Croizat is a free, user-friendly, cross-platform desktop software package which biologists can use to integrate and analyze spatial data on species or other taxa and to explore geographical patterns in diversity under a panbiogeographic and graph-theoretic approach.
Panbiogeography provides a method for analyzing the geographic structure of distributions in order to generate predictions about the evolution of species and other taxa in space and time. As of today, there is no standard, general-purpose software for the analysis of distributional data under a panbiogeographic approach. Croizat aims to solve that. It is based on the same database/analytical tools/map graphics model of many Geographic Information Systems (GIS). It does not have all the features and functions of a GIS, but this makes it much easier to use. Yet unlike GIS's, rather than concentrating on database and graphics flexibility, Croizat is designed to perform specialized biological analyses, many of which are not readily available from GIS's.
Additional features (as drawing of generalized tracks from the results of clique analysis and grid analysis for locating of main massings) will be included in future releases.
Croizat is written in Python, an interpreted, interactive, object-oriented programming language, coupled with the portable, multi-platform wxPython interface management library, and other free external libraries also written in Python and C/C++ (NetworkX, PIL, NumPy, Matplotlib and its Basemap module), as well as custom FORTRAN extensions. Therefore, the program is platform-independent, and runs without modifications on any PC compatible with the x86 architecture, under GNU/Linux, Mac OS X, and MS-Windows.
Click on the images to enlarge.
Croizat main screen (default view) under Ubuntu Linux
Croizat main screen (using NASA "Blue Marble" image as map background) under Ubuntu Linux
Croizat map parameters dialog under Microsoft Windows XP
Distribution of Zygodontomys rodents in northern South America represented as a track graph computed by Croizat (with satellite image background)
Croizat main screen under Mac OS X Tiger
Croizat taxon selection dialog under Mac OS X Tiger
Croizat main screen under Windows 7 RC
The Croizat distribution files come in either .tar.gz or .zip format. The .tar.gz format is most suitable for GNU/Linux and Mac OS X machines and the .zip format is most suitable for MS-Windows PCs.
To install the software, download and decompress the archive of the distribution corresponding to the target operating system. This procedure will create a directory (folder) called "Croizat" in which all the required files reside. To start Croizat under MS-Windows or Mac OS X, change to the program installation folder using Windows Explorer or Finder and double click on the file "Croizat.py". Under GNU/Linux, open a terminal window, change to the Croizat installation directory and type "python Croizat.py" (without quotes) on the command line.
In order to to run Croizat, a recent version (2.4 or higher) of the Python interpreter and the required external libraries (wxPython, PIL, NetworkX, NumPy, Matplotlib and its Basemap module) must be installed on the target computer. If Python is not already installed, a good option is to use the Enthought Python Distributon, which is free for academic use and includes everything needed to run Croizat.
It is highly recommended to install the latest version of the Basemap library (available from its SourceForge project page) in order to be able to use the program with full functionality.
For the GNU/Linux and MS-Windows versions, a computer with at least 256 MB of RAM, 200 MB hard disk space, and a mid-level Pentium processor or equivalent is recommended for running Croizat. Requirements for the Mac OS X version have not yet been determined. For analysis of large datasets, faster processors and more physical memory will be required for efficient computation.
The software is distributed as free software, under the GNU General Public License (GPL).
The online user's guide for Croizat is included in the distribution packages and also available here.
It is recommendable to join the Panbiog-L discussion list for discussions and exchanging questions about the software, as well as to get information about updates and bugs.
The correct citation suggested for Croizat in technical and scientific publications is as follows:
Cavalcanti, M.J. 2009. Croizat: a software package for quantitative analysis in Panbiogeography. Biogeografía 4: 4-6.
Scientific works which have used Croizat :
Moreira, G.R.P., Ferrari, A., Mondin, C. and Cervi, A. 2011. Panbiogeographical analysis of passion vines at their southern limit of distribution in the Neotropics. Revista Brasileira de Biociências 9: 28-40.
Previatelli, D. 2010. Phylogeny and biogeography of Neotropical Diaptominae. Unpublished PhD Thesis, Instituto Nacional de Pesquisas da Amazônia, Manaus. 204p.
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Many people have contributed to the development of Croizat: Brad McFall, Claudio Quezada, Douglas Riff, Eduardo Hajdu, Francisco Figueiredo, Gervásio Carvalho, Ian Henderson, John Grehan, José Maria Cardoso da Silva, Juan Morrone, Maria Lucia Lorini, Michael Heads, Renato Bernils, and Ronaldo Alperin (members of the original Croizat Review Panel) contributed knowledge and bug reports; Nicholas Matzke tested the Mac OS X version; Daniel Previatelli tested the MS-Windows 7 version; Jeffrey Whitaker, Scott Sinclair, John Hunter, Ryan May, Stef Mientki, and Aric Hagberg (members of the Matplotlib-users and NetworkX-discuss mailing lists) provided assistance and technical expertise. Special thanks to Robin Craw for encouragment and moral support. The development of Croizat was funded by a grant from Conservation International Brazil.
Mauro J. Cavalcanti
P.O. Box 46521
Rio de Janeiro, RJ, BRAZIL
Copyright © 2003-2011
Last updated October 28, 2011