ENV 226 Lab Online R Manual
2026-09-21
Chapter 1 Introduction
This course surveys the central concepts in ecology: evolution, population dynamics, community interactions, biogeochemical cycling, and limiting factors, as well as how those factors are measured, quantified, and interact with drivers of global environmental change. This course is required for the B.S. in Environmental Sciences degree program, and also the B.S. in Environmental and Sustainability Studies degree. This course acquaints students with foundational concepts and theories in ecology and provides a broad basis for more advanced courses in subdisciplines and applications of ecology.
In lab, we will conduct experiments and practice skills used in the ecological sciences. In addition to field and experimental techniques, these skills include data collection and analysis. Learning how to manage, manipulate and analyze data in R will serve your undergraduate career and beyond! In ENV 226 lab, we will ease you into using R for all your data needs!
How to use this resource
Each chapter in this online book corresponds to lab that you will complete. For most labs, you will download R code that you will use to analyze your data, and that can be also be used for other analyses and projects that you have in college and in the workplace.
How this manual is ordered
The chapters follow the same path the course does, from the smallest scale to the largest:
- Getting your tools working — R, RStudio, spreadsheets, and how to describe a set of numbers.
- Learning to work in the field — identifying what’s there, running a professional monitoring protocol, and then designing a study of your own.
- Organisms and populations — animal behavior, natural selection, estimating abundance, population structure, demography, and population growth.
- Communities — species interactions and diversity.
- Ecosystems and landscapes — decomposition, water quality, and modeling where species can live.
Statistical testing sits deliberately late, right before you analyze your own data, because tests make far more sense when you have a question you actually care about answering.
Three things about this order are worth knowing up front:
- Some chapters are alternatives, not additions. Dendrochronology is the spring substitute for the field methods lab, and the Crosstown Walk is an alternative to the Sinclair Wash study. You will do one of each pair, not both.
- Two labs do not run in chapter order, and both say so at the top. You plant the species interaction project early and visit the greenhouse weekly for six to eight weeks while the class works through other labs; the analysis and poster come at the end, in a separate chapter. The litter decomposition bags go out around week 3 and come back in around week 12, and need nothing from you in between.
- Weather reorders things. Flagstaff sits at 7,000 feet, and outdoor labs get moved when the forecast says so. Pay close attention to your TA, your Canvas shell and your email so that you don’t get lost.
Important downloads
Your rubrics for the lab report and final class project poster can be downloaded here:
These links are also embedded within the class projects for which you will create the lab report and the poster.
1.1 Skills you’ll build
Every chapter in this manual opens with a short box headed “Skills this lab builds.” These boxes tell you which professional competencies a given lab is training. Skills are drawn from two published frameworks that the ecology and biology education communities use to design and evaluate courses.
1.1.1 The two frameworks
4DEE — Four-Dimensional Ecology Education, from the Ecological Society of America. It describes ecology teaching along four dimensions, and its central claim is that good ecology education integrates them rather than teaching them separately.
| Dimension | What it covers |
|---|---|
| Core Ecological Concepts | Organisms · Populations · Communities · Ecosystems · Landscapes · Biomes · Biosphere |
| Ecology Practices | Natural history · Fieldwork · Designing, conducting, and critiquing investigations · Quantitative reasoning and computational thinking · Data analysis and interpretation · Working collaboratively · Communicating and applying ecology |
| Human–Environment Interactions | Human interdependence with the environment · Human impacts on the environment from local to global scales · Ecological ethics |
| Cross-Cutting Themes | Structure & function · Pathways & transformations of matter and energy · Systems · Evolution · Space & time |
The BioSkills Guide, a nationally validated set of learning outcomes that unpacks the Vision and Change core competencies into 77 specific, teachable statements. Its six competencies are:
- Process of Science — scientific thinking, information literacy, question formulation, study design, data interpretation and evaluation, doing research
- Quantitative Reasoning — numeracy, quantitative and computational data analysis
- Modeling & Simulation — purpose of models, model application, modeling
- Interdisciplinary Nature of Science — connecting scientific knowledge, interdisciplinary problem solving
- Communication & Collaboration — communication, collaboration, collegial review, metacognition
- Science & Society — ethics, societal influences, science’s impact on society
The two frameworks complement each other rather than overlapping. BioSkills emphasizes quantitative reasoning, communication and research ethics. It contains no outcome naming natural history or field observation, while those skills are highlighted in 4DEE.
1.1.2 Where this manual covers what
| Skill area | Where you practice it |
|---|---|
| Natural history and field observation | Tree walk · Field methods · Behavioral ecology · Population structure · Urban ecology |
| Fieldwork and protocol execution | Field methods · Ecological sampling · Plant population biology · Water quality · Species interactions I |
| Study design | Ecological sampling · Selecting statistical tests · Species interactions I · Urban ecology |
| Measurement error and uncertainty | Field methods (observer calibration) · Behavioral ecology (observer agreement) · Mark–recapture (assumption violations) · Population structure · Ecological sampling |
| Data management | Getting started · Working with data in a spreadsheet · Descriptive statistics · every lab with a shared class datasheet |
| Reproducible workflows | Working with data in a spreadsheet · every lab that ships an R script |
| Quantitative and statistical analysis | Basic statistical testing · Selecting statistical tests · Species diversity · every analysis chapter |
| Modeling and simulation | Plant population biology · Species distribution modeling · Population ecology · Dendrochronology |
| Communication and collaboration | Species interactions I and II · Urban ecology · the class project |
| Ethics and responsible conduct | Population ecology (culture disposal) · Species diversity (specimen collection) · Field methods (collecting permission) · Urban ecology (conduct in neighborhoods) |
| Science and society | Urban ecology · Invasive species · Water quality · Dendrochronology |
| Ecosystem processes | Litter decomposition · Water quality · Species diversity |
Sources. ESA 4DEE framework: https://esa.org/4dee/. Foundational paper: Klemow, K., A. Berkowitz, C. Cid, and G. Middendorf. 2019. Improving ecological education through a four-dimensional framework. Frontiers in Ecology and the Environment 17(2): 71. https://doi.org/10.1002/fee.2013
BioSkills Guide: Clemmons, A.W., J. Timbrook, J.C. Herron, and A.J. Crowe. 2020. BioSkills Guide: Development and national validation of a tool for interpreting the Vision and Change core competencies. CBE—Life Sciences Education 19(4): ar53. https://doi.org/10.1187/cbe.19-11-0259. The full list of 77 outcomes is freely available at https://qubeshub.org/publications/1305/5 under a CC BY-NC-ND 4.0 licence; outcome statements quoted in this manual are reproduced verbatim with attribution.