The output of cvodes is a matrix with number of rows equal to the length of the time vector ( time_vec) and the number of columns being equal to length of ( y \(\times\) p + 1). The additional arguments in cvodes specify the senstivity calculation method to be used ( STG for STAGGERED or SIM for SIMULATENOUS) and flag for error control (either T or F). Currently, SIMULATENOUS and STAGGERED methods of sensitivity calculations from the SUNDIALS library are supported in this package.ĭf1 <- cvodes(time_vec, IC, ODE_R, params, reltol, abstol, "STG",F) # using R df2 <- cvodes(time_vec, IC, ODE_Rcpp, params, reltol, abstol, "STG",F) # using Rcpp I plan to provide in future, an ability to specify specific particular parameters for which sensitivity is desired. However, in the future versions I will provide an ability to specify user-defined Jacobian as well as user-defined sensitivity equations.Īlso, currently, forward sensitivities are calculated with respect to all parameters of the system. Here, I have only included the numerical interpolation version and currently the user cannot specify the sensitivity equations. \] In the original CVODES interface from SUNDIALS, the sensitivity equations can either be provided by the user or can be calculated using numerical interpolation by the solver.
#Ode system of equations solver code#
One of the advantage of using this package is that all the source code of the SUNDIALS library is bundled with the package itself, so it does not require the SUNDIALS library to be installed on the machine separately (which is sometimes non trivial on a Windows machine).Īs described in the link above, the problem is from chemical kinetics, and consists of the following three rate equations: Right now, this package serves as a test case for providing an interface to the SUNDIALS library for R users. In future, we plan to provide interface for the other solvers (i.e., IDA/IDAS and ARCODE in the library also.
Ida - An interface to the IDA function in SUNDIALS to solve a system of Differential-Algebraic Equations (DAEs).Ĭvsolve - A convenient interface to solve a system of ODEs with discontinuities in solution.
The four exported functions from the package are:Ĭvode - An interface to the CVODE function in SUNDIALS to solve a system of ODEs.Ĭvodes - An interface to the CVODES function in SUNDIALS to calculate forward sensitivites with respect to parameters of the ODE system. There are many good C libraries available to solve (i.e., integrate systems of ODEs) and SUNDIALS available from the Lawrence Livermore National Laboratory is a one of the most popular and well-respected C library for solving non-stiff and stiff systems of ODEs.Ĭurrently, this package provides an interface to the CVODE and CVODES function (serial version) in the library which is used to solve ODEs (or Initial Value Problems) and calculate sensitivities. Ordinary Differential Equations (ODEs) describe the rate of change of dependent variables with respect to a single independent variable and are used in many fields to model behavior of the system.
0 kommentar(er)
