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
​- Georeferencing
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
This section will soon include the Instructor's guide, which will provide  a more detailed schedule and overview of each class session, and each of the assignments, codes, and other materials that can be individually downloaded.

Assignments

Protocols

R Scripts and Datasets

Class Slides