r interface to treebase
DESCRIPTION
My lightning talk at #ievobio 2011TRANSCRIPT
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Using Treebase from R
Carl Boettiger, @cboettig
UC Davis
June 22, 2011
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 1/18
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Informatics tools must reflectcurrent research methods
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 2/18
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Thank you
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 3/18
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Graduate Student
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 4/18
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Methods developer
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 5/18
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Teacher
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 6/18
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Bodega Phylogenetics Workshop
http://bodegaphylo.wikispot.org/
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 7/18
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Bodega Phylogenetics Workshop
No informatics software
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 8/18
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Bodega Phylogenetics Workshop
almost no internet
(we’re fixing that)
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 9/18
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Bodega Phylogenetics Workshop
almost no internet (we’re fixing that)
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 9/18
![Page 11: R interface to TreeBASE](https://reader034.vdocuments.site/reader034/viewer/2022042713/5498446bac7959292e8b5585/html5/thumbnails/11.jpg)
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
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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
![Page 13: R interface to TreeBASE](https://reader034.vdocuments.site/reader034/viewer/2022042713/5498446bac7959292e8b5585/html5/thumbnails/13.jpg)
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 11/18
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Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 12/18
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Why?
Education Journal club that repeats analysesMeta-Analyses that update themselvesTools the community could run with
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 13/18
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Why?
Education
Journal club that repeats analysesMeta-Analyses that update themselvesTools the community could run with
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 13/18
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Why?
Education Journal club that repeats analyses
Meta-Analyses that update themselvesTools the community could run with
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 13/18
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Why?
Education Journal club that repeats analysesMeta-Analyses
that update themselvesTools the community could run with
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 13/18
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Why?
Education Journal club that repeats analysesMeta-Analyses that update themselves
Tools the community could run with
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 13/18
![Page 20: R interface to TreeBASE](https://reader034.vdocuments.site/reader034/viewer/2022042713/5498446bac7959292e8b5585/html5/thumbnails/20.jpg)
Why?
Education Journal club that repeats analysesMeta-Analyses that update themselvesTools the community could run with
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 13/18
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See new paper (i.e. Derryberry et al. 2011)
Pull phylogeny into RRepeat analysis (diversification rate)Compare against newer methodsCompare against similar phylogenies
search_treebase(’Derryberry’, ’author’)[[1]]->treeplot(tree); metadata(tree$S.id)yule2rate(branching.times(tree))
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 14/18
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See new paper (i.e. Derryberry et al. 2011)Pull phylogeny into R
Repeat analysis (diversification rate)Compare against newer methodsCompare against similar phylogenies
search_treebase(’Derryberry’, ’author’)[[1]]->treeplot(tree); metadata(tree$S.id)yule2rate(branching.times(tree))
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 14/18
![Page 23: R interface to TreeBASE](https://reader034.vdocuments.site/reader034/viewer/2022042713/5498446bac7959292e8b5585/html5/thumbnails/23.jpg)
See new paper (i.e. Derryberry et al. 2011)Pull phylogeny into RRepeat analysis (diversification rate)
Compare against newer methodsCompare against similar phylogenies
search_treebase(’Derryberry’, ’author’)[[1]]->treeplot(tree); metadata(tree$S.id)yule2rate(branching.times(tree))
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 14/18
![Page 24: R interface to TreeBASE](https://reader034.vdocuments.site/reader034/viewer/2022042713/5498446bac7959292e8b5585/html5/thumbnails/24.jpg)
See new paper (i.e. Derryberry et al. 2011)Pull phylogeny into RRepeat analysis (diversification rate)Compare against newer methods
Compare against similar phylogenies
search_treebase(’Derryberry’, ’author’)[[1]]->treeplot(tree); metadata(tree$S.id)yule2rate(branching.times(tree))
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 14/18
![Page 25: R interface to TreeBASE](https://reader034.vdocuments.site/reader034/viewer/2022042713/5498446bac7959292e8b5585/html5/thumbnails/25.jpg)
See new paper (i.e. Derryberry et al. 2011)Pull phylogeny into RRepeat analysis (diversification rate)Compare against newer methodsCompare against similar phylogenies
search_treebase(’Derryberry’, ’author’)[[1]]->treeplot(tree); metadata(tree$S.id)yule2rate(branching.times(tree))
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 14/18
![Page 26: R interface to TreeBASE](https://reader034.vdocuments.site/reader034/viewer/2022042713/5498446bac7959292e8b5585/html5/thumbnails/26.jpg)
See new paper (i.e. Derryberry et al. 2011)Pull phylogeny into RRepeat analysis (diversification rate)Compare against newer methodsCompare against similar phylogenies
search_treebase(’Derryberry’, ’author’)[[1]]->treeplot(tree); metadata(tree$S.id)yule2rate(branching.times(tree))
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 14/18
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Into the hands of user/developer community
Scott Chamberlain
@recology
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 15/18
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Into the hands of user/developer community
Scott Chamberlain
@recology
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 15/18
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Now in the works
Dryad APIMendeley, PLoS, Springer APIsEoL API. . .
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 16/18
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Thanks
CollaboratorsScott Chamberlain (Rice)Duncan Temple-Lang (UC Davis, R-project)
Advice & SupportTodd Vision, Rutger Vos, Bill Peil, Hilmar LappTreeBASE & Dryad developer lists
Making it possiblePeter Wainwright (interested mentor)Alan Hastings (advisor)CSGF (funding)
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 17/18
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https://github.com/cboettig/treeBASE
Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 18/18