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Workshops/Field Trips: May 11

Workshops/Field Trips: Monday, May 11, 2026

Workshops: May 11, 2026 (workshop's description below)
Starting at 9:00 am:
- Introduction to version control with Git and GitHub
- Introduction to EcoClassify: Simplifying Image Classification for Ecological Applications
- Introduction to Storytelling in Science
- Urban Amphibian Population Ecology and Conservation Workshop
Starting at 1:00 pm:
- Developing a reproducible workflow in R using functions, {targets} and {renv}
- Connecting theory to data: Introduction to Bayesian statistics for ecologists
- From Absolute Zero to Coding Hero: An R Crash Course in Reproducible Research for Community Ecology
- Navigating Open Science: Pathways to transparency, replication, and access through scientific publishing

Field Trips:

Koffler Scientific Reserve of the University of Toronto (https://ksr.utoronto.ca/)
Hosts: Micah Freeman and John Stinchcombe
Departure at 9:00 am from 25 Willcocks Street, Toronto
Return at 4:00 pm (leave KSR at 3:00 pm)
With miles of trails through pristine wilderness, KSR offers unlimited opportunities for hiking, photography, birdwatching, and nature study.

Rouge National Urban Park (https://parks.canada.ca/pn-np/on/rouge)
Host: Stuart Livingstone
Departure at 8:30 am from 25 Willcocks street, Toronto
Return at 2:00 pm (leave Rouge Park at 1:00 pm)
Explore one of the largest urban parks in North America, conveniently located in the Greater Toronto Area. Discover the natural wonders of Canada through the park's rich assembly of forests, creeks, farms and trails as well as marshland, a beach on Lake Ontario and human history spanning 10,000 years.

Note that participation in the workshops will incur additional fees that must be paid upon registration (see details below), and that some workshops have a participant limit. Places in these workshops will be allocated on a first-come, first-served basis.
Please, make sure to consult the workshop and the field trip schedule to avoid booking two events at the same time.
No refunds will be issued for workshops and field trips EXCEPT in the case of cancellation by the local organizing committee. Some workshop organisers have specified a minimum number of participants. Those workshops may be cancelled if they are undersubscribed.  Field trips may be cancelled in the event of extreme adverse weather. 
The no-refund policy also applies if you accidentally double-book.

Workshops Starting at 9:00 am

Introduction to version control with Git and GitHub: 9:00 am
Presenter: Valentin Lucet
This workshop will introduce you to the version control software git, a popular tool used to manage code and collaborate with other coders. Git has become a standard in both industry and research for code management and sharing. You will learn the importance of using version control for the code you write as part of your degree, as git allows you to keep very strict control on what changes you bring to your code. You will also learn how to keep an online backup copy of your code by pairing git with Github, an online platform for software management. Finally, you will learn how to collaborate with others on the same code. You will learn how to do all this using Rstudio and your web browser.

Introduction to EcoClassify: Simplifying Image Classification for Ecological Applications: 9:00
Presenter: Alessandro Filazzola
Image classification is an increasingly important tool in ecology for mapping land cover, detecting habitat change, and monitoring environmental processes. Yet, many ecologists face challenges in applying these methods due to the technical complexity of machine learning tools and the lack of reproducible workflows. This interactive workshop introduces participants to the ecoClassify package for SyncroSim, an open-source platform that simplifies image classification and modeling for ecological applications. Participants will gain hands-on experience with an end-to-end workflow for segmented image classification, including preparing training data, building models, and interpreting outputs such as confusion matrices, accuracy metrics, and variable importance plots. The workshop will also explore how ecoClassify supports different modeling approaches, including random forest and convolutional neural networks, while emphasizing transparency and reproducibility. Designed for researchers, students, and practitioners, this workshop requires no prior experience with coding or SyncroSim. Step-by-step tutorials, sample datasets, and guided exercises will enable participants to run their own classifications and share results through SyncroSim Cloud. By focusing on open tools and accessible learning, the workshop lowers barriers to advanced remote sensing analyses, fostering broader participation in ecological research and data-driven decision-making.

Introduction to Storytelling in Science: 9:00 am
Presenter: Aerin Jacob
Storytelling is foundational to being human. People have been telling stories for thousands of years and a compelling narrative is one of our most powerful forms of communication, including in science. Effective grant proposals, presentations, and peer-reviewed papers all depend on some kind of story structure. But not everyone is a “born storyteller” … Why is one story easy to remember or emotionally moving while another one falls flat? Where do you start? That’s where this workshop comes in. Anyone can learn to tell a better story - there’s some even some science involved. This half-day interactive workshop is relevant for researchers, practitioners, and science enthusiasts at all career stages. Through lecture and individual and group work (written and spoken), you will learn concepts and practice techniques that strengthen your ability to inspire, inform, and build support for your science. This workshop requires 1-2h of homework ahead of time (mandatory). While this workshop would pair well with "Introduction to Science Communication", also taught by Aerin Jacob, you can take either one alone.

Urban Amphibian Population Ecology and Conservation: 9:00 am
Presenter: Meredith Swartwout
Due to their high sensitivity to environmental contamination, amphibian populations have been described as a crucial “canary in the coal mine” for the impact of human activities. However, monitoring amphibian populations can be challenging given their seasonal activity patterns and secretive behavior. In an urban environment, the task of monitoring amphibian populations can be even more difficult due to limited areas of suitable habitat, increased population barriers, and urban hazards (e.g., roads). In this workshop, we will review techniques for locating and monitoring amphibians, assessing population vitality, determining threats to populations, and, finally, implementing conservation actions in an urban setting. The workshop will have 3 parts: a 0.5 hr review of a field project and techniques, followed by 1.5 hrs of talks, and then 0.5 hr of discussion. The field project review will be covering a local scenario and field techniques for monitoring of an Endangered salamander population. We will discuss the research methods used, importance of historical context, habitat features, and conservation challenges. For the next 1.5 hrs, a variety of practitioners and amphibian researchers will give short talks. The final half hour will be spent discussing and practicing conservation problem-solving. This workshop emphasizes active learning and hands-on activities, challenging participants to engage in solving population modeling and conservation problems.

Workshops Starting at 1:00 pm

Navigating Open Science: Pathways to transparency, replication, and access through scientific publishing: 1:00 pm
Presenter: Natalie Sopinka
Science is increasingly moving towards openness: open data, open peer review, and open access publication. This workshop presented by Canadian Science Publishing, a proud partner of the Canadian Society for Ecology & Evolution, aims to demystify what it means to practice open science in the modern era. Workshop participants will be invited to take an active part in breakout activities to better understand components of open science, including how to follow funder requirements, better understand compliance routes, discover avenues for data deposition, and discuss how open practices can make an impact beyond the scientific community and reach global audiences.

Developing a reproducible workflow in R using functions, {targets} and {renv}: 1:00 pm
Presenter: Alec Robitaille
This workshop will cover key elements of reproducible workflows targeted at users with familiarity with the R programming language. The workshop will start with project management and move to function writing in R that is flexible and testable. Next attendees will combine data and functions to create a reproducible workflow using the R packages {targets}, {renv}, and {conflicted}. Workshop attendees will gain fundamental project management and workflow skills that they can apply to their own projects and take back to their labs and collaborators. Project management that develops cohesive and well structured projects from the start promotes easy sharing, publishing and understanding by other users. Building and using functions allows for the creation of independent, logical steps which are easily tested and extended to different contexts. Ecology and evolution analyses in particular are often complicated with many interconnected steps and diverse data types. This combination makes good project management, function writing skills, and reproducible workflows all the more important. An exciting part of this workshop is the introduction to the R package {targets}. Many ecology and evolution analyses have modifications throughout the scientific process, which results in analytical steps that need to be rerun. {targets} tracks dependencies between input files, analysis steps and outputs and as you modify your project, it only reruns the relevant pieces. {targets} is an effective way to produce and manage a reproducible workflow, and is one of the first pipeline tools designed specifically for R, the main coding language of many CSEE attendees. As a relatively new tool, not many R users have taken advantage of it yet and this workshop provides an opportunity to get familiar.

From Absolute Zero to Coding Hero: An R Crash Course in Reproducible Research for Community Ecology: 1:00 pm
Presenter: Robert Colautti
The Absolute Zero to Coding Hero (AZ2CH) workshops are created by, and for, biologists. We assume no prior coding knowledge as participants are guided from the most fundamental syntax and coding concepts up to publication-ready analyses and data visualizations, with all tutorials provided free online for review during and after the workshop. In this workshop, we introduce coding in R with R Studio for the analysis of species communities, from large collaborative field surveys down to microbial communities reconstructed from high-throughput sequencing. This workshop is targeted at trainees and active researchers with little, if any, prior coding experience. Students working on original species community data are particularly encouraged to attend, but all are welcome and we will provide datasets to guide participants through a complete workflow for organizing, inspecting, restructuring, analyzing, and visualizing ecological data in R with R Studio. Based on the free and open textbook “R Crash Course for Biologists”, we will quickly introduce participants to key syntax and concepts for programming in R with R Studio, and using R markdown, with knitr, ggplot2, and dplyr for open and reproducible research with publication-ready graphics. After introducing these core skills, the second half of the course focuses on approaches for normalizing micro- and macro-ecology datasets, measuring species richness and evenness (alpha diversity), and constructing dissimilarity matrices to visualize and analyze community differences (beta diversity). This workshop will also emphasize reproducibility in ecological research, introducing the baRcodeR package for generating unique sample identifiers with scannable barcodes, and demonstrating how to build open and collaborative workflows in R Studio with Git and GitHub. By the end of the workshop, participants will gain conceptual and practical coding skills to analyze community ecology data and conduct open, reproducible, and data-driven ecological research.

Connecting theory to data: Introduction to Bayesian statistics for ecologists: 1:00 pm
Presenter: Andrew MacDonald
Have you ever found yourself with a detailed ecological dataset, an hypothesis you're excited to test -- but struggled to find a statistical procedure to connect the two? Bayesian statistics are exciting for ecologists because they offer us the ability to design a model that meets the full complexity of our dataset and our ecological ideas. An amazing array of models can be built, fit, and assessed using the same flexible toolkit. This workshop will cover the basics of applied Bayesian modelling for ecology. We will discuss some of the theory behind the Bayesian framework, and explore some common models using simulated. We'll learn how to fit, interpret, diagnose and visualize a Bayesian model using plots, and study a wide variaty of models useful to ecologists. These will include generalized linear models for count data and presence-absence data, as well as hierarchical, nonlinear, and zero-inflated models. All models will be illustrated using ecological examples and published datasets. We'll explore these model types using a combination of brms, rstanarm (two leading R packages) as well as some Stan code. Some prior experience in R is encouraged, but none with statistics nor with Bayesian approaches specifically.
This workshop is sponsored by the Canadian Institute of Ecology and Evolution - Institut canadien d’écologie et d’évolution.

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