Thursday Meetings: Duncan; Alan

Duncan Meeting

  • ROAuth/RCurl question.  Mendeley is OAuth 1, github is OAuth 2 (simpler).  Both are implemented in pure R in another package, may be good.  OAuth 1 constructs complicated http urls with secret, and token, and random key, need to escape chars, etc.  OAuth 2 is https, just uses token.
  • Authentication options: Jeff’s ROAuth/Duncan’s mod, other OAuth package.
  • RMendeley– windows binary, competition?
  • socialR – discussed strategy to get a figure with matching code and data.  Tracing, codeDepends, defining syntax.
  • TreeBASE – iEvoBio lightning talk, data integration competition?  integrate 3 sources: TreeBASE, Dryad, Mendeley?  Github share scripts?
  • Dryad: Scott on board.

Alan Meeting

  • Finding requisite sampling density.
  • Switching to ROC curves?  Yup.  Include graphic illustrating how they are computed.
  • Rephrasing critique of what’s done: quantifying it’s performance vs understanding it’s performance (move latter to appendix).
  • Data/lit.

Coding and writing

  • Working on updating manuscript figures
  • MCMCMC routine on wrightscape example still manages to throw errors sometimes, not clear why.  more debugging.

Misc

Always takes me a moment to remember how to grab a deleted or changed file from an earlier commit to the repository, thought I better write it down.  Now tracking these useful bits under code-tricks (maybe should keep them as gists too?  If only gists could have tag structure, etc)

git checkout 81e8a9fac4a862ca097ae2ef693fbfe33a0970c5 roc_curve_ex.R

Reuse of phylogenetic info: Looking at MIAPA project (Leebens-Mack et. al. 2006), NSF ABI.  Wonder if the TreeBASE project (maybe with Dryad+Mendeley interfaces) can be turned into aiEvoBio challenge entry (deadline June 13!)

References

  • Leebens-Mack J, Vision T, Brenner E, Bowers J, Cannon S, Clement M, Cunningham C, DePamphilis C, DeSalle R, Doyle J, Eisen J, Gu X, Harshman J, Jansen R, Kellogg E, Koonin E, Mishler B, Philippe H, Pires J, Qiu Y, Rhee S, Sjölander K, Soltis D, Soltis P, Stevenson D, Wall K, Warnow T and Zmasek C (2006). “Taking The First Steps Towards A Standard For Reporting on Phylogenies: Minimum Information About A Phylogenetic Analysis (Miapa).” Omics: A Journal of Integrative Biology, 10. ISSN 1536-2310, https://dx.doi.org/10.1089/omi.2006.10.231.