Frontiers in Climate‑Sensitive Vector Modelling – Tutorial Hub¶

Welcome to the central hub for modelling tutorials from the Frontiers in Climate-Sensitive Vector Modelling Workshops, most recently held in Nicosia, Cyprus (2025). These resources are designed to support participants, students, and researchers engaging with advanced approaches to simulating vector population dynamics, analysing climate-driven risk, and investigating the processes underlying climate-sensitive vector dynamics and associated disease transmission

All tutorials are accessible under:

➡️ Nicosia 2025 Tutorials

🔍 About the Workshops¶

The Frontiers in Climate-Sensitive Vector Modelling series brings together researchers working at the interface of climate-driven vector ecology, infectious disease modelling, climate data integration, and early-warning systems. The 2025 workshop in Nicosia offered a fully hands-on training environment focused on:

Model integration of climate relationships and environmental factors that shape vector biology
Mechanistic mosquito population models using deterministic and stochastic methods
Emerging methodologies, including phenotypic plasticity models, structured population dynamics, and physics-informed neural networks
Spatial modelling and integration with early-warning systems

The full programme is available at:

📄 https://vectormodelling.com/Nicosia2025/program

📦 Included Tutorials¶

Below is an overview of the tutorials delivered during the Nicosia 2025 workshop. Each section links to the corresponding notebook in VEClim's tutorial viewer. For an interactive session, please visit VEClim's tutorials, which include a work directory to copy, edit, and execute the instructions as you wish

1. Copernicus Data Store – Environmental Data for Disease Modelling¶

Folder: CDS

A practical introduction to accessing and using environmental datasets from the Copernicus Data Store (CDS) for vector dynamics modelling. The tutorial covers:

Navigating the CDS catalogue and identifying relevant climate and environmental variables
Downloading data programmatically via the CDS API
Working with environmental datacubes for modelling workflows
Additional user-friendly climate data tools, including the WMO–KNMI Climate Explorer and the IPCC Atlas

Tutorial: CDS_tutorial.ipynb

2. bayesTPC – Bayesian Thermal Performance Curves¶

Folder: bayesTPC

A concise introduction to fitting thermal performance curves (TPCs) using the bayesTPC R package. The tutorial demonstrates how to:

Load temperature–trait data and choose a TPC model
Fit the curve using Bayesian inference (via nimble)
Inspect posterior distributions and diagnostic plots
Generate predicted thermal responses with uncertainty
Suitable for participants interested in temperature-dependent trait estimation for climate-sensitive vector models

Tutorial: bayesTPC_tutorial.ipynb

3. arbocartoR – Spatial ODE Model of Aedes Ecology & Control¶

Folder: arbocartoR

An R‑based spatial mosquito and arbovirus model, covering:

Parcel‑based population dynamics
Meteorological inputs
Preventive control evaluation
Human mobility and intervention scenarios

Tutorial: arbocartoR_tutorial.ipynb

4. Physics-Informed Neural Networks (PINNs) for Vector Population Dynamics¶

Folder: PINN

A brief introduction to applying PINNs in vector population modelling. The tutorial covers:

Embedding ODE-based biological constraints inside neural networks
Using PINNs for forward simulation and inverse parameter estimation
Comparing PINN performance with traditional ODE parameterisation
Insights from ablation studies on how network design influences accuracy
Advantages of hybrid mechanistic–data-driven approaches for recovering hard-to-measure biological parameters

Please note that this particular tutorial requires the interactive VEClim's tutorials to run and display properly

Tutorial: PINN_tutorial.ipynb

5. dynamAedes – Spatially Explicit Mosquito Invasion Modelling¶

Folder: dynamAedes

A stochastic modelling framework for Aedes aegypti and Aedes albopictus allowing:

Climate‑driven population dynamics
Introduction scenarios
Spatial spread across Cyprus
Multiple simulations & uncertainty quantification

Tutorial: dynamAedes_tutorial.ipynb

6. sPop / PopJSON Modelling¶

Folder: sPop

A modern refinement of degree‑day models using flexible, data‑driven pseudo‑stages. Includes:

Using PopJSON to build complex, modular population models
Running Population C‑based simulations from R or Python
Modelling Aedes aegypti using experimental and climate data

Tutorial (R): sPop_R_tutorial.ipynb

Tutorial (Python): sPop_py_tutorial.ipynb

3. Delay‑Differential Equations for Vector Ecology (DDE Tutorial)¶

Folder: DDE

Introduces DDEs for temperature‑sensitive vector systems, including:

Comparison of ODE vs DDE behaviour
Variable delays using temperature time series
Multi‑stage mosquito population modelling
Blowfly system as the classical DDE benchmark

Tutorial: DDE_tutorial.ipynb

🧭 How to Navigate in Tutorials Viewer¶

The tutorials viewer is structured as follows:

/tutorials-viewer/localfile/
   ├── CDS/
   ├── bayesTPC/
   ├── arbocartoR/
   ├── PINN/
   ├── dynamAedes/
   ├── sPop/
   └── DDE/

If you see a README.ipynb inside a folder, click it directly to start.

📬 Contact¶

For questions, please contact the VEClim modelling team or the workshop organisers.

🌐 https://vectormodelling.com

📄 Download¶

You can download this README notebook directly from the link in the header.