Data Visualization for Plant Pathologists

Syllabus

Course

Data Visualization for Plant Pathologists

PLP 6921, 1 Credits, Spring 2022

Instructor

Drs. Nicholas S. Dufault & James C. Fulton

Office: Zoom, Teams, Phone or In-person if possible

Email: nsdufault@ufl.edu & pcvgt@ufl.edu

Phone: 352-273-4623

Location

Fifield 2564 and Zoom

Times

Thursday 4:05-4:55 pm ET

Office Hours

Times: Wednesday & Thursday 2-3 pm ET

Location: Zoom through Canvas or In-person by appointment (if possible)

Note: our schedules get very busy during the semester so please try to schedule appointments as far in advance as possible. In general, it will be very difficult to set up appointments less than 24 hours in advance.

Websites

The syllabus, assignments and their due dates, grades and course updates can be found on the course website through Canvas. https://elearning.ufl.edu.

Online lectures and other relevant class information and resources will be posted at https://ufvegpathology.github.io/phyto-data-viz. Changes to the schedule will be posted on both sites so please try to check them periodically for updates.

Course Communications

Communication via Canvas is prefered.

Required Texts

There is no required textbook for this class.

All needed material is openly available on the course websites. If you are interested in additional reading on the topics we are covering then we highly recommend:

Learning R:

Learning Data Visualizations in R:

  • Fundamentals of Data Visualization: A Primer on Making Informative and Compelling Figures by Claus O. Wilke (978-1492031086) https://clauswilke.com/dataviz/
  • Data Visualisation with R – 111 Examples by Thomas Rahlf (978-3030284435) http://www.datavisualisation-r.com/
  • Data Visualization (A Practical Introduction) by Kieran Healy (978-0691181622) https://socviz.co/index.html
  • ggplot2: Elegant Graphics for Data Analysis (Use R!) by Hadley Wickham (978-0387981406) https://ggplot2-book.org/
  • How Charts Lie: Getting Smarter about Visual Information Hardcover by Alberto Cairo (978-1324001560)

Course Description

Data visualization makes it easier for researchers to communicate ideas and findings to their peers and the public. Producing your own communicative plots from data will allow you to understand plots made by others and identify what are effecitve and ineffective methods for data visualization. In this course, we will discuss what we mean by data visualization, what our goals as scientists are and should be, what tools are available to present/visualize your data using the software “R”, and how to critique/evaluate presented data. This colloquium course is one in a series of required courses provided to graduate students in the department of plant pathology, however, many plant science students will benefit from the information presented here.

Prerequisite Knowledge and Skills

Knowledge of basic biology to provide context for exercises.

Purpose of Course

As scientists and data consumers we are exposed to data visualization every single day. Whether the data is presented as a chart describing everyone’s favorite ice cream, a figure showing the change in the stock market over time, or an illustration in a popular science magazine demonstrating the most recent advances in our understanding of black holes and astrophysics, every single of us must interpret, develop, and communicate thoughts and data in clear, understandable, and aesthetically-pleasing ways. But how many of us stop to consider the underlying principles of how we present our data? Whether our intended messages are being conveyed accurately? Or whether we’re being misled by seemingly plausible sounding explanations of data depicted in erroneous ways? Join us this semester’s adventure to discuss these topics and others including: research reproducibility, data storage, and data carpentry.

Course Objectives and Goals

After completing this colloquium students will be empowered to:

  • Conceptualize data visualizations and how they are implemented to convey an author’s intended message
  • Identify basic rules/guidelines to accurately convey data without misleading or distorting data 
  • Utilize different tools and applications that can help you design attractive and compelling data visualizations
  • Have a sound grasp of data management strategies and increased comfort with data storage and accessibility
  • Be familiar with R data carpentry tools DPLYER and the TIDYverse suite of applications for data manipulation
  • Evaluate data visualizations and recommend effective adjustments to peers and friends

Teaching Philosophy

This class is taught using a flipped, learner-centered, approach, because learning to program and work with data requires actively working on computers. Flipped classes work well for all kinds of content, but we think they work particularly well for computer-oriented classes. If you’re interested in knowing more take a look at this website: https://teach.ufl.edu/resource-library/flipped-classroom/.

Instructional Methods

As a flipped classroom, students are provided with either reading or video material that they are expected to view/read prior to class. Classes will involve brief refreshers on new concepts followed by working on exercises in class that cover that concept. While students are working on exercises the instructor will actively engage with students to help them understand materials they find confusing, clarify misunderstandings and help identify mistakes that are preventing students from completing the exercises, and discuss novel applications and alternative approaches to the data analysis challenges students are attempting to solve. For more challenging topics class may start with 20-30 minute demonstrations on the concepts followed by time to work on exercises.

-Course Policies-

Our goal is to help you learn, while recognizing that most people have limitations.

This will be a hybrid course that will have online and in-person/zoom lecture components. To provide maximum flexibility the course material can be engaged with in three ways:

  1. Fully synchronous: Attend class during the scheduled class periods. Follow each lesson, which combine video lectures and exercises, during the class periods and ask for help as you run into questions. This is the closest approximation to how the course normally runs in-person.
  2. Synchronous Q&A: Follow each lesson before class, watching the videos and doing the exercises you can. Stop if you get confused. Come to class during the class periods and ask for help on challenges you encountered.
  3. Asynchronous: Follow the lessons online and ask for help via Canvas chat or email. This is the least ideal approach because the course is generally based around the benefits of direct student-instructor interaction to work through misunderstandings, but we’ll do our best to make it work for you.

The course always has flexible deadline policies (see below) and will continue to do so to support students learning under these difficult circumstances. There is an automatic (no request needed) 48 hour extension on all assignments for those who need it. If you need more time just let us know. You never need to disclose personal information to us to get an extension. Just let us know how long you need as early as you can.

Class Recording

Our class sessions may be audio visually recorded for students in the class to refer back and for enrolled students who are unable to attend live. Students who participate with their camera engaged or utilize a profile image are agreeing to have their video or image recorded. If you are unwilling to consent to have your profile or video image recorded, be sure to keep your camera off and do not use a profile image. Likewise, students who un-mute during class and participate orally are agreeing to have their voices recorded. If you are not willing to consent to have your voice recorded during class, you will need to keep your mute button activated and communicate exclusively using the “chat” feature, which allows students to type questions and comments live. The chat will not be recorded or shared. As in all courses, unauthorized recording and unauthorized sharing of recorded materials is prohibited.

Attendance Policy

Attendance will not be taken or factor into the grades for this class. However, experience suggests that students who regularly miss class often struggle to learn the material.

Quiz/Exam Policy

There are no quizzes or exams in this course.

Make-up policy

Life happens and therefore there is an automatic grace period of 48 hours for the submission of late assignments with no need to request an extension. However, it is highly recommended that you submit assignments on time when possible because assignments build on one another and it can be hard to catch up if you fall behind. Reasonable requests for longer extensions will also be granted. Assignments turned in after the 48 hour grace period without an extension will be be graded with a 10% penalty.

Assignment policy

Assignments are due Monday night by 11:59 pm Eastern Time as indicated on Canvas. This timing allows you to be finished with one week’s material before starting the next week’s material. Assignments should be submitted via Canvas as word documents or through the Perusall app.

Course Technology

Students are required to provide their own laptops and to install free and open-source software on those laptops (see Setup for installation instructions). Support will be provided by the instructor in the installation of required software. If you don’t have access to a laptop please contact the instructor and they will do their best to provide you with one.

Materials and Supplies Fees

There are no materials and supplies fees for this course.

-UF Policies-

University Policy on Accommodating Students with Disabilities

The Disability Resource Center coordinates the needed accommodations of students with disabilities. This includes registering disabilities, recommending academic accommodations within the classroom, accessing special adaptive computer equipment, providing interpretation services and mediating faculty-student disability related issues.Students requesting classroom accommodation must first register with the Dean of Students Office. The Dean of Students Office will provide documentation to the student who must then provide this documentation to the Instructor when requesting accommodation. For more information contact 352-392-8565 or through their website https://disability.ufl.edu/.

My policy: If you are in my class, I want to help you learn and will happily work with you to make the learning environment equitable for you and others.

Online Course Evaluation Process

Students are expected to provide professional and respectful feedback on the quality of instruction in this course by completing course evaluations online via GatorEvals. Guidance on how to give feedback in a professional and respectful manner is available at https://gatorevals.aa.ufl.edu/students/. Students will be notified when the evaluation period opens, and can complete evaluations through the email they receive from GatorEvals, in their Canvas course menu under GatorEvals, or via https://ufl.bluera.com/ufl/. Summaries of course evaluation results are available to students at https://gatorevals.aa.ufl.edu/public-results/.

University Policy on Academic Misconduct

Academic honesty and integrity are fundamental values of the University community. Students should be sure that they understand the UF Student Honor Code at https://sccr.dso.ufl.edu/policies/student-honor-code-student-conduct-code/.

Netiquette and Communication Courtesy

All members of the class are expected to follow rules of common courtesy in all email messages, threaded discussions and chats. https://teach.ufl.edu/wp-content/uploads/2020/04/NetiquetteGuideforOnlineCourses.docx

Academic Honesty

As a student at the University of Florida, you have committed yourself to uphold the Honor Code, which includes the following pledge:“We, the members of the University of Florida community, pledge to hold ourselves and our peers to the highest standards of honesty and integrity.”You are expected to exhibit behavior consistent with this commitment to the UF academic community, and on all work submitted for credit at the University of Florida, the following pledge is either required or implied: “On my honor, I have neither given nor received unauthorized aid in doing this assignment.”

It is assumed that you will complete all work independently in each course unless the instructor provides explicit permission for you to collaborate on course tasks (e.g. assignments, papers, quizzes, exams). Furthermore, as part of your obligation to uphold the Honor Code, you should report any condition that facilitates academic misconduct to appropriate personnel. It is your individual responsibility to know and comply with all university policies and procedures regarding academic integrity and the Student Honor Code. Violations of the Honor Code at the University of Florida will not be tolerated. Violations will be reported to the Dean of Students Office for consideration of disciplinary action. For more information regarding the Student Honor Code, please see: https://sccr.dso.ufl.edu/policies/student-honor-code-student-conduct-code/.

Software Use

All faculty, staff and students of the university are required and expected to obey the laws and legal agreements governing software use. Failure to do so can lead to monetary damages and/or criminal penalties for the individual violator. Because such violations are also against university policies and rules, disciplinary action will be taken as appropriate.

Student Privacy

There are federal laws protecting your privacy with regards to grades earned in courses and on individual assignments. For more information, please see:https://registrar.ufl.edu/ferpa/.

-Grading Policies-

Grading for this course is based on 6 equally weighted assignments and one final presentation.

Exercises in assignments will be graded as follows:

  • Produces the correct answer using the requested approach: 100%
  • Generally uses the right approach, but a minor mistake results in an incorrect answer: 90%
  • Attempts to solve the problem and makes some progress using the core concept: 50%
  • Answer demonstrates a lack of understanding of the core concept: 0%

Perusall assignments will be graded using the AI with the program and presentations will be graded according to the Canvas instructions. Please check the Canvas site for all assignment instructions.

Grading scale

  • A 93-100
  • A- 90-92.9
  • B+ 87-89.9
  • B 83-86.9
  • B- 80-82.9
  • C+ 77-79.9
  • C 73-76.9
  • C- 70-72.9
  • D+ 67-69.9
  • D 60-66.9
  • E <60

UF grading policies for assigning grade points

Grading policies can be found at: https://catalog.ufl.edu/UGRD/academic-regulations/grades-grading-policies/

-Campus Helping Resources-

Students experiencing mental health and personal issues that interfere with their general well-being are encouraged to utilize the university’s counseling resources. The Counseling& Wellness Center provides confidential counseling services at no cost for currently enrolled students. Resources are available on campus for students having mental health and well-being issues or lacking clear career or academic goals, which interfere with their academic performance.

Health and Wellness

U Matter, We Care: If you or a friend is in distress, please contact umatter@ufl.edu or 352 392-1575 so that a team member can reach out to the student.

Counseling and Wellness Center: http://www.counseling.ufl.edu/, 352-392-1575.

Sexual Assault Recovery Services (SARS): https://umatter.ufl.edu/helping-students/sexual-violence-response/; Student Health Care Center, 352-392-1161.

University Police Department: 392-1111 (or 9-1-1 for emergencies), or http://www.police.ufl.edu/.

Academic Resources

E-learning technical support: 352-392-4357 or e-mail to helpdesk@ufl.edu. https://elearning.ufl.edu/.

Career Connections Center: Reitz Union, 352-392-1601. Career assistance and counseling. https://career.ufl.edu/.

Library Support: https://uflib.ufl.edu/. Various ways to receive assistance with respect to using the libraries or finding resources.

Teaching Center: Turlington Hall, 352-392-2010. General study skills and tutoring. https://teachingcenter.ufl.edu/.

University Writing Program: Turlington Hall, 352-846-1138. Help brainstorming, formatting, and writing papers. https://writing.ufl.edu/writing-studio/.

Student Complaints

Student Complaints (Campus):https://registrar.ufl.edu/complaint.html.

Student Complaints (On-Line): https://distance.ufl.edu/state-authorization-status/#student-complaint.

Course Schedule

The details course schedule is available on the course website at: https://ufvegpathology.github.io/phyto-data-viz/schedule.