Using Treebase from R

Carl Boettiger, @cboettig

UC Davis

June 22, 2011

Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 1/18

Informatics tools must reflectcurrent research methods

Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 2/18

Thank you

Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 3/18

Graduate Student

Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 4/18

Methods developer

Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 5/18

Teacher

Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 6/18

Bodega Phylogenetics Workshop

http://bodegaphylo.wikispot.org/

Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 7/18

Bodega Phylogenetics Workshop

No informatics software

Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 8/18

Bodega Phylogenetics Workshop

almost no internet

(we’re fixing that)

Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 9/18

Bodega Phylogenetics Workshop

almost no internet (we’re fixing that)

Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 9/18

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

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

Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 11/18

Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 12/18

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

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

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

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

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

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

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

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

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

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

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

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

Into the hands of user/developer community

Scott Chamberlain

@recology

Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 15/18

Into the hands of user/developer community

Scott Chamberlain

@recology

Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 15/18

Now in the works

Dryad APIMendeley, PLoS, Springer APIsEoL API. . .

Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 16/18

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

https://github.com/cboettig/treeBASE

Carl Boettiger, @cboettig, UC Davis Treebase, R, & Meta-Analyses 18/18