Graduate Students: Aeran Coughlin and Richard J Wong
Sponsoring Faculty: Danae Diaz
Undergraduate Course: Biology 290S – 3: “Biology By Design”
This data expedition focused on plant communities, ecological data exploration, quantifying diversity, linear and generalized linear models, and ordination. Prior to the data expedition, students collected field data in Anderson Woods. We began class with a short lecture describing community ecology, community structure metrics, and how to analyze them. As a class, we then went through a pre-written R Markdown demonstrating how to organize and visualize data and quantify community metrics. After a discussion of what our variables mean and how they relate to each other, we had the students work in groups to answer one of our guiding questions on their own by creating a figure and building a model. They were asked to generate a hypothesis and prediction, customize a code chunk to build their model and plot, then interpret the statistical output and figure. As a class, we came together and had each group present their findings, discussing the ecological context of their results. Finally, we had one person per group knit the R Markdown file into a PDF to turn in as credit.
This class was part of a seminar focused on experimental design in ecology. The students had varying levels of exposure to statistics and coding, so we focused on:
- How to organize and understand field collected data
- Choose an ecological diversity index and describe what it means
- Interpret a multi-dimensional scaling ordination plot
- Read model summaries
- Create hypotheses
- Build a model and render a figure
- Interpret its results in a broader context
Guiding Questions for Visualization and Hypothesis Testing
- How does Shannon Diversity change over a soil moisture gradient?
- How does Total Vegetation change over a soil moisture gradient?
- How does Shannon Diversity change across elevation?
- How does Total Vegetation change across elevation?
- Are areas with higher Total Vegetation more diverse?
Homework
There was no formal homework assigned for this class; however, if students did not complete the data analysis and interpretation portion of the exercise, then they were asked to complete it for homework and submit the knitted PDF file.
Classroom Exercise
This data expedition allowed students to conduct analyses that they had collected themselves in Anderson Woods. Here, we use an annotated R Markdown file with guiding questions to help the students understand what the collected information means in an ecological context. The short lecture at the beginning of class primed students to think of both abiotic and biotic interactions and how they may influence a plant community’s diversity and composition.
The students then followed the annotated R Markdown file on their own computers to understand how to organize and model the data, as well as calculate ecological metrics such as the Shannon Diversity Index. After a discussion on whether the data collected fit our assumptions for linear models and NMDS, we have the students create a hypothesis and prediction for one of our five guiding questions. The students then had to fill in variable names to complete an R chunk with the correct statistical analysis and figure rendering mode. As a group, these students have to interpret the summary results and figure and accept or reject their hypothesis with an explanation.
Lastly, we had each group knit the R Markdown file with all of their answers into a PDF, which they then submit on canvas.
