Articles

General-purpose optimisation

General-purpose optimisation interfaces: optim()-style optimisation with extensions (optim2), and heuristic optimisation with standardised arguments (optimh).

General optimisation with optim2()

Heuristic optimisation with optimh()

Optimisation recipes and diagnostics (optim2 and optimh)

Parallel computing for optimisation in calibrar

Model calibration

Parameter estimation examples and workflows based on calibrate(), including deterministic and ODE-based models.

Sequential calibration with calibrate()

Using the `calibrate()` function for parameter estimation

Parameter estimation for ODE systems

Model-specific workflows

Examples tailored to specific modelling platforms.

Preparing and running OSMOSE calibrations with calibrar