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Workshop Agenda

Critical Skills to Scale Up Ecology

This workshop is a collaboration between ESA SEEDS and NEON, with support from Data Carpentries and is  made possible with a grant from the National Science Foundation. 

Instructors:

Jessica Guo, Phd

Dr. Jessica Guo is a scientific programmer and plant ecophysiologist at the University of Arizona. Her interests include plant water relations, plant sensor technology, Bayesian modeling, and data dashboards. Over the past 10 years, Jessica has taught many coding and statistics workshops, and she is a recently certified Carpentries instructor. 

 

Kristina Reimer, PhD

Kristina Riemer is a scientific programmer in the University of Arizona ALVSCE Data Science Team. She teaches computational skills and creates scientific software for ecological and agricultural research. She has been a Carpentries instructor since 2016 and has taught at ten workshops, and also contributed to Carpentry lesson curriculum.

 

Claire Lunch, PhD

Dr. Claire Lunch is a data scientist with the National Ecological Observatory Network. Her focus is on open data and open science, improving reproducibility via open platforms, and expanding coding and quantitative skills in the ecological community. At NEON, she works on data processing pipelines, public code resources, and other public resources to facilitate NEON data use.

 

Agenda

Segment I: Data Carpentries  

I. Collaboration with code

  1. Command line shell scripting within the RStudio terminal window
  2. git/GitHub in RStudio (part I)
  3. git/GitHub in RStudio (part II)

II. Reproducibility and project management

  1. Project management and best practices for R
  2. Data manipulation using tidyverse
  3. Functions in R
  4. Control flow in R

III. Documentation and publishing

  1. Best practices and publishing with RMarkdown

Our primary teaching method will be “code-along”, so that students practice the steps needed to code independently. We will have breakout rooms (particularly for troubleshooting), small assignments, and a collaborative note-taking document. 

 

Segment II: NEON Data Exploration 

  1. Overview of NEON – finding your way around the NEON website and data portal
  2. Accessing NEON utilities
  3. Spatial Data and Observatory spatial design
  4. NEON Data processing and QA/QC
  5. Develop your independent projects with support from NEON science team
  6. Presentation of a culmination project through small group-designed research projects on a topic of interest. Work starting as capstone projects from similar workshops have resulted in publications or graduate thesis for participants.