R package rodeo

Basic information

rodeo is an add-on package for the statistical computing software R. It facilitates the implementation of mechanistic models built on ordinary differential equations (ODE). Its heart is a code generator whose output (Fortran95+ or R) can be passed to numerical solvers, namely those from the packages deSolve and rootSolve.

The extended documentation (PDF) for the rodeo package describes basic functionality and contains many examples. A brief overview on the package’s objectives and concepts is given in this presentation (PDF). Interactive modeling examples some of which are implemented with rodeo are hosted at a dedicated server maintained by TU Dresden, Institute of Hydrobiology.

The latest version is available in the project’s source code repository. It can be installed as follows:

library('devtools')
install_github('dkneis/rodeo')

There is also a release version of rodeo on CRAN. However, due to ongoing development, this version may be somewhat outdated.

Demo examples

A set of demo examples is contained in the package vignette (see link above). The related data and scripts are shipped with the package (see folder rodeo/doc/examples after installation). To find the actual location of that folder, use

system.file("doc/examples",package="rodeo")

To run the examples, you need

  • the development version of the package (see above),

  • a recent version of R,

  • the developer tools to compile Fortran code.

Regarding the last point, I prepared a short PDF document with minimalistic instructions. In case of problems, please consult the official administration and installation guide, especially the appendices.

Other R packages

The following packages are not ‘officially’ released and they are not uploaded on CRAN. The links direct to the respective source code repositories.

Other software

  • The ECHSE framework for rapid development of hydrological model engines (implemented in C++).