odemodeling

R-package for building and fitting Bayesian ODE models in Stan. The package might still have some sharp corners but:

1. once you have learned how to use it, coding up new ODE models should be faster with it than raw Stan
2. once you have created a model with it, you can do the fitting using different ODE solvers (adaptive, non-adaptive) without needing to write new Stan code
3. once you have fitted a model with it, you can

• quickly visualize the ODE solutions without needing to extract them yourself
• quickly solve and visualize the ODE solutions using a different solver or at a different set of time points without needing to write new Stan code yourself
• quickly assess whether the solver used during fitting was accurate enough, or if you need to do the fitting again with a more accurate one (see https://arxiv.org/abs/2205.09059)

Installation

• Install cmdstanr following the instructions here.
• Install odemodeling using

remotes::install_github("jtimonen/odemodeling", ref = "main", build_vignettes = TRUE)

Building the vignette takes around one minute. You can skip it with build_vignettes = FALSE.

Getting started

If you built the vignette, you can view it using

browseVignettes("odemodeling")

It is also available online here. The vignette is perhaps the best place to start. More detailed info is in documentation, that you can view with

library(odemodeling)
?odemodeling