Green Creek Paradigms, LLC

      Schuyler, VA  22969  USA  

      Thomas Olivier, Ph.D. ( tom.olivier@alumni.duke.edu)


CRITTRZ Population Simulation Kit Home Page

CRITTRZ is a Python language library that supports construction of models of  demographic, genetic and infectious disease processes in animal populations subdivided by space or social groupings.  Development of CRITTRZ has been motivated particularly by an interest in processes in populations of Old World monkeys.  The library includes an interface to the Idrisi geographic information system (GIS).   CRITTRZ is designed for use by research biologists  and conservation biologists.  It is open-source software and can be downloaded freely.  The current release is a beta test release.  It  targets computers running Windows XP and Linux operating systems. 

The tenth version of CRITTRZ  ( Version 0.9.5 ) was released on 1-14-2011.  This latest release adds the ability to write to a file the distances between subpopulations in spatially structured simulations, a harness that allows a simulation series to be run in segments,  more detailed logging of modes of individual migration in Old World monkey models and transmission of mitochondrial DNA.  

Version 0.9.5 is the second beta release of  CRITTRZ.  Earlier versions are obsolete.  Release of version 1.0 is planned to take place during 2011..

Documentation:

            CRITTRZ.0.9.5.doc.pdf

Reports:

Oral presentation at the 2003 PyCon  Python language developers' conference.  Discusses purpose and initial design of CRITTRZ.  Appendices provide details of data structures employed, examples of code, input and output files.

Poster presented at the 2003 Society for Conservation Biology meetings.  Summarizes purpose, design of CRITTRZ and assumptions of model of cercopithecine monkey population.  Presents some analyses of  group fusions and fissions in simulated growing, declining and stable populations and simulated spread of sexually transmitted diseases.

Poster presented at the 2004 Society for Conservation Biology meetings.  Summarizes CRITTRZ system and cercopithecine multi-male population model.  Analyses genetic differentiation between social groups in simulated populations that are growing, declining and stable in size, with different group fusion and fission size thresholds.  Simulated populations are socially subdivided, but groups are not isolated by space.

Oral presentation at the 2005 Society for Conservation Biology meetings.  Reports on simulated effects of varied demographic conditions and depth of kinship reckoning on matriline numbers and genetic differentiation in cercopithecine multi-male social groups .  Examines genetic differentiation for entire groups, group natal segments, matrilines within groups and fission product groups. Simulated populations are socially subdivided, but groups are not isolated by space.

Oral presentation at the NKS 2006 Wolfram Science Conference.  Reviews rationale for use of simulations in primate population studies, issues presented by varied social group organizations in different monkey species,  precursors of CRITTRZ written in FORTH and C in 1980's, and CRITTRZ.

Oral presentation at the 2007 Virginia GIS Conference.  Explains CRITTRZ interface to the Idrisi GIS. Examples of CRITTRZ raster uses include group home ranges, cost of movement surfaces affecting migration, resources influencing survival and reproduction.  Simulations illustrate invasion of network and planar shaped habitats by monkey populations, infectious disease spread within and between sympatric monkey species.

Poster presented at the 2008 Society for Conservation Biology meetings.  Summarizes CRITTRZ system, GIS usage, cercopithecine multi-male population model.  Illustrates gene frequency surfaces generated in simulations of monkey populations occupying planar and Y-shaped habitats.

Poster presented at the 2010 Congress of the International Primatological Society.  Examines genetic differentiation in simulated populations composed of cercopithecine multi-male groups. Populations subjected to density-dependent size regulation, with some spatial isolation of groups.  Version posted here includes correction of title typo. 

Oral presentation at the 2011 meetings of the American Society of Primatologists.  Investigates genetic adaptation to disease at one autosomal locus in simulated populations composed of cercopithecine multi-male groups.  The genetic adaptation reduces disease effects in infected individuals. Considers associated demographic, social and disease prevalence changes.

Oral presentation at the 2012 Congress of the International Primatological Society.  Models adaptation to infectious disease in simulated populations composed of cercopithecine multi-male groups.  The genetic adaptation is by increased resistance to infection in uninfected individuals.  Considers associated demographic, social and disease prevalence changes. Many conditions in this study resemble those in the 2011 presentation to the American Society of Primatologists.  However, the mode of genetic adaptation differs.

Note that the discussions in the PyCon and 2003 SCB presentations refer to development versions of CRITTRZ as they existed at two points in  2003. Some architectural  features of Versions 0.7.0  onward are different.  

Download Information

CRITTRZ is available now in three distribution files.  CRITTRZ.0.9.5.Win.zip contains the new core system for installation on Windows computers.  CRITTRZ.0.9.5.WinIdr.zip contains the core system and modules that provide and use an interface to the Idrisi GIS ( sold by Clark Labs ) for Windows computers.  CRITTRZ.0.9.5.Lin.tar.gz contains the core system for installation on Linux computers.  

To download a distribution file, press on the link provided below:

CRITTRZ.0.9.5.Win.zip

CRITTRZ.0.9.5.WinIdr.zip

CRITTRZ.0.9.5.Lin.tar.gz

Distribution files include source code, documentation and sample applications.  These downloads also include a copy of  Python source code and documentation for rv Version 1.1, an open source random number generator developed by Ivan Frohne and used by CRITTRZ.  Downloads of some previous distributions of CRITTRZ are available at http://sourceforge.net/projects/crittrz.

Feedback

Comments on CRITTRZ  and bug reports are welcome by the author, Tom Olivier ( tom.olivier@alumni.duke.edu ).


Page updated 09-15-2012.          Green Creek Home