7 Packaging odin models

So far, we have compiled odin code as we have needed it, using the odin() function. This works well for many uses, but has its limitations:

It requires that anyone who uses your code has a working C++ compiler; they will need to compile your model and load it into R to run things
Compilation of the model is quite slow; large models can take more than 10s to compile. We generally will only compile a system once per R session, but this is still quite a large fixed cost to pay
If you need to work with HPC systems, then your tasks all need to compile your code. This slows down tasks, but also means you need to take care that everyone writes to different places
We try to paper over this, but the models that we compile on-the-fly may not always play nicely with parallel frameworks (e.g., future)
As your model grows, you will accumulate a number of coupled support functions that go along with it, and a package is the easiest mechanism for supporting this
Packages are much easier for other people to use than standalone R scripts
There is nice tooling available to packages for configuring dependencies, tests and other automatic checks (see below).

library(odin2)

7.1 A basic package skeleton

Many tools exist to create packages; here we will use usethis, but there’s nothing magic here - you could create these files by hand if you prefer (see Writing R Extensions for the official guide on R packages if this is the approach you prefer).

path <- tempfile()
usethis::create_package(
  path,
  fields = list(Package = "pkg",
                Title = "My Odin Model",
                Description = "An example odin model"))
#> ✔ Creating '/tmp/RtmpzGtnYb/file1c652ed74a82/'.
#> ✔ Setting active project to "/tmp/RtmpzGtnYb/file1c652ed74a82".
#> ✔ Creating 'R/'.
#> ✔ Writing 'DESCRIPTION'.
#> Package: pkg
#> Title: My Odin Model
#> Version: 0.1.0
#> Authors@R (parsed):
#>     * An Author <a.author@example.com> [aut, cre]
#> Description: An example odin model
#> License: CC0
#> Encoding: UTF-8
#> Language: en-GB
#> Roxygen: list(markdown = TRUE)
#> RoxygenNote: 7.3.2
#> ✔ Writing 'NAMESPACE'.
#> ✔ Setting active project to "<no active project>".
usethis::proj_set(path)
#> ✔ Setting active project to "/tmp/RtmpzGtnYb/file1c652ed74a82".

Our package now contains:

fs::dir_tree(path)
#> /tmp/RtmpzGtnYb/file1c652ed74a82
#> ├── DESCRIPTION
#> ├── NAMESPACE
#> └── R

usethis has created some skeleton files for us. The DESCRIPTION contains:

Package: pkg
Title: My Odin Model
Version: 0.1.0
Authors@R: 
    person("An", "Author", , "a.author@example.com", role = c("aut", "cre"))
Description: An example odin model
License: CC0
Encoding: UTF-8
Language: en-GB
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2

and the NAMESPACE file contains

# Generated by roxygen2: do not edit by hand

7.2 Adding odin code

The odin code needs to go within this package in the inst/odin directory. Code saved as inst/odin/myname.R will create a generator called myname. Here, we create a file inst/odin/sir.R containing the SIR model from Chapter 1:

deriv(S) <- -beta * S * I / N
deriv(I) <- beta * S * I / N - gamma * I
deriv(R) <- gamma * I

initial(S) <- N - I0
initial(I) <- I0
initial(R) <- 0

N <- parameter(1000)
I0 <- parameter(10)
beta <- parameter(0.2)
gamma <- parameter(0.1)

We also need to make some changes to our package:

We need to include dust2 as an Imports dependency
We need to include dust2, monty and cpp11 as LinkingTo dependencies
We need to arrange our package so it loads the shared library that we build

If you run odin_package() before setting this up, it will error and indicate where the problem lies:

odin_package(path)
#> ℹ Found 1 odin code file in 'inst/odin'
#> ✔ Wrote 'inst/dust/sir.cpp'
#> Error:
#> ! Expected package 'dust2' as 'Imports' in DESCRIPTION

usethis::use_package("dust2", "Imports")
#> ✔ Adding dust2 to 'Imports' field in DESCRIPTION.
#> ☐ Refer to functions with `dust2::fun()`.
usethis::use_package("dust2", "LinkingTo")
#> ✔ Adding dust2 to 'LinkingTo' field in DESCRIPTION.
usethis::use_package("monty", "LinkingTo")
#> ✔ Adding monty to 'LinkingTo' field in DESCRIPTION.

Setting up to use cpp11 is a bit more involved because of the changes that we need to make to ensure that everything links together correctly; for details see the packaging section of the cpp11 “Getting started” vignette

usethis::use_package_doc()
#> ✔ Writing 'R/pkg-package.R'.
#> ☐ Run `devtools::document()` to update package-level documentation.
usethis::use_cpp11()
#> ✔ Creating 'src/'.
#> ✔ Adding "*.o", "*.so", and "*.dll" to 'src/.gitignore'.
#> ✔ Adding "@useDynLib pkg, .registration = TRUE" to 'R/pkg-package.R'.
#> ☐ Run `devtools::document()` to update 'NAMESPACE'.
#> ✔ Adding cpp11 to 'LinkingTo' field in DESCRIPTION.
#> ✔ Writing 'src/code.cpp'.
devtools::document(path)
#> ℹ Updating pkg documentation
#> Writing 'NAMESPACE'
#> ℹ Loading pkg
#> ℹ 1 functions decorated with [[cpp11::register]]
#> 
#> ✔ generated file 'cpp11.R'
#> 
#> ✔ generated file 'cpp11.cpp'
#> 
#> ℹ Re-compiling pkg (debug build)
#> ── R CMD INSTALL ───────────────────────────────────────────────────────────────
#> * installing *source* package ‘pkg’ ...
#> ** using staged installation
#> ** libs
#> using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
#> g++ -std=gnu++17 -I"/opt/R/4.4.2/lib/R/include" -DNDEBUG  -I'/home/runner/work/_temp/Library/cpp11/include' -I'/home/runner/work/_temp/Library/dust2/include' -I'/home/runner/work/_temp/Library/monty/include' -I/usr/local/include    -fpic  -g -O2  -UNDEBUG -Wall -pedantic -g -O0  -c code.cpp -o code.o
#> g++ -std=gnu++17 -I"/opt/R/4.4.2/lib/R/include" -DNDEBUG  -I'/home/runner/work/_temp/Library/cpp11/include' -I'/home/runner/work/_temp/Library/dust2/include' -I'/home/runner/work/_temp/Library/monty/include' -I/usr/local/include    -fpic  -g -O2  -UNDEBUG -Wall -pedantic -g -O0  -c cpp11.cpp -o cpp11.o
#> g++ -std=gnu++17 -shared -L/opt/R/4.4.2/lib/R/lib -L/usr/local/lib -o pkg.so code.o cpp11.o -L/opt/R/4.4.2/lib/R/lib -lR
#> installing to /tmp/RtmpzGtnYb/devtools_install_1c655f161ec1/00LOCK-file1c652ed74a82/00new/pkg/libs
#> ** checking absolute paths in shared objects and dynamic libraries
#> * DONE (pkg)
#> Writing 'pkg-package.Rd'
fs::file_delete(file.path(path, "src/code.cpp"))

We can now generate our odin code:

odin_package(path)
#> ℹ Found 1 odin code file in 'inst/odin'
#> ℹ 'inst/dust/sir.cpp' is up to date
#> ℹ Working in package 'pkg' at '/tmp/RtmpzGtnYb/file1c652ed74a82'
#> ℹ Found 1 system
#> ✔ Wrote 'src/sir.cpp'
#> ✔ Wrote 'R/dust.R'
#> ✔ Wrote 'src/Makevars'
#> ℹ 13 functions decorated with [[cpp11::register]]
#> ✔ generated file 'cpp11.R'
#> ✔ generated file 'cpp11.cpp'

The package now contains more files:

fs::dir_tree(path)
#> /tmp/RtmpzGtnYb/file1c652ed74a82
#> ├── DESCRIPTION
#> ├── NAMESPACE
#> ├── R
#> │   ├── cpp11.R
#> │   ├── dust.R
#> │   └── pkg-package.R
#> ├── inst
#> │   ├── dust
#> │   │   └── sir.cpp
#> │   └── odin
#> │       └── sir.R
#> ├── man
#> │   └── pkg-package.Rd
#> └── src
#>     ├── Makevars
#>     ├── code.o
#>     ├── cpp11.cpp
#>     ├── cpp11.o
#>     ├── pkg.so
#>     └── sir.cpp

Almost every new file here should not be edited directly (and all contain a line at the start to that effect).

Our DESCRIPTION now contains

Package: pkg
Title: My Odin Model
Version: 0.1.0
Authors@R: 
    person("An", "Author", , "a.author@example.com", role = c("aut", "cre"))
Description: An example odin model
License: CC0
Encoding: UTF-8
Language: en-GB
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Imports: 
    dust2
LinkingTo: 
    cpp11,
    dust2,
    monty

and NAMESPACE contains

# Generated by roxygen2: do not edit by hand

useDynLib(pkg, .registration = TRUE)

In R/:

cpp11.R is the glue code generated by cpp11
dust.R is glue code generated by dust2
pkg-package.R was generated by usethis::use_package_doc() and holds the special roxygen2 comments that caused devtools::document() to write our NAMESPACE file (you can edit this file!)

#' @keywords internal
"_PACKAGE"

## usethis namespace: start
#' @useDynLib pkg, .registration = TRUE
## usethis namespace: end
NULL

In inst/dust, sir.cpp contains the dust interface for our model (see the “Writing dust2 systems” vignette if you are curious)

In man/, pkg-package.Rd contains help files generated by roxygen2

In src/

Makevars contains code to allow OpenMP to work to parallelise the system
cpp11.cpp is glue code generated by cpp11
sir.cpp is the full system code generated by dust2
code.cpp was added by cpp11 and can be removed
The .o and .so (or .dll on Windows) files are generated by the compiler

7.3 Development of the package

Once your odin code is in a package, you will want to iterate over it. Previously you might have had scripts that you used source() on to load into the session. Now your workflow looks like:

Edit the odin code in inst/odin
Run odin_package()
Load the package with pkgload::load_all()

If you edit code in R/ you don’t need to run step 2, and running step 3 is enough.

pkgload::load_all(path)
#> ℹ Loading pkg
#> ℹ 13 functions decorated with [[cpp11::register]]
#> 
#> ✔ generated file 'cpp11.R'
#> 
#> ✔ generated file 'cpp11.cpp'
#> 
#> ℹ Re-compiling pkg (debug build)
#> ── R CMD INSTALL ───────────────────────────────────────────────────────────────
#> * installing *source* package ‘pkg’ ...
#> ** using staged installation
#> ** libs
#> using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
#> g++ -std=gnu++17 -I"/opt/R/4.4.2/lib/R/include" -DNDEBUG  -I'/home/runner/work/_temp/Library/cpp11/include' -I'/home/runner/work/_temp/Library/dust2/include' -I'/home/runner/work/_temp/Library/monty/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -UNDEBUG -Wall -pedantic -g -O0  -c cpp11.cpp -o cpp11.o
#> g++ -std=gnu++17 -I"/opt/R/4.4.2/lib/R/include" -DNDEBUG  -I'/home/runner/work/_temp/Library/cpp11/include' -I'/home/runner/work/_temp/Library/dust2/include' -I'/home/runner/work/_temp/Library/monty/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -UNDEBUG -Wall -pedantic -g -O0  -c sir.cpp -o sir.o
#> g++ -std=gnu++17 -shared -L/opt/R/4.4.2/lib/R/lib -L/usr/local/lib -o pkg.so cpp11.o sir.o -fopenmp -L/opt/R/4.4.2/lib/R/lib -lR
#> installing to /tmp/RtmpzGtnYb/devtools_install_1c6514a93627/00LOCK-file1c652ed74a82/00new/pkg/libs
#> ** checking absolute paths in shared objects and dynamic libraries
#> * DONE (pkg)

If you are using RStudio then Ctrl-Shift-l will load the package for you.

7.4 Next steps

Once you have a model in a package, then you are within the realms of normal R package development, and nothing here is specific to odin. However, if you are not familiar with package development we hope these tips will be useful.

A good place to look for information on package development is Hadley Wickham and Jenny Bryan’s “R packages” book, and to avoid repeating their material we’ll just link to it:

Create an RStudio project for your new package
Write some tests for your model and its support code. We’ll document some basic ideas for this later.
Create a git repository for your package and put it on GitHub. For more discussion see this chapter in “R packages”, and this guide on configuring R, RStudio and git to work well together.
Set up continuous integration so that your tests are run automatically when you make changes to your package
Put your package into an R universe to make it easy for others to install. Your organisation may already have one (for DIDE users, please see this repo), or you can start your own

This looks like a lot of work, but most of the setup here can be configured in a few lines. Writing tests is the only part that requires more than configuration, and that is something that you will tend to get better at over time.