Github projects of

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 However, due to ongoing development, this version may be somewhat outdated.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.

• Generic GUI for rodeo-based 0-dimensional models; deprecated (2016-08-01)
• Some utilities for 1D diagenetic modeling

R-related material

Topics	Description
Sensitivity analysis	Analyzing the sensitivity of models with respect to input parameters is a common task. I wrote a minimalistic guide on that topic which is a reference for myself but also a kind of tutorial. The described methods are applicable to models implemented with rodeo, for example. You can help to improve the document by sending me feedback (bug reports, suggestions for simplification or extension).

Other software

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