Fast and simple iteration of stochastic models. Designed to work as a component of a particle filter.
Stochastic models appear in many domains as they are easy to write out, but hard to analyse without running many realisations of the process. dust provides a light interface to run models that are written in C++ in parallel from R. It provides very little functionality aside from a random number generator that is designed to be run in parallel, and is mostly interested in providing an interface, with which more powerful tools can be developed.
See vignette("dust") for instructions for using dust to create basic models. See the mcstate for a package that uses dust to implement a particle filter and particle MCMC.
As a (much) higher-level interface, the odin.dust provides a way of compiling stochastic odin models to work with dust.
To install dust:
# install.packages("drat") # -- if you don't have drat installed
drat:::add("ncov-ic")
install.packages("dust")You will need a compiler to install dependencies for the package, and to build any models with dust. dust uses pkgbuild to build its shared libraries so use pkgbuild::check_build_tools() to see if your system is ok to use.
The development version of the package can be installed directly from GitHub if you prefer with:
remotes::install_github("mrc-ide/dust", upgrade = FALSE)MIT © Imperial College of Science, Technology and Medicine