User:Carl Boettiger/Notebook/Comparative Phylogenetics/2010/05/13

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Adaptive Dynamics

Public code hosting

  • Project code now available through Github.
  • Advantages to public hosting: Replication of adaptive dynamics simulations can be difficult, particularly in matching various nuisance parameters. While there is certainly much pedagogical value in individual researchers implementing their own simulations, verification and reproducibility of scientific results would be greatly facilitated by adapting an accepted open source code base and adding branches, etc. Researchers could much more immediately benefit from the work of their colleagues and spend more time implementing novel research and less reproducing it. Many eyes would ensure more robust, efficient and bug-free code.
  • Current code has a long way to come, particularly in terms of documentation.
  • The C-Matrix approach lacks the desired level of generality, though it does accelerate the calculations significantly compared to the straight forward implementation that would recalculate competition coefficients after each birth or death event instead of only after each mutation.
  • Motivation for public hosting partly comes partly from email request for the code from my fluctuation domains paper, in which a researcher pointed out the difficulty in replicating certain branching results.


  • Most work today in Stochastic Population Dynamics (second day of beetle workshop).
  • Migrated Firefox bookmarks to delicious. Should encourage me to bookmark more frequently, slowly entering the modern world here.
  • Enterprise 2.0 competition for enterprise solutions, have much in common with challenges in science. Wonder what we're already doing well vs what could be transfered from here.
  • Search history is an interesting source of statistics -- apparently I view 100-300 pages a day? Many are gmail/wiki/notebook pages, still.
  • Looked into website polling / voting schemes that can be added to websites, i.e. Facebook's like button and the digg button. A colleague was looking into ways to get students to rank the usefulness of various course content. Probably many other, possibly better solutions but an intriguing idea.