Skip to content

Latest commit

 

History

History
48 lines (38 loc) · 2.66 KB

README.md

File metadata and controls

48 lines (38 loc) · 2.66 KB

Species interaction models with Stan (and R)

This collection contains code for fitting common species interaction models using Hamiltonian Monte Carlo in Stan. It is intended as a learning resource, rather than flexible "production-ready" implementations. Expect that the code may contain errors and inefficiencies--use at your own risk!

Each model is contained in a sub-folder. The naming convention specifies each model as three components separated by underscores:

  • the interaction type (compet_* for competitive, conres_* for consumer-resource)
  • the time framework (*_disc_* for discrete, *_cont_* for continuous)
  • the common name of the model in the ecological literature

Each folder has a GitHub-viewable Markdown document (.md), the RMarkdown document (.Rmd) that generated it, and a stand-alone Stan file (.stan) containing the portable model source code. R is used to either generate or import example data and interfaces Stan via the cmdstanr package. The posterior distribution of the model parameters are presented, and when possible a meaningful calculation on the posterior parameters is performed (e.g., finding the posterior distribution of the equilibrium point).

Models available

Competition (compet_*)

  • Lotka-Volterra (discrete time)
  • Lotka-Volterra (continuous time)
  • Beverton-Holt
  • Leslie-Gower
  • Law-Watkinson
  • Ricker
  • Hassell

Consumer-Resource (conres_*)

  • Lotka-Volterra (discrete time)
  • Lotka-Volterra (continuous time)
  • Rosenzweig-MacArthur
  • Beverton-Holt
  • Leslie-Gower
  • Nicholson-Bailey
  • Arditi-Ginzburg
  • Yodzis-Innes
  • DeAngelis-Beddington
  • Wangersky-Cunningham

Similar resources

Stan ecology page: additional case studies, event materials, & collected peer-reviewed papers

Spatial models for plant neighborhood dynamics in Stan: a spatially-explicit competition model wherein competitors affect focals more when they are larger and closer

Ecology tag on Stan Discourse

Contributing

We welcome contributions to this example model base. Please use model_template.Rmd in the home directory to format your contribution. Please include the following in your pull request:

  • an RMarkdown source file
  • a rendered Markdown file with *_files subfolder (e.g., containing images of plots)
  • a stand-alone Stan file

We also welcome bug reports & ideas to make the models more efficient.

Please note our code of conduct for contributors.