Exploring Plant Phenology Using Herbarium Specimens

An undergraduate research course developed by the California Phenology Network
In this course, students will design and conduct original research to examine the effect of climate on plant phenological events (e.g., flowering) using herbarium specimen data. Students will augment existing specimen records with phenological and georeference data in the CCH2 data portal. They will then visualize, clean, and analyze herbarium specimen data and climate data using Excel and R code (through RStudio). Each student will present their research as a scientific report, poster, and/or a lightning talk. During weekly class meetings, important topics and guidance regarding the research process will be discussed.

Course Overview
This course was designed for a relatively small class of advanced undergraduate students for a 10-week quarter. No previous experience with R or herbarium specimens is necessary, but students should have basic knowledge about the scientific method and be comfortable reading scientific literature. The weekly schedule of topics is shown below.
Week
Class topics
1
- Course introduction and background
​- Scientific questions​
- Independent and dependent variables
2
- Refining your research question
- Sources of data and their limitations
- Collecting phenological data in CCH2
3
- Methods and assumptions in data analysis
​- Linear models in RStudio
4
- Questions about R
5
- Writing a scientific paper / creating a research poster
​- Data collection and troubleshooting
6
- Data cleaning
7
- Describing results
- Designing additional analyses
8
- Interpreting results (discussion and conclusion)
9
- Giving and receiving feedback
10
- Paper or poster presentations

Course Materials
The Instructor's Guide provides a more detailed schedule and overview of each class session, as well as the materials available for the course. These materials are also individually listed below. Click the name of the assignment to download the assignment instructions and any related materials.

Assignments

Assignment 1: Course Introduction Readings
Students will read three articles that provide critical background information about how phenological research is conducted using herbarium specimens: a practical primer, a review article, and a primary research article of their choice from our research page.

Assignment 2: Independent and Dependent Variables Research
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Assignment 3: Phenological Scoring Guide
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Assignment 4: Preparing and Analzying Data in R
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Annotated Bibliography
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Final Paper / Poster

Final Poster Guidelines and Template
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Final Report Guidelines
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Protocols

Protocol 1: Using the CCH2 Data Portal
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Protocol 2: Preparing to Use RStudio
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Protocol 3: Using the Phenological Scoring Tools in CCH2
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R Scripts and Datasets

Class 3 Demonstration Code and Example Dataset
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Assignment 4 Code and Example Dataset (also provided in Assignment 4 above)
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Final Data Cleaning and Analyses Code
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Class Slides

Class 1: Introduction to Course
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Class 2: Refining your Research Question
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Class 3: Data Analysis in R
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