@Misc{W3C_2014,
  url = {http://www.w3.org/TR/rdf-sparql-query/},
  title = {SPARQL Query Language for RDF},
  journal = {W3C},
  howpublished = {\url{http://www.w3.org/TR/rdf-sparql-query/}},
  author = {Eric Prud'hommeaux},
  archived = {http://greycite.knowledgeblog.org/?uri=http%3A%2F%2Fwww.w3.org%2FTR%2Frdf-sparql-query%2F},
  year = {2014},
}

@article{Parr2011,
abstract = {The accelerating growth of data and knowledge in evolutionary biology is indisputable. Despite this rapid progress, information remains scattered, poorly documented and in formats that impede discovery and integration. A grand challenge is the creation of a linked system of all evolutionary data, information and knowledge organized around Darwin's ever-growing Tree of Life. Such a system, accommodating topological disagreement where necessary, would consolidate taxon names, phenotypic and geographical distributional data across clades, and serve as an integrated community resource. The field of evolutionary informatics, reviewed here for the first time, has matured into a robust discipline that is developing the conceptual, infrastructure and community frameworks for meeting this grand challenge.},
author = {Parr, Cynthia S and Guralnick, Robert and Cellinese, Nico and Page, Roderic D M},
doi = {10.1016/j.tree.2011.11.001},
file = {:home/cboettig/Documents/Mendeley/Trends in ecology \& evolution/2011/Parr et al. - 2011 - Trends in ecology \& evolution.pdf:pdf},
issn = {0169-5347},
journal = {Trends in ecology \& evolution},
mendeley-groups = {Evolutionary Theory/Phylogenetic Methods},
month = dec,
number = {2},
pages = {94--103},
pmid = {22154516},
publisher = {Elsevier Ltd},
title = {{Evolutionary informatics: unifying knowledge about the diversity of life.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22154516},
volume = {27},
year = {2011}
}



@Article{Revell_2012,
  title = {phytools: An R package for phylogenetic comparative biology (and other things).},
  author = {Liam J. Revell},
  journal = {Methods in Ecology and Evolution},
  year = {2012},
  volume = {3},
  pages = {217-223},
}

@Book{Xie_2013,
  title = {Dynamic Documents with {R} and knitr},
  author = {Yihui Xie},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2013},
  note = {ISBN 978-1482203530},
  url = {http://yihui.name/knitr/},
}

@Article{Vos_2012,
  doi = {10.1093/sysbio/sys025},
  url = {http://dx.doi.org/10.1093/sysbio/sys025},
  year = {2012},
  month = {Feb},
  publisher = {Oxford University Press (OUP)},
  volume = {61},
  number = {4},
  pages = {675-689},
  author = {R. A. Vos and J. P. Balhoff and J. A. Caravas and M. T. Holder and H. Lapp and W. P. Maddison and P. E. Midford and A. Priyam and J. Sukumaran and X. Xia and A. Stoltzfus},
  title = {NeXML: Rich, Extensible, and Verifiable Representation of Comparative Data and Metadata},
  journal = {Systematic Biology},
}

@Article{Harmon_2008,
  title = {GEIGER: investigating evolutionary radiations},
  author = {LJ Harmon and JT Weir and CD Brock and RE Glor and W Challenger},
  journal = {Bioinformatics},
  year = {2008},
  volume = {24},
  pages = {129-131},
}

@Article{Rausher_2010,
  doi = {10.1111/j.1558-5646.2009.00940.x},
  url = {http://dx.doi.org/10.1111/j.1558-5646.2009.00940.x},
  year = {2010},
  month = {Mar},
  publisher = {Wiley-Blackwell},
  volume = {64},
  number = {3},
  pages = {603-604},
  author = {Mark D. Rausher and Mark A. McPeek and Allen J. Moore and Loren Rieseberg and Michael C. Whitlock},
  title = {Data Archiving},
  journal = {Evolution},
}

@Article{Boettiger_2012,
  doi = {10.1111/j.2041-210x.2012.00247.x},
  url = {http://dx.doi.org/10.1111/j.2041-210x.2012.00247.x},
  year = {2012},
  month = {Oct},
  publisher = {Wiley-Blackwell},
  volume = {3},
  number = {6},
  pages = {1060-1066},
  author = {Carl Boettiger and Duncan {Temple Lang}},
  editor = {Luke Harmon},
  title = {Treebase: an R package for discovery, access and manipulation of online phylogenies},
  journal = {Methods Ecol Evol},
}

@Manual{R,
  title = {R: A Language and Environment for Statistical Computing},
  author = {{R Core Team}},
  organization = {R Foundation for Statistical Computing},
  address = {Vienna, Austria},
  year = {2014},
  url = {http://www.R-project.org/},
}

@Manual{phylobase,
  title = {phylobase: Base package for phylogenetic structures and comparative data},
  author = {{NESCENT R Hackathon Team}},
  year = {2014},
  note = {R package version 0.6.8},
  url = {http://CRAN.R-project.org/package=phylobase},
}

@Article{Tenopir_2011,
  doi = {10.1371/journal.pone.0021101},
  url = {http://dx.doi.org/10.1371/journal.pone.0021101},
  year = {2011},
  month = {Jun},
  publisher = {Public Library of Science (PLoS)},
  volume = {6},
  number = {6},
  pages = {e21101},
  author = {Carol Tenopir and Suzie Allard and Kimberly Douglass and Arsev Umur Aydinoglu and Lei Wu and Eleanor Read and Maribeth Manoff and Mike Frame},
  editor = {Cameron Neylon},
  title = {Data Sharing by Scientists: Practices and Perceptions},
  journal = {PLoS ONE},
}

@Manual{Boettiger_2014,
  title = {knitcitations: Citations for knitr markdown files},
  author = {Carl Boettiger},
  note = {R package version 1.0-1},
  url = {https://github.com/cboettig/knitcitations},
  year = {2014},
}

@InCollection{Hartig_2012,
  doi = {10.1007/978-3-642-31753-8_56},
  url = {http://dx.doi.org/10.1007/978-3-642-31753-8_56},
  year = {2012},
  publisher = {Springer Science + Business Media},
  pages = {506-507},
  author = {Olaf Hartig},
  title = {An Introduction to SPARQL and Queries over Linked Data},
  booktitle = {Web Engineering},
}

@Article{Chamberlain_2013,
  doi = {10.12688/f1000research.2-191.v2},
  url = {http://dx.doi.org/10.12688/f1000research.2-191.v2},
  year = {2013},
  month = {Oct},
  publisher = {F1000 Research, Ltd.},
  author = {Scott A. Chamberlain and Eduard Sz{\"o}cs},
  title = {taxize: taxonomic search and retrieval in R},
  journal = {F1000Research},
}

@Article{Drew_2013,
  doi = {10.1371/journal.pbio.1001636},
  url = {http://dx.doi.org/10.1371/journal.pbio.1001636},
  year = {2013},
  month = {Sep},
  publisher = {Public Library of Science (PLoS)},
  volume = {11},
  number = {9},
  pages = {e1001636},
  author = {Bryan T. Drew and Romina Gazis and Patricia Cabezas and Kristen S. Swithers and Jiabin Deng and Roseana Rodriguez and Laura A. Katz and Keith A. Crandall and David S. Hibbett and Douglas E. Soltis},
  title = {Lost Branches on the Tree of Life},
  journal = {PLoS Biol},
}

@Article{Bollback_2006,
  doi = {10.1186/1471-2105-7-88},
  url = {http://dx.doi.org/10.1186/1471-2105-7-88},
  year = {2006},
  publisher = {Springer Science + Business Media},
  volume = {7},
  number = {1},
  pages = {88},
  author = {JonathanP Bollback},
  journal = {BMC Bioinformatics},
}

@Article{Cranston_2014,
  doi = {10.1371/currents.tol.bf01eff4a6b60ca4825c69293dc59645},
  url = {http://dx.doi.org/10.1371/currents.tol.bf01eff4a6b60ca4825c69293dc59645},
  year = {2014},
  publisher = {Public Library of Science (PLoS)},
  author = {Karen Cranston and Luke J. Harmon and Maureen A. O'Leary and Curtis Lisle},
  title = {Best Practices for Data Sharing in Phylogenetic Research},
  journal = {PLoS Curr},
}

@Article{Huelsenbeck_2003,
  doi = {10.1080/10635150390192780},
  url = {http://dx.doi.org/10.1080/10635150390192780},
  year = {2003},
  month = {Apr},
  publisher = {Oxford University Press (OUP)},
  volume = {52},
  number = {2},
  pages = {131-158},
  author = {John P. Huelsenbeck and Rasmus Nielsen and Jonathan P. Bollback},
  title = {Stochastic Mapping of Morphological Characters},
  journal = {Systematic Biology},
}

@Article{Stoltzfus_2012,
  doi = {10.1186/1756-0500-5-574},
  url = {http://dx.doi.org/10.1186/1756-0500-5-574},
  year = {2012},
  publisher = {Springer Science + Business Media},
  volume = {5},
  number = {1},
  pages = {574},
  author = {Arlin Stoltzfus and Brian O'Meara and Jamie Whitacre and Ross Mounce and Emily L Gillespie and Sudhir Kumar and Dan F Rosauer and Rutger A Vos},
  title = {Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis},
  journal = {BMC Research Notes},
}

@Article{Stodden_2014,
  doi = {10.2139/ssrn.1550193},
  url = {http://dx.doi.org/10.2139/ssrn.1550193},
  publisher = {Social Science Electronic Publishing},
  author = {Victoria Stodden},
  title = {The Scientific Method in Practice: Reproducibility in the Computational Sciences},
  journal = {SSRN Journal},
  year = {2014},
}

@Article{Paradis_2004,
  title = {{APE}: analyses of phylogenetics and evolution in {R} language},
  author = {E. Paradis and J. Claude and K. Strimmer},
  journal = {Bioinformatics},
  year = {2004},
  volume = {20},
  pages = {289-290},
}

@Misc{taskview,
  url = {http://cran.r-project.org/web/views/Phylogenetics.html},
  author = {Brian O'Meara},
  title = {CRAN Task View: Phylogenetics, Especially Comparative Methods},
  howpublished = {\url{http://cran.r-project.org/web/views/Phylogenetics.html}},
  archived = {http://greycite.knowledgeblog.org/?uri=http%3A%2F%2Fcran.r-project.org%2Fweb%2Fviews%2FPhylogenetics.html},
  year = {2014},
}


@ARTICLE{Maddison_1997,
  title    = "{NEXUS}: an extensible file format for systematic information",
  author   = "Maddison, D and Swofford, D and Maddison, W",
  journal  = "Syst. Biol.",
  volume   =  46,
  number   =  4,
  pages    = "590--621",
  month    =  dec,
  year     =  1997,
  url      = "http://www.ncbi.nlm.nih.gov/pubmed/11975335",
  keywords = "data standard",
  issn     = "1063-5157",
  pmid     = "11975335"
}

@INCOLLECTION{Piel_2002,
  title     = "{TreeBASE}: a database of phylogenetic information",
  booktitle = "The Interoperable ``Catalog of Life''",
  author    = "Piel, W H and Donoghue, M J and Sanderson, Michael J",
  editor    = "Shimura, J and Wilson, K L and Gordon, D",
  abstract  = "Phylogenetic systematics brings added value to the species lists
               and taxonomic inventories that form the groundwork of our
               understanding of biodiversity. But this added value is lost
               without a central database to store what we know about
               historical patterns and evolutionary relationships. TreeBASE was
               developed to harness this information and to provide a tool to
               study the evolution of biodiversity. Access to phylogenetic
               trees, and to the data underlying them, is needed for a wide
               variety of purposes, including comparative studies of
               morphological and molecular evolution, biogeography,
               coevolution, and studies of congruence of results based on
               different sources of evidence. Such data are also needed to
               monitor progress in phylogenetic research, to test new methods
               of analysis, and to address immediate practical problems in
               conservation of biodiversity. TreeBASE stores published
               phylogenetic trees, character and molecular data matrices,
               bibliographic information, and some details on taxa, characters,
               algorithms used, and analyses performed. The database is
               designed to be explored interactively and to allow retrieval and
               recombination of trees and data from different studies. TreeBASE
               therefore provides a means of assessing and synthesizing
               knowledge of phylogenetic information and biodiversity. The URL
               is: http://phylogeny.harvard.edu/treebase.",
  publisher = "National Institute for Environmental Studies",
  number    =  171,
  pages     = "41--47",
  series    = "Research Report",
  year      =  2002,
  url       = "http://donoghuelab.yale.edu/sites/default/files/124_piel_shimura02.pdf",
  address   = "Tsukuba, Japan"
}

@Manual{XML,
	title = {XML: Tools for parsing and generating XML within R and S-Plus.},
	author = {Duncan Temple Lang},
	year = {2013},
	note = {R package version 3.98-1.1},
	url = {http://CRAN.R-project.org/package=XML},
}

