R Hackathon 1/Teleconferences

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Revision as of 08:31, 17 November 2007 by Bco (talk) (1st Teleconference 11/16/2007)
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1st Teleconference 11/16/2007

Please note the planning steps page for additional information on specific items.


Note for participants: all of the items following the first two are topics posed for discussion, rather than decisions already made. We encourage you to voice any and all feedback, including that pursuing the topic is not desirable (if that is what you feel).

  1. Welcome, review of purpose and general objectives (TJV)
  2. Outline of planning schedule ahead (HL)
  3. Introductions (everyone)
  4. Priorities and subgroups (SK, BCO) (5mins)
  5. Preparations by participants (HL) (25mins)
    • Presentations
      • Lightning (< 5-10mins) talks - purpose(s), topics, and presenters
      • Needs for full-length (> 15min) talks?
      • Brainstorming current or future challenges - useful topics, presenters?
    • Bootcamps - purpose, needs, and presenters
    • Compiling package-specific information on the wiki - e.g., overview, relevant programming info, future goals
    • Tabulating metadata across packages (as started by Brian O'Meara) - methods, supported formats and analysis methods, visualization capabilities
    • Describing internal representation of data from test files in each package on the wiki
    • Reading list - suggestions (both for possible gaps and for recommended reading)
    • Other preparations we or others can facilitate or help with?
  6. Documentation & testing (SP, SK) (5mins)
    • R documentation and vignette writing - who has experience, and would be willing to help train the users? Examples to draw from?
    • Collection of data for testing and validation (such as tree files for testing)
  7. Source code repository (or repositories) (HL) (5mins)
    • Survey of current source code repository and versioning setup for participating packages
    • Assessing need for help with publicly accessible repository
    • Assessing need(s) for NESCent-run repository
    • Code branching needs
    • Other source code-related preparation needs
  8. IT logistics (HL)
    • Computers - will we need loaners?
    • Network access - will anyone need wired network?
    • File share needs
  9. Other homework? (5mins)
  10. Q & A (10mins)


Action Items:

    • begin work on crafting data standards: what do we want, what formats should we consider
    • convert test set of sample trees and datasets to internal representation for each package, summarizing info here.
    • write package overviews, including future goals
    • send help files for functions not already available here to Brian O'Meara
    • learn how to write documentation, including vignettes, for R. This may include learning LaTex, though there are various programs to make using this easier.
    • start emailing each other for discussions
    • misc.: investigate R->Java (Mesquite) process (see rJava); look into linking to CIPRES, perhaps inviting additional participants for this; start prioritizing which new methods to add; think about source code repositories (rforge? sourceforge? Google Code?) .