PPATH 542: Epidemiology of Plant Diseases (Spring 2018)


  • Plant Pathology and Environmental Microbiology


Course Logistics

Instructor: Dr. Paul Esker, Assistant Professor, Department of Plant Pathology and Environmental Microbiology
Office: 219 Buckhout Lab
Phone: 814-865-0680

Class meeting times: Tues/Thurs | 8:00-9:55 a.m.
Class location: 201 Buckhout Lab
Course credits: 3
Course prerequisites: PPATH 401, MATH 111 or MATH 141 or 3 credits in statistics

Course Objectives

  1. To increase understanding regarding how plant disease epidemics occur and change over time and space.
  2. To increase knowledge about the different tools and methods that can be applied for monitoring and quantification of plant pathogens and diseases.
  3. To demonstrate the importance of crop losses, as well as the methods used to quantify, predict, and reduce crop losses.
  4. To improve computational skills related to modeling and analysis of epidemiological data.

Course Materials

  • Primary readings from: The Study of Plant Disease Epidemics, L.V. Madden, G. Hughes, and F. van den Bosch (2007).
  • Various book chapters and journal articles.
  • Students should have access to a personal computer and either R or SAS software. We will also use some examples based on Stella, but no additional special software will be required (see isee Exchange Directory).

Course Grading

Two exams (midterm and final) 50
Problem assignments 30
Course Project 20

Course Topics

  1. Introduction to plant disease epidemiology:
    1. History and importance
    2. General terminology
  2. Monitoring diseases and epidemics:
    1. Methods to measure disease incidence and severity
    2. Host measurements
  3. Brief introduction to the analysis of epidemiological data:
    1. Concepts in modeling
    2. Mathematical and statistical methodology applied to epidemiology
  4. Temporal disease progress:
    1. Disease progress over time
    2. Models and analysis
  5. Spatial patterns and disease spread:
    1. Aggregation and plant diseases
    2. Pathogen and disease dispersal
    3. Spatial scale and disease monitoring
    4. Sampling
  6. Crop loss assessment:
    1. History and importance
    2. Types of yield
    3. Quantification and modeling
  7. Decision-making based on epidemiological principles

Course Project

Epidemiology is best learned by practice. In this course, students will have the opportunity to develop a group project related to the plant disease epidemiology, including, the following possibilities:

  1. Development of a white paper on the future needs in plant disease epidemiology.
  2. Development of a Shiny app illustrating a specific concept in plant disease epidemiology.
  3. Development of a teaching article related to a specific concept in plant disease epidemiology.

    Penn State Statements

    The Penn State Principles

    The Pennsylvania State University is a community dedicated to personal and academic excellence. The Penn State Principles were developed to embody the values that we hope our students, faculty, staff, administration, and alumni possess. At the same time, the University is strongly committed to freedom of expression. Consequently, these Principles do not constitute University policy and are not intended to interfere in any way with an individual's academic or personal freedoms. We hope, however, that individuals will voluntarily endorse these common principles, thereby contributing to the traditions and scholarly heritage left by those who preceded them, and will thus leave Penn State a better place for those who follow.

    Academic Integrity

    Penn State and the College of Agricultural Sciences take violations of academic integrity very seriously. Faculty, alumni, staff and fellow students expect each student to uphold the University's standards of academic integrity both in and outside of the classroom. Academic integrity is the pursuit of scholarly activity in an open, honest and responsible manner. Academic integrity is a basic guiding principle for all academic activity at The Pennsylvania State University, and all members of the University community are expected to act in accordance with this principle. Consistent with this expectation, students should act with personal integrity, respect other students' dignity, rights and property, and help create and maintain an environment in which all can succeed through the fruits of their efforts. Academic integrity includes a commitment not to engage in or tolerate acts of falsification, plagiarism, misrepresentation or deception. Such acts of dishonesty violate the fundamental ethical principles of the University community and compromise the worth of work completed by others (see Faculty Senate Policy 49‐20 and G‐9 Procedures.)

    Code of Conduct and Student Conduct Procedures

    Academic Integrity Guidelines for the College of Agricultural Sciences

    A lack of knowledge or understanding of the University's Academic Integrity policy and the types of actions it prohibits and/or requires does not excuse one from complying with the policy.

    Nondiscrimination Statement

    The University is committed to equal access to programs, facilities, admission and employment for all persons. It is the policy of the University to maintain an environment free of harassment and free of discrimination against any person because of age, race, color, ancestry, national origin, religion, creed, service in the uniformed services (as defined in state and federal law), veteran status, sex, sexual orientation, marital or family status, pregnancy, pregnancy-related conditions, physical or mental disability, gender, perceived gender, gender identity, genetic information or political ideas. Discriminatory conduct and harassment, as well as sexual misconduct and relationship violence, violates the dignity of individuals, impedes the realization of the University's educational mission, and will not be tolerated. Direct all inquiries regarding the nondiscrimination policy to Dr. Kenneth Lehrman III, Vice Provost for Affirmative Action, Affirmative Action Office, The Pennsylvania State University, 328 Boucke Building, University Park, PA 16802-5901, Email:, Tel (814) 863-0471.


    Penn State welcomes students with disabilities into the University's educational programs. Every Penn State campus has an office for students with disabilities. The Office for Disability Services (ODS) Web site provides contact information for every Penn State campus. For further information, please visit the Office for Disability Services Web site.

    In order to receive consideration for reasonable accommodations, you must contact the appropriate disability services office at the campus where you are officially enrolled, participate in an intake interview, and provide documentation. 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.

    Mental Health 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.

    Counseling and Psychological Services at University Park (CAPS)

    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

    Educational Equity/Report Bias

    Consistent with University Policy AD29, students who believe they have experienced or observed a hate crime, an act of intolerance, discrimination, or harassment that occurs at Penn State are urged to report these incidents as outlined on the University's Report Bias webpage

    Contact one of the following offices:

    • University Police Services, University Park: 814-863-1111
    • Multicultural Resource Center, Diversity Advocate for Students: 814-865-1773
    • Office of the Vice Provost for Educational Equity: 814-865-5906
    • Office of the Vice President for Student Affairs: 814-865-0909
    • Affirmative Action Office: 814-863-0471