Population Genetics |
Field stats
IRES: Costa Rica
Statistical Training in the field
P.I. Laura may-collado; co-P.I. Joaquin Nunez
Welcome to
IRES Costa Rica
An NSF-funded learning experience for students passionate about marine biology and ecology
(NSF Award Number 2246323)
2024 Offering: June (Virtual); July 1-31
This IRES program takes place in Santa Elena Bay, located on the northwest Pacific coast of Costa Rica. A unique oceanographic feature of this region is the seasonal upwelling also known as the “Papagayo Upwelling” which brings deep cold and nutrient-rich water to the surface during the trade wind season, driving high productivity and biodiversity in the area. Because of these unique oceanographic and biological characteristics, the gulf is part of the Guanacaste Conservation Area and a UNESCO Heritage Nature site, protecting coral reefs, seagrass, and mangroves ecosystems, which are critical habitats for sharks and rays, northern and southern hemisphere humpback whales and several species of dolphins.
statistical training
As part of the IRES experience, students will learn data analysis skills using the R programming language. This training will occur through a series of workshops. The first of which will be a pre-field-work online workshop in June. Four more workshops will take place while students are in the field. These "computational nights" will occur on July 6, 7, 13, and 14.
Students will find all relevant information about the IRES computational and statistical training on this page. These workshops are powered by:
Biological Data Science Program
at The University of Vermont
Accessing the VACC
Basic steps to access UVM computational resources from afar
To access the VACC while off-campus you will need to install and activate UVM's VPN client (link)
Also, you must ensure that the DUO two-factor authentication system is installed and set up in your device before fieldwork!
To access the VACC and create a virtual desktop use the following instructions:
Link to the VACC: https://vacc-ondemand.uvm.edu/
The basics of R
Workshop 1 (June): The basics of R and a refresher of statistics
This day-long intensive workshop will introduce students to the basics of the R programming language through a series of guided practicums. Along the way, students will revisit basic concepts of probability and statistics. These will be key skills for their IRES analyses.
Resources:
1. The basics of R, pt 1. (Video [15 min], Code)
2. The basics of R, pt 2. (Video [17 min], Code)
3. Data structures (Video [18 min], Code)
4. Libraries and built-in data (Video [9 min], Code)
5. Tidyverse (Video [16 min], Website, Code)
6. Loops (Video [25 min], Code)
7. Functions (Video [15 min], Code)
8. GGplot (Video [10 min], Website, Code)
9. Inputs and Outputs (Video [21 min], Code)
10. Basic Statistics (Video [22 min], Code) *
* Rusty or New to stats? Please see the extra resources below for some guides on the basic concepts. Stat basics (good resources from the web; Statquest's "clearly explained" series on YouTube): Mean and Standard deviation; Correlations; P-values; confidence intervals.
Power analysis
Workshops 2 & 3 (July 7-8): Basic statistics and power analyses
Multivariate tools
Workshops 4 & 5 (July 11): Multivariate statistics. Principal component analysis and spatial visualization
During the third and fourth "computing nights," we will explore tools to answer another important question in stats: "How can I derive insight from multiple measurements (i.e., variables) of my study system?"
Pre-workshop assignment:
Please watch this quick 5-minute video about PCA from StatQuest (Video).
Activities:
1. Principal component analysis and Geo-spatial visualizations (Code)
After fieldwork
Data analysis, write-ups, and "office hours"
Once we complete our field season we need to analyze the data to derive biological meaning. To do this, we create virtual office hours to discuss the next steps.
Schedule Office hours:
Reach out to Joaquin.Nunez[at]uvm.edu to set up virtual office hours