@article{fisher2010,
abstract = {Property rights of shared scientific data are often analyzed by applying formal intellectual property law. However, the scales at which these laws apply are not necessarily relevant to data sharing practice among individuals (e.g., in virtual, social communities). Rather, the data sharing communities and their members often form their own policies, practices and norms governing data sharing. Using common property theory, our research objectives were to determine: (1) parallels between data sharing communities and natural resource-sharing communities; (2) factors that lead to successful data sharing; (3) circumstances under which rules, laws and policies govern data sharing. We used cases from two emerging data sharing communities in the environmental sciencesa micrometeorology community (FLUXNET) and a satellite remote sensing community. Cases of data sharing without conflict or irresolvable disputes had more principles in common with a successfully managed natural resource commons than did those characterized by conflict. Successful data sharing requires that biophysical scientists be more attentive to the social nature of data sharing.},
author = {Fisher, Joshua B and Fortmann, Louise},
doi = {10.1016/j.im.2010.04.001},
file = {:home/cboettig/Documents/Mendeley/Fisher, Fortmann - 2010 - Information \& Management.pdf:pdf},
issn = {03787206},
journal = {Information \& Management},
keywords = {common pool resources,data-citation},
mendeley-tags = {data-citation},
month = may,
number = {4},
pages = {237--245},
publisher = {Elsevier B.V.},
title = {{Governing the data commons: Policy, practice, and the advancement of science}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0378720610000376},
volume = {47},
year = {2010}
}
@article{markcostello2009,
abstract = {Despite policies and calls for scientists to make data available, this is not happening for most environmental- and biodiversity-related data because scientists' concerns about these efforts have not been answered and initiatives to motivate scientists to comply have been inadequate. Many of the issues regarding data availability can be addressed if the principles of ``publication'' rather than ``sharing'' are applied. However, online data publication systems also need to develop mechanisms for data citation and indices of data access comparable to those for citation systems in print journals.},
author = {Costello, Mark J},
doi = {10.1525/bio.2009.59.5.9},
file = {:home/cboettig/Documents/Mendeley/Costello - 2009 - BioScience(2).pdf:pdf},
isbn = {0006356815253244},
issn = {0006-3568},
journal = {BioScience},
month = may,
number = {5},
pages = {418--427},
publisher = {American Institute of Biological Sciences},
title = {{Motivating Online Publication of Data}},
url = {http://caliber.ucpress.net/doi/abs/10.1525/bio.2009.59.5.9 http://www.jstor.org/stable/25502450},
volume = {59},
year = {2009}
}
@Article{	  alfaro2009a,
  abstract	= {The uneven distribution of species richness is a
		  fundamental and unexplained pattern of vertebrate
		  biodiversity. Although species richness in groups like
		  mammals, birds, or teleost fishes is often attributed to
		  accelerated cladogenesis, we lack a quantitative conceptual
		  framework for identifying and comparing the exceptional
		  changes of tempo in vertebrate evolutionary history. We
		  develop MEDUSA, a stepwise approach based upon the Akaike
		  information criterion for detecting multiple shifts in
		  birth and death rates on an incompletely resolved
		  phylogeny. We apply MEDUSA incompletely to a diversity tree
		  summarizing both evolutionary relationships and species
		  richness of 44 major clades of jawed vertebrates. We
		  identify 9 major changes in the tempo of gnathostome
		  diversification; the most significant of these lies at the
		  base of a clade that includes most of the coral-reef
		  associated fishes as well as cichlids and perches. Rate
		  increases also underlie several well recognized tetrapod
		  radiations, including most modern birds, lizards and
		  snakes, ostariophysan fishes, and most eutherian mammals.
		  In addition, we find that large sections of the vertebrate
		  tree exhibit nearly equal rates of origination and
		  extinction, providing some of the first evidence from
		  molecular data for the importance of faunal turnover in
		  shaping biodiversity. Together, these results reveal living
		  vertebrate biodiversity to be the product of volatile
		  turnover punctuated by 6 accelerations responsible for
		  >85\% of all species as well as 3 slowdowns that have
		  produced "living fossils." In addition, by revealing the
		  timing of the exceptional pulses of vertebrate
		  diversification as well as the clades that experience them,
		  our diversity tree provides a framework for evaluating
		  particular causal hypotheses of vertebrate radiations.},
  annote	= {Medusa paper},
  author	= {Alfaro, Michael E and Santini, Francesco and Brock, Chad D
		  and Alamillo, Hugo and Dornburg, Alex and Rabosky, Daniel L
		  and Carnevale, Giorgio and Harmon, Luke J},
  doi		= {10.1073/pnas.0811087106},
  file		= {:home/cboettig/Documents/Mendeley//Alfaro et al. - 2009 -
		  Proceedings of the National Academy of
		  Sciences.pdf:pdf;:home/cboettig/Documents/Mendeley/Alfaro
		  et al. - 2009 - Proceedings of the National Academy of
		  Sciences(2).pdf:pdf},
  issn		= {1091-6490},
  journal	= {Proceedings of the National Academy of Sciences},
  keywords	= {Animals,Biodiversity,Biological Evolution,Diversification
		  Rates,Jaw,Jaw: anatomy \& histology,Likelihood
		  Functions,Phylogeny,Vertebrates,Vertebrates:
		  genetics,medusa},
  mendeley-tags	= {Diversification Rates,medusa},
  month		= aug,
  number	= {32},
  pages		= {13410--14},
  pmid		= {19633192},
  title		= {{Nine exceptional radiations plus high turnover explain
		  species diversity in jawed vertebrates.}},
  url		= {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2715324\&tool=pmcentrez\&rendertype=abstract}
		  ,
  volume	= {106},
  year		= {2009}
}

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

@InCollection{	  bellwood2002,
  address	= {San Diego},
  author	= {Bellwood, D. R. and Wainwright, Peter C},
  booktitle	= {Coral Reef Fishes. Dynamics and diversity in a complex
		  ecosystem},
  editor	= {Sale, P. F.},
  file		= {:home/cboettig/Documents/Mendeley/Bellwood, Wainwright -
		  2002 - Coral Reef Fishes. Dynamics and diversity in a
		  complex ecosystem.pdf:pdf},
  pages		= {5--32},
  publisher	= {Academic Press},
  title		= {{The history and biogeography of fishes on coral reefs}},
  year		= {2002}
}

@Article{	  felsenstein1985,
  author	= {Felsenstein, Joseph},
  doi		= {10.1086/284325},
  file		= {:home/cboettig/Documents/Mendeley//Felsenstein - 1985 -
		  The American Naturalist.pdf:pdf},
  issn		= {0003-0147},
  journal	= {The American Naturalist},
  keywords	= {evolution,phylogenetics},
  mendeley-tags	= {evolution,phylogenetics},
  month		= jan,
  number	= {1},
  pages		= {1--15},
  publisher	= {UChicago Press},
  title		= {{Phylogenies and the Comparative Method}},
  url		= {http://www.journals.uchicago.edu/doi/abs/10.1086/284325},
  volume	= {125},
  year		= {1985}
}

@Misc{		  fishbase2012,
  author	= {Froese, R. and Pauly, Daniel},
  publisher	= {World Wide Web electronic publication.},
  title		= {{FishBase}},
  url		= {www.fishbase.org},
  year		= {2012}
}

@Book{		  friedl2006,
  abstract	= {Regular expressions are an extremely powerful tool for
		  manipulating text and data. They are now standard features
		  in a wide range of languages and popular tools, including
		  Perl, Python, Ruby, Java, VB.NET and C\# (and any language
		  using the .NET Framework), PHP, and MySQL. If you don't use
		  regular expressions yet, you will discover in this book a
		  whole new world of mastery over your data. If you already
		  use them, you'll appreciate this book's unprecedented
		  detail and breadth of coverage. If you think you know all
		  you need to know about regular expressions, this book is a
		  stunning eye-opener. As this book shows, a command of
		  regular expressions is an invaluable skill. Regular
		  expressions allow you to code complex and subtle text
		  processing that you never imagined could be automated.
		  Regular expressions can save you time and aggravation. They
		  can be used to craft elegant solutions to a wide range of
		  problems. Once you've mastered regular expressions, they'll
		  become an invaluable part of your toolkit. You will wonder
		  how you ever got by without them. Yet despite their wide
		  availability, flexibility, and unparalleled power, regular
		  expressions are frequently underutilized. Yet what is power
		  in the hands of an expert can be fraught with peril for the
		  unwary. Mastering Regular Expressionswill help you navigate
		  the minefield to becoming an expert and help you optimize
		  your use of regular expressions. Mastering Regular
		  Expressions, Third Edition, now includes a full chapter
		  devoted to PHP and its powerful and expressive suite of
		  regular expression functions, in addition to enhanced PHP
		  coverage in the central "core" chapters. Furthermore, this
		  edition has been updated throughout to reflect advances in
		  other languages, including expanded in-depth coverage of
		  Sun's java.util.regexpackage, which has emerged as the
		  standard Java regex implementation.Topics include: A
		  comparison of features among different versions of many
		  languages and tools How the regular expression engine works
		  Optimization (major savings available here!) Matching just
		  what you want, but not what you don't want Sections and
		  chapters on individual languages Written in the lucid,
		  entertaining tone that makes a complex, dry topic become
		  crystal-clear to programmers, and sprinkled with solutions
		  to complex real-world problems, Mastering Regular
		  Expressions, Third Edition offers a wealth information that
		  you can put to immediate use. Reviews of this new edition
		  and the second edition: "There isn't a better (or more
		  useful) book available on regular expressions." --Zak
		  Greant, Managing Director, eZ Systems "A real tour-de-force
		  of a book which not only covers the mechanics of regexes in
		  extraordinary detail but also talks about efficiency and
		  the use of regexes in Perl, Java, and .NET...If you use
		  regular expressions as part of your professional work (even
		  if you already have a good book on whatever language you're
		  programming in) I would strongly recommend this book to
		  you." --Dr. Chris Brown, Linux Format "The author does an
		  outstanding job leading the reader from regex novice to
		  master. The book is extremely easy to read and chock full
		  of useful and relevant examples...Regular expressions are
		  valuable tools that every developer should have in their
		  toolbox. Mastering Regular Expressionsis the definitive
		  guide to the subject, and an outstanding resource that
		  belongs on every programmer's bookshelf. Ten out of Ten
		  Horseshoes." --Jason Menard, Java Ranch},
  author	= {Friedl, Jeffrey E. F.},
  isbn		= {0596528124},
  publisher	= {O'Reilly Media, Inc.},
  title		= {{Mastering regular expressions}},
  url		= {http://books.google.com/books?id=NYEX-Q9evKoC\&pgis=1},
  year		= {2006}
}

@Manual{	  geiger,
  annote	= {R package version 1.3-2},
  author	= {Harmon, Luke and Weir, Jason and Brock, Chad and Glor,
		  Rich and Challenger, Wendell and Hunt, Gene},
  title		= {{geiger: Analysis of evolutionary diversification}},
  url		= {http://cran.r-project.org/package=geiger},
  year		= {2009}
}

@Book{		  ggplot2,
  author	= {Wickham, Hadley},
  isbn		= {978-0-387-98140-6},
  publisher	= {Springer New York},
  title		= {ggplot2: elegant graphics for data analysis},
  url		= {http://had.co.nz/ggplot2/book},
  year		= {2009}
}

@Article{	  hanson2011,
  author	= {Hanson, Brooks and Sugden, Andrew and Alberts, Bruce},
  doi		= {10.1126/science.1203354},
  file		= {:home/cboettig/Documents/Mendeley//Hanson, Sugden, Alberts
		  - 2011 - Science (New York, N.Y.).pdf:pdf},
  issn		= {1095-9203},
  journal	= {Science (New York, N.Y.)},
  month		= feb,
  number	= {6018},
  pages		= {649},
  pmid		= {21310971},
  title		= {{Making data maximally available.}},
  url		= {http://www.ncbi.nlm.nih.gov/pubmed/21310971},
  volume	= {331},
  year		= {2011}
}

@Article{	  jones2006,
  author	= {Jones, Matthew B. and Schildhauer, Mark P. and Reichman,
		  O.J. and Bowers, Shawn},
  doi		= {10.1146/annurev.ecolsys.37.091305.110031},
  file		= {:home/cboettig/Documents/Mendeley//Jones et al. - 2006 -
		  Annual Review of Ecology, Evolution, and
		  Systematics.pdf:pdf},
  issn		= {1543-592X},
  journal	= {Annual Review of Ecology, Evolution, and Systematics},
  keywords	= {data integration,data
		  sharing,ecoinformatics,metadata,ontology,scientific
		  workflows,semantics},
  mendeley-tags	= {ecoinformatics},
  month		= dec,
  number	= {1},
  pages		= {519--544},
  title		= {{The New Bioinformatics: Integrating Ecological Data from
		  the Gene to the Biosphere}},
  url		= {http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.ecolsys.37.091305.110031}
		  ,
  volume	= {37},
  year		= {2006}
}

@Article{	  kneib2007,
  author	= {Kneib, Thomas},
  file		= {:home/cboettig/Documents/Mendeley/Kneib - 2007 - Journal
		  of Statistical Software.pdf:pdf},
  journal	= {Journal of Statistical Software},
  keywords	= {ecological modelling,ecology,r,statistical computation},
  number	= {1},
  pages		= {1--7},
  title		= {{Introduction to the Special Volume on 'Ecology and
		  Ecological Modelling in R'}},
  url		= {http://www.jstatsoft.org/v22/i01/paper},
  volume	= {22},
  year		= {2007}
}

@Manual{	  knitr,
  annote	= {R package version 0.4.2},
  author	= {Xie, Yihui},
  title		= {{knitr: A general-purpose package for dynamic report
		  generation in R}},
  url		= {http://yihui.name/knitr/},
  year		= {2012}
}

@Article{	  merali2010,
  author	= {Merali, Zeeya},
  file		= {:home/cboettig/Documents/Mendeley/Merali - 2010 -
		  Nature.pdf:pdf},
  journal	= {Nature},
  pages		= {6--8},
  title		= {{Why Scientific programming does not compute}},
  year		= {2010}
}

@Article{	  michener2012,
  author	= {Michener, William K. and Jones, Matthew B.},
  doi		= {10.1016/j.tree.2011.11.016},
  file		= {:home/cboettig/Documents/Mendeley/Michener, Jones - 2012 -
		  Trends in Ecology \& Evolution.pdf:pdf},
  issn		= {01695347},
  journal	= {Trends in Ecology \& Evolution},
  keywords	= {open science},
  mendeley-tags	= {open science},
  month		= jan,
  number	= {2},
  pages		= {85--93},
  publisher	= {Elsevier Ltd},
  title		= {{Ecoinformatics: supporting ecology as a data-intensive
		  science}},
  url		= {http://linkinghub.elsevier.com/retrieve/pii/S0169534711003399}
		  ,
  volume	= {27},
  year		= {2012}
}

@Article{	  parr2011a,
  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/Parr et al. - 2011 -
		  Trends in ecology \& evolution.pdf:pdf},
  issn		= {0169-5347},
  journal	= {Trends in ecology \& evolution},
  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{	  peng2011b,
  author	= {Peng, R. D.},
  doi		= {10.1126/science.1213847},
  file		= {:home/cboettig/Documents/Mendeley/Peng - 2011 -
		  Science.pdf:pdf},
  issn		= {0036-8075},
  journal	= {Science},
  month		= dec,
  number	= {6060},
  pages		= {1226--1227},
  title		= {{Reproducible Research in Computational Science}},
  url		= {http://www.sciencemag.org/cgi/doi/10.1126/science.1213847}
		  ,
  volume	= {334},
  year		= {2011}
}

@Manual{	  rcurl,
  annote	= {R package version 1.91-1},
  author	= {Lang, Duncan Temple},
  title		= {{RCurl: General network (HTTP/FTP/...) client interface
		  for R}},
  url		= {http://cran.r-project.org/package=RCurl},
  year		= {2012}
}

@Article{	  reichman2011,
  abstract	= {Ecology is a synthetic discipline benefiting from open
		  access to data from the earth, life, and social sciences.
		  Technological challenges exist, however, due to the
		  dispersed and heterogeneous nature of these data.
		  Standardization of methods and development of robust
		  metadata can increase data access but are not sufficient.
		  Reproducibility of analyses is also important, and
		  executable workflows are addressing this issue by capturing
		  data provenance. Sociological challenges, including
		  inadequate rewards for sharing data, must also be resolved.
		  The establishment of well-curated, federated data
		  repositories will provide a means to preserve data while
		  promoting attribution and acknowledgement of its use.},
  author	= {Reichman, O J and Jones, Matthew B. and Schildhauer, Mark
		  P.},
  doi		= {10.1126/science.1197962},
  file		= {::},
  issn		= {0036-8075},
  journal	= {Science},
  keywords	= {Access to Information,Data
		  Collection,Databases,Ecology,Factual,Information
		  Dissemination,Information Management,Information Storage
		  and Retrieval,Information Systems,Internet},
  month		= feb,
  number	= {6018},
  pages		= {703--705},
  pmid		= {21311007},
  title		= {{Challenges and Opportunities of Open Data in Ecology}},
  url		= {http://www.sciencemag.org/cgi/doi/10.1126/science.1197962
		  http://www.ncbi.nlm.nih.gov/pubmed/21311007},
  volume	= {331},
  year		= {2011}
}

@Misc{		  rteam2012,
  address	= {Vienna, Austria},
  author	= {{R Development Core Team}, The},
  publisher	= {R Foundation for Statistical Computing},
  title		= {{R: A language and environment for statistical
		  computing.}},
  url		= {http://www.r-project.org/},
  year		= {2012}
}

@Article{	  westneat2005,
  abstract	= {The family Labridae (including scarines and odacines)
		  contains 82 genera and about 600 species of fishes that
		  inhabit coastal and continental shelf waters in tropical
		  and temperate oceans throughout the world. The Labridae
		  (the wrasses) is the fifth largest fish family and second
		  largest marine fish family, and is one of the most
		  morphologically and ecologically diversified families of
		  fishes in size, shape, and color. Labrid phylogeny is a
		  long-standing problem in ichthyology that is part of the
		  larger question of relationships within the suborder
		  Labroidei. A phylogenetic analysis of labrids was conducted
		  to investigate relationships among the six classical tribes
		  of wrasses, the affinities of the wrasses to the
		  parrotfishes (scarines), and the broad phylogenetic
		  structure among labrid genera. Four gene fragments were
		  sequenced from 98 fish species, including 84 labrid fishes
		  and 14 outgroup taxa. Taxa were chosen from all major
		  labrid clades and most major global ocean regions where
		  labrid fishes exist, as well as cichlid, pomacentrid, and
		  embiotocid outgroups. From the mitochondrial genome we
		  sequenced portions of 12S rRNA (1000 bp) and 16S rRNA (585
		  bp), which were aligned by using a secondary structure
		  model. From the nuclear genome, we sequenced part of the
		  protein-coding genes RAG2 (846 bp) and Tmo4C4 (541 bp).
		  Maximum likelihood, maximum parsimony, and Bayesian
		  analyses on the resulting 2972 bp of DNA sequence produced
		  similar topologies that confirm the monophyly of a family
		  Labridae that includes the parrotfishes and butterfishes
		  and strong support for many previously identified taxonomic
		  subgroups. The tribe Hypsigenyini (hogfishes, tuskfishes)
		  is the sister group to the remaining labrids and includes
		  odacines and the chisel-tooth wrasse Pseudodax moluccanus,
		  a species previously considered close to scarines.
		  Cheilines and scarines are sister-groups, closely related
		  to the temperate Labrini, and pseudocheilines and cheilines
		  are split in all phylogenies. The razorfishes (novaculines)
		  and temperate pseudolabrines form successive sister clades
		  to the large crown group radiation of the Julidini. The
		  cleaner wrasses (Labrichthyini) are nested within this
		  radiation and several julidine genera do not appear to be
		  monophyletic (e.g., Coris and Halichoeres). Invasion of
		  temperate water by this predominantly tropical group has
		  occurred multiple times and the reconstruction of
		  biogeography assuming an Indo-Pacific ancestor results in
		  five different lineages invading the Atlantic/Caribbean
		  region. Functional novelties in the feeding apparatus have
		  allowed labrid fishes to occupy nearly every feeding guild
		  in reef environments, and trophic variation is a central
		  axis of diversification in this family.},
  author	= {Westneat, Mark W and Alfaro, Michael E},
  doi		= {10.1016/j.ympev.2005.02.001},
  file		= {:home/cboettig/Documents/Mendeley/Westneat, Alfaro - 2005
		  - Molecular phylogenetics and evolution.pdf:pdf},
  issn		= {1055-7903},
  journal	= {Molecular phylogenetics and evolution},
  keywords	= {16S,16S: genetics,Animals,Bayes Theorem,Cell Nucleus,Cell
		  Nucleus: genetics,DNA,DNA-Binding Proteins,DNA-Binding
		  Proteins: genetics,DNA: chemistry,DNA:
		  genetics,Evolution,Fish Proteins,Fish Proteins:
		  genetics,Geography,Mitochondrial,Mitochondrial:
		  chemistry,Mitochondrial: genetics,Molecular,Molecular
		  Sequence Data,Oceans and Seas,Perciformes,Perciformes:
		  classification,Perciformes:
		  genetics,Phylogeny,RNA,Ribosomal,Ribosomal:
		  genetics,Sequence Analysis},
  month		= aug,
  number	= {2},
  pages		= {370--90},
  pmid		= {15955516},
  title		= {{Phylogenetic relationships and evolutionary history of
		  the reef fish family Labridae.}},
  url		= {http://www.ncbi.nlm.nih.gov/pubmed/15955516},
  volume	= {36},
  year		= {2005}
}

@Manual{	  xml,
  annote	= {R package version 3.9-4},
  author	= {Lang, Duncan Temple},
  title		= {{XML: Tools for parsing and generating XML within R and
		  S-Plus.}},
  url		= {http://cran.r-project.org/package=XML},
  year		= {2012}
}
