SpaDES modules

This is the catalogue of SpaDES modules. It is a place to find pieces of model code that other people have already written, and a place to list your own so that others can find them.

👉 Browse the module list

The list is grouped by subject — forests, fire, carbon, wildlife, disturbance, climate data, and so on. Each entry gives the name of the people who wrote it and a link to its code.

Almost every module lives in its own GitHub repository, not in this one. You do not need to download anything from here.

New to SpaDES? Start here

• Robust and nimble scientific workflows, using SpaDES — the book. How to install R and the packages, how to set up your first project, and full worked examples you can copy and run.
• SpaDES.project — the package that builds a project for you: it fetches the modules you asked for, installs the R packages they need, and makes the folders.

How you use a module

You give setupProject() the GitHub locations of the modules you want. It gets them and everything they depend on, then you run them.

repos <- c("https://predictiveecology.r-universe.dev", getOption("repos"))
options(repos = repos)
if (!require("pak")) install.packages("pak")
pak::pak("SpaDES.project", ask = FALSE)

out <- SpaDES.project::setupProject(
  paths = list(projectPath = "~/myFirstProject"),
  modules = c(
    "PredictiveEcology/Biomass_speciesData@main",
    "PredictiveEcology/Biomass_borealDataPrep@main",
    "PredictiveEcology/Biomass_core@main"
  ),
  times = list(start = 2011, end = 2031)
)

simOut <- SpaDES.core::simInitAndSpades2(out)

Use any entry from the module list in modules. The part after @ is the branch, and you can leave it off. Some repositories hold several modules in folders, so you point at the folder:

modules = file.path("PredictiveEcology/scfm@development/modules",
                    c("scfmLandcoverInit", "scfmRegime", "scfmDriver",
                      "scfmIgnition", "scfmEscape", "scfmSpread"))

The book explains all of this in more detail: Setting up a project.

Writing your own module

The book walks through it, starting at Creating a new module. In short, SpaDES.core::newModule("myModule", path = "modules") writes the skeleton files for you, and you fill in the parts that do the work.

Adding your module to the list

Put your module in a public GitHub repository, then either

• edit the module list yourself (it is a wiki page, anyone can edit it), or
• open an issue telling us the repository name and what the module does.

What else is in this repository

A handful of small, old demonstration modules sit in modules/ (for example gameOfLife and LCC2005). They are kept for teaching and for historical reasons, and are no longer maintained. Anything you are likely to want for real work is in the module list.

Where to get help

• predictiveecology.org — news, projects, manuals, workshops
• SpaDES package documentation
• Ask a question or report a problem