RCALI: R package Calculation of the Integrated Flow of Particles between Polygons

RCALI R package for CALculation of the Integrated flow of particles between polygons

What is RCALI?

RCALI is a R package that makes interface between CaliFloPP and R.
CaliFloPP is a software that calculates flows of particles between pairs of polygons, when given a so-called individual dispersal function. The individual dispersal function describes the particle dispersion between pairs of points, and CaliFloPP deduces the total flows between pairs of polygons.
Moreover, RCALI allows to take into account the angle of the current point with the horizontal, and so, to analyze anisotropic dispersal function.

This package is developed in the MaIAGE Lab. of INRA - Jouy-en-Josas, France.

Some more details

The integration problem is solved by reducing the dimension of the integral and by using algorithms from computational geometry.

Two general methods for numerical integration are implemented:

a simple randomized discretization of the integral,
an two-dimensional adaptive cubature method.

The first method, denoted by grid method, involves simple discretizations of the integral based on regular grids. The approximation is an unbiased estimator of the integral. Furthermore, by using independent replicates, it is possible to assess the precision of the result. This method is quite robust (it is unbias and converges even for non-smooth integrands) but it is rather time consuming.
The second method is based on the algorithm DCUTRI. The approximation errors are estimated. Compared to the grid method, this method is very fast.

Input and output

Input: The user should provide the polygons coordinates in a text file. He can define his own individual dispersal functions in R or by customizing C-programs.
Output: The results are output on the screen (or standard output unit), and/or on a result-file.

References

Main reference paper

A. Bouvier, K. Kiêu, K. Adamczyk, and H. Monod. Computation of integrated flow of particles between polygons. Environmental Modelling & Software, 24:843--849, 2009. [DOI| http]

Other reference

J. Berntsen, T.O Espelid. DCUTRI: Algorithm 706, An algorithm for adaptive cubature over a collection of triangles. ACM Transactions on Mathematical Software, 18(3):329--342, 1992.

Licence
RCALI is an open source, freely available software released under the CeCILL-C Licence. Please, read the LICENSE file.

Requirements
R system, a C compiler, and the R-package splancs.

Documentation
An introduction and other documents are provided in the directory doc of the package.

Download
Download the last version here (uncompress the file before installation) or from the CRAN site.

What's new
* 2017-03-03: What's new in RCALI version 0.2-18

Contact
Annie.Bouvier at inra.fr