Add Runge-Kutta temporal discretization schemes for r-deFBA

HannesBaukmann / pyrrrateFBA

Package for the analysis of (regulatory) deFBA models.

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Add Runge-Kutta temporal discretization schemes for r-deFBA #1

Open YannickDuport opened 1 year ago

YannickDuport commented 1 year ago

Currently, the only way to discretise the r-deFBA problem is by using the trapezoidal rule. However, several Runge-Kutta schemes are already implemented for deFBA. Add the option to use these schemes for r-deFBA as well.

YannickDuport commented 1 year ago

RK time discretization now works for r-deFBA. cp_rk_linprog() now also creates a vector f_bar_all and a matrix abarineq, containing regulatory constraints, that can be passed to sparse_mip_model_setup()

YannickDuport commented 1 year ago

Maybe someone should have a quick look at the implementation to make sure everything is correct. Several test runs indicate that it should work correctly.