- Package: populationdynamics
- Title: An R package with tools to simulate various population dynamics models in ecology
- Version: 0.0-1
- Date: 2012-02-13
- Author: Carl Boettiger email@example.com
- Maintainer: Carl Boettiger firstname.lastname@example.org
- Description: Simulation tools, largely for individual based models using the Gillespie algorithm and fast C code.
- License: BSD
- URL: https://github.com/cboettig/populationdynamics
- BugReports: https://github.com/cboettig/populationdynamics/issues
- SystemRequirements: Gnu Scientific Library version >= 1.8
This package has been developed to house functions that I commonly use in my own research. It is not intended as a general-purpose toolbox and thus may not have the polish or robustness you might expect from an R package intended for the use of others, such as you find on CRAN.
These functions are provided as an R package only to provide a module for my own various research projects. Nonetheless, the package is licensed under permissive BSD license and you are more then welcome to adapt it as you will. The most successful reuse may involve extracting particular bits of code, such as the Gillespie C engine, to extend rather than installing the package whole-cloth.
Many functions in this toolbox make use of fast, parallelized (OpenMP) C code for improved performance of the exact, continuous time individual-based stochastic simulations using the Gillespie algorithm, including the generation of many replicate simulations. Unfortunately, this adds additional hurdles to installation and portability of the package.
Note that the package requires the GNU Scientific C Library be installed to run. The package will attempt to find and link the libary automatically using autoconf tools, though sometimes manual intervention is required. See R manuals on installing R packages with autoconf for more details. The package has been tested exclusively on Linux systems, including the high performance computing facility Carver operated by the NERSC supercomputing center in Berkeley.
One Mac user found it necessary to add a symbolic link to the appropriate C compiler to successfully install this package on Maverick. See https://github.com/cboettig/prosecutors-fallacy/issues/2#issue-27830362