What is CaliFloPP?

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 flow between pairs of polygons using an integration algorithm.
The R-package RCALI is an interface between CaliFloPP and R. In addtion, it allows the treatment of anisotropic dispersal functions.

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. The application that motivated the development of CaliFloPP concerns gene flow between crop fields and their borders at landscape scale, which involves the dispersion of pollen and seed particles. Thus, CaliFloPP has allowed an extension to very general field shapes of Genesys, a model and software on the population dynamics of cultivated and feral oilseed rape in an agricultural landscape (Colbach et al., 2001). Since then, CaliFloPP has been used in other agro-ecological applications dealing with plant health or the coexistence between different types of agriculture.

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 by modifying C-programs. The parameters of the methods and the various options can be specified, either in a parameter-file, or via an interactive dialogue with the program. Default values are catered.
Output: The results are output on the screen (or standard output unit). The user can ask the creation of a result-file, in a format suitable for further analysis.

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 articles quoted in the presentation

• N. Colbach, and all. Genesys: a model of the influence of cropping system on gene escape from herbicide tolerant rapeseed crops to rape volunteers. II. Genetic exchanges among volunteer and cropped populations in a small region. Agriculture, Ecosystems and Environnement, 83:255--270, 2001.
• 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.

Articles and reports using CaliFloPP (selection)

• J. Papaix. Structure du paysage agricole et risque épidémique, une approche démo-génétique. Thèse de Doctorat, ABIES (UMR 1290 BIOGER, F-78850 Thiverval Grignon et UR 341 MIAJ, F-78352- Jouy-en-Josas), 2011.
• A. Baux, N. Colbach, D. Pellet (2011). Crop management for optimal low-linolenic rapeseed oil production-Field experiments and modelling. European Journal of Agronomy, 35, 144-153. [DOI|
• N. Colbach. (2009). How to model and simulate the effects of cropping systems on population dynamics and gene flow at the landscape level: example of oilseed rape volunteers and their role for co-existence of GM and non-GM crops. Environmental Science and Pollution Research, 16, 348-360. [DOI|
• Y. Tricault, R. Fealy, N. Colbach, E. Mullins (2011). Towards an optimal management regime to facilitate the coexistence of GM herbicide tolerant and non-GM oilseed rape. European Journal of Agronomy, 34, 26-34. [DOI|
• N. Colbach, C. Devaux, F. Angevin (2009). Comparative study of the efficiency of buffer zones and harvest discarding on gene flow containment in oilseed rape. A modelling approach. European Journal of Agronomy, 30, 187-198. [DOI| http]
• N. Colbach, H. Monod, C. Lavigne (2009). A simulation study of the medium-term effects of field patterns on cross-pollination rates in oilseed rape (Brassica napus L.). Ecological Modelling, 220, 662-672. [DOI| http]

 

Licence
CaliFloPP is an open source, freely available software released under the CeCILL Licence Version 2. Please, read the COPYING file.

Download
Download the last version.

OS Requirements
Installation of CaliFloPP needs a C++ compiler, and, optionally, for installation of the R-packages, the R system.

What's new
* 2012-01-19: What's new in CaliFloPP 3.3

Contact
Annie.Bouvier at inra.fr