Day 3: Ecological Modeling -- Wednesday 17 July 2024 14:00-18:00 UTC
Introductory talk: Clear, flexible, and fast: implementing ODE-based models with R package “rodeo”
David Kneis (Institute of Hydrobiology, TU Dresden)
The video recaps basic concepts of ordinary differential equations in the context of ecological modeling.
After watching it, you should be familiar with the nature of simultaneous ODE, the initial value problem, and
concepts to obtain dynamic and steady-state solutions. The video also highlights common practical issues
encountered in ODE-based ecological modeling. We will resolve the latter by a dedicated R package (“rodeo”) in
the corresponding workshop.
14:00-14:45 UTC - Keynote: Role of a trophic group in a plankton community
Patch Thongthaisong (Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB))
In this presentation, I show a model mimicking interactions between plankton trophic groups (a plankton food web)
and how I use it to obtain mechanistic insights into the roles of a parasite in plankton ecology.
A live stream of the pre-recorded keynote will begin at 14:00 UTC, followed immediately by a live Question and
Answer session with the speakers.
14:45-15:00 UTC - Break
15:00-17:00 UTC - Workshop: Clear, flexible, and fast: implementing ODE-based models with R package “rodeo”
David Kneis (Institute of Hydrobiology, TU Dresden)
Differential equations (DE) provide a means to simulate the dynamics of a wide range of ecological systems. Basic
DE-based models are nowadays fairly easy to implement. As system become more complex, however, obstacles pop up: How
to communicate a model with 10 state variables and 20 processes to users, students, or the scientific audience? How can
we validate and debug the equations step-by-step? How to make models fit for re-use? How to minimize computation times such
that sensitivity analysis and parameter estimation become actually feasible? The workshop gives an introduction the R package
rodeo which address all of the raised issues by two simple concepts: a standard notation and a code generator. The package
helps both beginners and experts to build comprehensible, high-performance DE models with a minimum of coding. Hence, rodeo
allows you to spend more time on identifying your system and gathering valuable observations.
This workshop will be live.
Materials for this workshop can be found in this slidedeck.
17:00-18:00 UTC Breakout/Working Groups Sessions
A traditional part of AEMON-J meetings in the past has been to openly discuss ideas for new, joint projects.
This time in the schedule is to bring up such ideas, perhaps inspired by the workshops earlier that day, and discuss.
If no such ideas are pitched, this time can also be used for small talk, networking, and other social activities.
