odin has grown from just one package to a series of
packages; this document aims to help orient you to the right place to
understand how pieces fit together and where to find help.
dustcontains an engine for running odin-style models in parallel. It supports both continuous time and discrete time models, but does not “know” anything about odin. This is the lower level support that many users will end up engaging with eventually.
odin.dustis a package for compiling
odinmodels to work with
dust. It will likely merge into
dustis on CRAN.
mcstateis a package for performing inference with
odinmodels compiled to work with
dust. It implements a particle filter, particle MCMC and other statistical methods.
odin: a brief summary of available functions in odin. This applies to both
odin.dustmodels, but with the conditions discussed in the porting guide
odincode: this applies to both
odin.dust: shows how to use
odin.dustto explore a stochastic SIR model, without doing inference on it
odin.dust: Differences between the original version of
odinand the subset of the DSL supported by
The documentation for
mcstate concerns mostly performing
pompusers, comparison of our particle filter with a Kalman filter.
The documentation for
dust is typically
more advanced, but will be useful at times for users of
dust: discusses what
dustmodels can do, and how they try to help you.
dustmodel (which you are unlikely to want to do) but also covers what
dustmodels can do, by example.
dustRNG in other packages and generating random numbers in highly-parallel situations.
Each package also comes with reference documentation, which contains examples and detailed help for individual functions.
In addition to the above, we are growing our ability to work with
odin models on the web, which you can see at
wodin: wodin itself
dopri-js: an ODE solver in TypeScript allowing smooth interpolation of its solutions
dfoptim: derivative-free optimisation methods for TypeScript
odin-js: TypeScript support for running continuous time
dust-js: An implementation of part of the
dustinterface in TypeScript
dustis on CRAN)
mcstateto make the inference part of the system nicer to work with; this will include an overhaul of the nested models.