odelia: ODE solver using Runge-Kutta 4-5 adaptive step, C++ header files

The odelia package for R is an ODE solver in C++ header files, using RK4-5. There's potential to link to R via Rcpp. Code was first developed by Rich FitzJohn as part of the plant package. I'm spinning that code out into a package, as I want to use it elsewhere.

Vocabulary

• system
• stepper
• solver
• runner

License

This package is released under the GNU Affero General Public License v3 (AGPL-3).

Contributing

Contributions are welcome. By submitting a pull request or code to this repository, you agree to the terms of the Contributor License Agreement.

ODE System Structure

An ODE system in odelia consists of:

• A system header (inst/include/odelia/examples/*.hpp) — C++ class defining the ODE. Must implement ode_size(), set_ode_state(), ode_state(), and ode_rates(). Template on scalar type for AD support.

• An Rcpp interface (src/*_interface.cpp) — [[Rcpp::export]] functions exposing the system to R.

• An R wrapper (R/*-interface.R, optional) — R6 classes providing a friendlier API around the external pointers.

• A demo script (examples/*/demo.R) — Runnable demonstration.

Testing variants

Use the Makefile targets below depending on the level of test coverage you want.

make test

Runs package tests after local compile. Fast default for day-to-day work.

make test-local

Runs testthat::test_local() from the source tree.

make test-installed

Installs with tests and runs testthat::test_package() against the installed package copy.