

Week 3

There is no weekly assignment this week to give you time to obtain the data you will be using in your project and develop your project proposal. Post a final proposal to the 'Term Project Discussion - Peer-review' board.

Week 4

Refine project proposals and post to forum for peer-review (Week 5). If you have not already done so, post a final proposal to the 'Term Project Discussion - Peer-review' board.

Week 5

Peer-review of term project proposals. You will each be asked to provide comments on two other students' current proposals. These are intended to help you further refine your project idea and plans. Also, your commentaries on other students' project proposals will be assessed. Your comments should be posted to the ''Term Project Discussion - Peer-review' board as responses to the message outlining the project in question.

Week 6

A revised (final) project proposal is due this week (about 600-800 words). This will commit you to some targets in your project and will be used as a basis for assessment of how well you have done. The final proposal should be submitted through the 'Final Project Proposal (Wk 6)' Assessment box.

Week 7

You should aim to make steady progress on the project this week.

Week 8

You should aim to make steady progress on the project this week.
Week 9 This week you should complete your project work and post it as a PDF attachment on the 'Term Project Discussion - Final Project' forum that you are finished. This should be suitable for anyone involved with the course to read and understand. Note that there are no other course activities at all this week, to give you plenty of time to work on completion of the project. You should also submit the final term project to the 'Final Project Submission (Wk 9)' Assessment box.
WEEK 10 Finally, the whole class, including the instructor, will use the posted project reports as a basis for reviewing what we have all learned (hopefully!) from the course. Contributions to discussions of one another's projects will be evaluated as well as the projects themselves. Think of this as a virtual version of an in-class presentation of your project with an opportunity for members of the class (and the instructor) to ask questions, make suggestions, share experiences, review ideas, and so on.

Course Policies

Technical Requirements

For this course, we recommend the minimum technical requirements outlined on our "Program Technical Requirements" page. If you need technical assistance at any point during the course, please contact the Outreach Helpdesk (for World Campus students) or the IT Service Desk (for students at all other campus locations).

Internet Connection

Access to a reliable broadband Internet connection is required for this course. A problem with your Internet access may not be used as an excuse for late, missing, or incomplete coursework. If you experience problems with your Internet connection while working on this course, it is your responsibility to find an alternative Internet access point, such as a public library or wireless hotspot.

Mixed Content

This site is considered a secure website, which means that your connection is encrypted. We do, however, link to content that isn't necessarily encrypted. This is called mixed content. By default, mixed content is blocked in Internet Explorer, Firefox and Chrome. This may result in a blank page or a message saying that only secure content is displayed. Follow the directions on our technical requirements page to view the mixed content.

Equations

This course must be viewed using one of the following browsers: Firefox (any version), Safari (versions 5.1 or 6.0), Chrome (0.3 or later), or Internet Explorer with the MathPlayer PlugIn. If you use any other browser, there will be pages containing equations that do not render properly. If you need technical assistance at any point during the course, please contact the Outreach Helpdesk (for World Campus students) or the IT Service Desk (for students at all other campus locations).

Penn State E-mail Accounts

All official communications from the Penn State World Campus are sent to students' Penn State e-mail accounts. Be sure to check your Penn State account regularly, or forward your Penn State e-mail to your preferred e-mail account, so you don't miss any important information.

Academic Integrity

This course follows the guidelines for academic integrity of Penn State's College of Earth and Mineral Sciences. Penn State defines academic integrity as "the pursuit of scholarly activity in an open, honest and responsible manner." Academic integrity includes "a commitment not to engage in or tolerate acts of falsification, misrepresentation, or deception." In particular, the University defines plagiarism as "the fabrication of information and citations; submitting others' work from professional journals, books, articles, and papers; submission of other students' papers, lab results or project reports and representing the work as one's own." Penalties for violations of academic integrity may include course failure. To learn more, see Penn State's "Plagiarism Tutorial for Students."

Course Copyright

All course materials students receive or to which students have online access are protected by copyright laws. Students may use course materials and make copies for their own use as needed, but unauthorized distribution and/or uploading of materials without the instructor’s express permission is strictly prohibited. University Policy AD 40, the University Policy Recording of Classroom Activities and Note Taking Services addresses this issue. Students who engage in the unauthorized distribution of copyrighted materials may be held in violation of the University’s Code of Conduct, and/or liable under Federal and State laws.

For example, uploading completed labs, homework, or other assignments to any study site constitutes a violation of this policy.

Accommodations for Students with Disabilities

Penn State welcomes students with disabilities into the University's educational programs. Every Penn State campus has an office for students with disabilities. The Student Disability Resources (SDR) website provides contact information for every Penn State campus: Contacts for Disability Resources at all Penn State Campuses. For further information, please visit the Student Disability Resources (SDR) website.

In order to receive consideration for reasonable accommodations, you must contact the appropriate disability services office at the campus where you are officially enrolled. You will participate in an intake interview and provide documentation, see Applying for Services from Student Disability Resources. If the documentation supports your request for reasonable accommodations, your campus’s disability services office will provide you with an accommodation letter. Please share this letter with your instructors and discuss the accommodations with them as early in your courses as possible. You must follow this process for every semester that you request accommodations.

Counseling and Psychological Services

Many students at Penn State face personal challenges or have psychological needs that may interfere with their academic progress, social development, or emotional wellbeing.  The university offers a variety of confidential services to help you through difficult times, including individual and group counseling, crisis intervention, consultations, online chats, and mental health screenings.  These services are provided by staff who welcome all students and embrace a philosophy respectful of clients’ cultural and religious backgrounds, and sensitive to differences in race, ability, gender identity and sexual orientation. Services include the following:

Counseling and Psychological Services at University Park  (CAPS): 814-863-0395
Counseling and Psychological Services at Commonwealth Campuses
Penn State Crisis Line (24 hours/7 days/week): 877-229-6400
Crisis Text Line (24 hours/7 days/week): Text LIONS to 741741

Reporting Bias-Motivated Incidents

Penn State takes great pride to foster a diverse and inclusive environment for students, faculty, and staff. Acts of intolerance, discrimination, or harassment due to age, ancestry, color, disability, gender, gender identity, national origin, race, religious belief, sexual orientation, or veteran status are not tolerated (Policy AD29 Statement on Intolerance) and can be reported through Educational Equity via the Report Bias webpage.

Military Personnel

Veterans and currently serving military personnel and/or spouses with unique circumstances (e.g., upcoming deployments, drill/duty requirements, disabilities, VA appointments, etc.) are welcome and encouraged to communicate these, in advance if possible, to the instructor in the case that special arrangements need to be made.

Inclement Weather

In case of weather-related delays at the University, this online course will proceed as planned. Your instructor will inform you if there are any extenuating circumstances regarding content or activity due dates in the course due to weather delays. If you are affected by a weather-related emergency, please contact your instructor at the earliest possible time to make special arrangements.

Connect Online with Caution

Penn State is committed to educational access for all. Our students come from all walks of life and have diverse life experiences. As with any other online community, the lack of physical interaction in an online classroom can create a false sense of anonymity and security. While one can make new friends online, digital relationships can also be misleading. Good judgment and decision making are critical when choosing to disclose personal information with others whom you do not know.

Deferred Grades

If you are prevented from completing this course within the prescribed amount of time, it is possible to have the grade deferred with the concurrence of the instructor. To seek a deferred grade, you must submit a written request (by e-mail or U.S. post) to your instructor describing the reason(s) for the request. It is up to your instructor to determine whether or not you will be permitted to receive a deferred grade. If, for any reason, the course work for the deferred grade is not complete by the assigned time, a grade of "F" will be automatically entered on your transcript.

Attendance

This course will be conducted entirely online. There will be no set class meeting times, but you will be required to complete weekly assignments with specific due dates. Many of the assignments are open for multiple days, so it is your responsibility to complete the work early if you plan to travel or participate in national holidays, religious observances or University approved activities.

If you need to request an exception due to a personal or medical emergency, contact the instructor directly as soon as you are able. Such requests will be considered on a case-by-case basis.


Disclaimer

Please note that the specifics of this Course Syllabus can be changed at any time, and you will be responsible for abiding by any such changes. All changes will be communicated with you via e-mail, course announcement and/or course discussion forum.