Projects

msatsnippets

This site contains (often) full scripts/programs (command-line driven) used for the analysis of microsatellite data for population genetic studies. It also contains some python scripts for social data and home range analysis using ArcView. In most cases, all of these scripts were incorporated as ... [More] part of my dissertation, thus their storage here. I have put these here for 3 main purposes: So that others may use them w/o having to re-invent the wheel For review and refactoring by others For the purposes of archival Code bits (all in the Subversion Trunk at this site): Data Management convertGenepop.py (convert data to genepop format) convertR.py (convert data to R genetics format) merImport.py (import output from MER to database) pairwise coveyPairwiseFormatter.py (format data to pairwise relatedness/relationship format) queller QandGFormatter2.py (format data for queller and goodnight relatedness 5.0) Data Simulation genDataGen.py (microsatellite data generator, dirichlet and multinomial based) Group Membership coveyRetention.py (determine carryover for social groups across seasons) Home Range hValueEstimator.py (estimate LSCV h for a number of individuals - for computing avg. h) hrOverlap.py (ArcGIS script to determine home range overlap) Logistic Combinations logitCombos.py (compute combinations of parameters for logistic regression - INCOMPLETE) Random Selection errorSampling.py (randomly sample from a dbase table some individuals for genotype error testing) Relatedness QandG.py (permutation based, group relatedness testing) mleRelatedness.py (pairwise relatedness by group) mleRelationship.py (pairwise relationship by group) Social Mates social3Weeks.py (determine social mates from telemetry data 3 weeks prior to incubation) ocialSeason,py (determine social mates from telemetry data for entire breeding season) Timing Tests timeTest.py (some time tests i was doing for relatedness estimation) Per usual, I am not responsible for these working correctly or incorrectly (particularly given code in subversion branches). It is up to you to validate the code using your own data or eyeballs. That being said, I use these versions with my data. Take that as you will. ALL of this software is largely undocumented!!! I will get around, at some point, to making it more user friendly and prettier. I needed most of these quickly and had little time to spare on making things pretty. If you would like to use a particular bit of code, email me and i can help you out. The project owner name precedes @gmail.com. [Less]

dancelabs

The Dance Labs' mission is to explore human potential for expression, relatedness, and connection using experimental methods based on music & dance. Because the nature of our work is very methodical and engineered, we've decided to use modern code development paradigms and technology ... [More] to advance our mission. We feel the open source community will relate to what we do and bring sound principles to building a sustainable community. For more information, please visit: http://www.dancelabs.com [Less]