Parameter Space Partitioning MCMC for Global Model Evaluation (Pitt, Kim, Navarro & Myung, 2006).

CRAN page of psp

To cite package ‘psp’ in publications use:

Lenard Dome and Andy Wills (2021). psp: Parameter Space Partitioning MCMC for Global Model Evaluation. R package version 0.1. https://CRAN.R-project.org/package=psp

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {psp: Parameter Space Partitioning MCMC for Global Model Evaluation},
    author = {Lenard Dome and {Andy Wills}},
    year = {2023},
    note = {R package version 1.0.2},
    url = {https://CRAN.R-project.org/package=psp},
  }

Disclaimer

This package only recieves maintenance updates. It is not actively developed. If you would like to contribute, please contact me (@lenarddome).

Install

For the stable version

install.packages("psp")

For the developmental version:

devtools::install_github("lenarddome/psp")

About psp

• A short intro and manual
• A brief blog post

Philosophy

A big influence on this implementation is an instantiation of the Open Models Initiative, catlearn. Watch the talk of Andy Wills: “The OpenModels project” from Open Research Working Group (ORWG) virtual meeting 08/09/20.

The project's architecture is also influenced by DEoptim. DEoptim implements a Differential Evolutionary Optimization algorithm formodel-fitting.

We are completely open-source and free. Anyone can contribute. If you would like to raise an issue or contribute code, use Github, message or email me (@lenarddome).

Code Style

We use Google’s R Style Guide with some extra caveats:

• Do not use roxygen. Write your documentation from scratch as an Rdocumentation file. It is desirable to avoid writing test units for converting your comments to documentation.
• We have a 100 characters per line policy. You are still encouraged to keep line lengths to 80 characters, but sometimes going over 80 can be better than the alternative.
• Use TODO, FIXME, HACK, BUG, WARNING, NOTE comments for code that is temporary, a short-term solution, or good-enough but not perfect.
  • TODO comments must adhere to the following format: ## TODO: change this to use matrix operations.
• Use spaces!
  • Good practice: if (makeup == TRUE) list(variable = runif(100), id = rep(letters, 5)[1:100]).
  • Bad practice: if(makeup==TRUE) list(variable=runif(100),id=rep(letters,5)[1:100]).
• Do not number your files. File naming conventions are pretty straightforward:
  • Files are prefixed by their relation to groups of functions. For example, the prefix psp means that the file contains function relevant for the parameter space partitioning routines.
  • Files use camelCase.
  • File names must not contain spaces.
• Apply the same conventions to C++ code as well. While we do not militantly adhere to this, study Google's C++ Style Guide.