R interface to TreeBASE

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My lightning talk at #ievobio 2011

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R interface to TreeBASE

  1. 1. Using Treebase from R Carl Boettiger, @cboettig UC Davis June 22, 2011Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 1/18
  2. 2. Informatics tools must reflect current research methodsCarl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 2/18
  3. 3. Thank youCarl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 3/18
  4. 4. Graduate StudentCarl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 4/18
  5. 5. Methods developerCarl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 5/18
  6. 6. TeacherCarl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 6/18
  7. 7. Bodega Phylogenetics Workshop http://bodegaphylo.wikispot.org/Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 7/18
  8. 8. Bodega Phylogenetics Workshop No informatics softwareCarl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 8/18
  9. 9. Bodega Phylogenetics Workshop almost no internetCarl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 9/18
  10. 10. Bodega Phylogenetics Workshop almost no internet (we’re fixing that)Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 9/18
  11. 11. Bodega Phylogenetics Workshop Students required to bring their own data.Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 10/18
  12. 12. Bodega Phylogenetics Workshop Students required to bring their own data. (we’re proud of that.)Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 10/18
  13. 13. Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 11/18
  14. 14. Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 12/18
  15. 15. Why?Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 13/18
  16. 16. Why? EducationCarl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 13/18
  17. 17. Why? Education Journal club that repeats analysesCarl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 13/18
  18. 18. Why? Education Journal club that repeats analyses Meta-AnalysesCarl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 13/18
  19. 19. Why? Education Journal club that repeats analyses Meta-Analyses that update themselvesCarl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 13/18
  20. 20. Why? Education Journal club that repeats analyses Meta-Analyses that update themselves Tools the community could run withCarl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 13/18
  21. 21. See new paper (i.e. Derryberry et al. 2011)Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 14/18
  22. 22. See new paper (i.e. Derryberry et al. 2011) Pull phylogeny into RCarl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 14/18
  23. 23. See new paper (i.e. Derryberry et al. 2011) Pull phylogeny into R Repeat analysis (diversification rate)Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 14/18
  24. 24. See new paper (i.e. Derryberry et al. 2011) Pull phylogeny into R Repeat analysis (diversification rate) Compare against newer methodsCarl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 14/18
  25. 25. See new paper (i.e. Derryberry et al. 2011) Pull phylogeny into R Repeat analysis (diversification rate) Compare against newer methods Compare against similar phylogeniesCarl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 14/18
  26. 26. See new paper (i.e. Derryberry et al. 2011) Pull phylogeny into R Repeat analysis (diversification rate) Compare against newer methods Compare against similar phylogenies search_treebase(’Derryberry’, ’author’)[[1]]->tree plot(tree); metadata(tree$S.id) yule2rate(branching.times(tree))Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 14/18
  27. 27. Into the hands of user/developer communityCarl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 15/18
  28. 28. Into the hands of user/developer community Scott Chamberlain @recologyCarl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 15/18
  29. 29. Now in the works Dryad API Mendeley, PLoS, Springer APIs EoL API ...Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 16/18
  30. 30. Thanks Collaborators Scott Chamberlain (Rice) Duncan Temple-Lang (UC Davis, R-project) Advice & Support Todd Vision, Rutger Vos, Bill Peil, Hilmar Lapp TreeBASE & Dryad developer lists Making it possible Peter Wainwright (interested mentor) Alan Hastings (advisor) CSGF (funding)Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 17/18
  31. 31. https://github.com/cboettig/treeBASECarl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 18/18

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