pkgbuild::has_build_tools(debug = TRUE)
#> Trying to compile a simple C file
#> Running /opt/R/4.4.2/lib/R/bin/R CMD SHLIB foo.c
#> using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
#> gcc -I"/opt/R/4.4.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c foo.c -o foo.o
#> gcc -shared -L/opt/R/4.4.2/lib/R/lib -L/usr/local/lib -o foo.so foo.o -L/opt/R/4.4.2/lib/R/lib -lR
#>
#> [1] TRUEOdin and Monty
Preface
This is a book about writing models in the odin “domain specific language” (DSL) and fitting these models to data using monty. These tools can be used entirely separately; you can create a dynamical model (or “system”) in odin and never fit it to data, or you can use monty to fit models that are written in plain R code. We’ll structure the book to cover the tools fairly separately at first, then describe their intersection. Along the way, you’ll also use dust, which powers odin, so we’ll spend some time describing how to use that, and also how to write models directly in dust if you need more control than odin provides.
History
Originally, we designed odin around describing and solving systems of differential equations, with a small amount of support for working with discrete-time stochastic systems. Over time, and particularly during the COVID-19 response, we expanded the stochastic support and introduced the ability to fit these models using particle filters and other sequential Monte Carlo algorithms. You may have used odin.dust and mcstate through this period. As of 2024 we have rationalised our tools into a new set of packages which are currently called odin2, dust2 and monty
Slide decks
Installation
You can install these packages in one go from our R-universe:
install.packages(
c("monty", "dust2", "odin2"),
repos = c("https://mrc-ide.r-universe.dev", "https://cloud.r-project.org"))You will also need a functioning C++ toolchain; you can test this by running
About this book
This book exists to supplement the package documentation, and we will try to link extensively to it. It is designed as a fairly friendly walk-through of the tools, and to mirror courses that we run.