User:Carl Boettiger/Notebook/Comparative Phylogenetics

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New Approaches for Comparative Phylogenetics with Continuous Traits

This notebook continues in my new notebook instead of the calendar-linked wiki pages above. All new entries can be seen through the embedded frame above. The OWW notebook remains my archive on this topic from the beginning of February 2010 to October 20th, 2010. Many improved features, including nice handling of categories and tags, better search, clean rss feeds of posts, easy control over backups, support for mobile devices, and control over format and layout have led me to explore this change. The notebook remains open.

Abstract

Phylogenetically based comparative methods are an established and rapidly expanding area of research in macroevolution. Existing approaches may produce misleading results when the traits under consideration reflect different niche specialization across the taxa in question. I propose a method that addresses these difficulties and extends our ability to ask new questions using phylogenetic comparative data, such as the inferring number of niches represented in the data and rate of evolutionary transitions between niches.

Notes

  • If you're new to OpenWetWare Lab Notebooks, you can find my entries by clicking on the appropriate day on the calendar above. The first entry in this notebook starts on February 3rd, 2010. Of course you can also search the notebook.
  • This project is being conducted at the University of California, Davis, in collaboration with the Wainwright Lab. Professors Graham Coop, Brian Moore, Michael Turelli, and Dr. Peter Ralph to provide helpful guidance.
  • If you're interested in this work don't hesitate to contact me. Potential exists for collaborating on software development, software testing, or suggesting potential datasets for analysis, as well as general feedback on structure of the project and the notebook itself.

Recent commits to codes

Wrightscape

<xfeeds feedlimit="2"> http://github.com/cboettig/wrightscape/commits/master.atom </xfeeds>


Comparative-Phylogenetics

General methods for comparative phylogenetics, includes Monte Carlo likelihood ratio methods <xfeeds feedlimit="2"> http://github.com/cboettig/Comparative-Phylogenetics/commits/master.atom </xfeeds>

Project Idea Log

  • I've implemented a uservoice forum to record ideas for methods development in comparative phylogenetics. The feedback widget on the left edge of the screen allows me or others interested in this research to quickly submit or record an idea. Researchers can vote for ideas they'd most like to see, or add comments about implementation of any of the ideas through the forum. I can record progress around each idea in the forum. This organizes my research around the principle ideas and goals, which is a nice compliment to this lab notebook which provides the more detailed record of research organized in time.



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