Modules & structure
The exact layout of the repository is intentionally flexible. The structure below represents a lightweight organisation that works well for both teaching exercises and rapid research prototyping.
scripts/
Basic radiative transfer examples using ToolsRTM and SCOPEinR, including single-run scripts, parameter sweeps, and small lookup table (LUT) generators. These scripts are intended for rapid experimentation, method testing, and teaching, and can be run independently or used as building blocks for more advanced workflows, notebooks, or Shiny applications.
apps/
Interactive Shiny applications that link biochemical and structural plant traits to simulated spectra. These apps are designed for rapid exploration of model behaviour, and interactive teaching and prototyping. They allow users to adjust key biophysical parameters in real time, visualise spectral and physiological responses across different radiative transfer models.
LUTs/
The Lookup tables and input parameter files used to run different radiative transfer and eco-physiological models within the Virtual Biophysical Lab. The LUTs support multiple modelling frameworks, including leaf-, canopy-, and top-of-atmosphere simulations (e.g. PROSAIL, INFORM, FLUSPECT, Liberty, SCOPE), and are used to ensure reproducibility and consistency across scripts.
notebooks/
R or Python notebooks used for interactive exploration, teaching demonstrations, and quick checks of model behaviour.
assets/
logos, plots and diagrams generated by the lab, designed for reuse in lectures, presentations, or scientific papers.
docs/
Short notes, mini-tutorials, and descriptions of example scripts or exercises intended for students and new users.