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160621_package_citations.bib
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@Article{,
author = {Paul J. McMurdie and Susan Holmes},
journal = {PLoS ONE},
pages = {e61217},
title = {phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data},
volume = {8},
number = {4},
year = {2013},
url = {http://dx.plos.org/10.1371/journal.pone.0061217},
}
@Manual{,
title = {biom: An interface package (beta) for the BIOM file format.},
author = {Paul J. McMurdie and the biom-format team http://biom-format.org/},
year = {2014},
note = {R package version 0.3.12},
url = {http://CRAN.R-project.org/package=biom},
}
@Article{,
title = {The Split-Apply-Combine Strategy for Data Analysis},
author = {Hadley Wickham},
journal = {Journal of Statistical Software},
year = {2011},
volume = {40},
number = {1},
pages = {1--29},
url = {http://www.jstatsoft.org/v40/i01/},
}
@Manual{,
title = {dplyr: A Grammar of Data Manipulation},
author = {Hadley Wickham and Romain Francois},
year = {2015},
note = {R package version 0.4.2},
url = {http://CRAN.R-project.org/package=dplyr},
}
@Manual{,
title = {vegan: Community Ecology Package},
author = {Jari Oksanen and F. Guillaume Blanchet and Roeland Kindt and Pierre Legendre and Peter R. Minchin and R. B. O'Hara and Gavin L. Simpson and Peter Solymos and M. Henry H. Stevens and Helene Wagner},
year = {2015},
note = {R package version 2.3-0},
url = {http://CRAN.R-project.org/package=vegan},
}
@Manual{,
title = {gplots: Various R Programming Tools for Plotting Data},
author = {Gregory R. Warnes and Ben Bolker and Lodewijk Bonebakker and Robert Gentleman and Wolfgang Huber Andy Liaw and Thomas Lumley and Martin Maechler and Arni Magnusson and Steffen Moeller and Marc Schwartz and Bill Venables},
year = {2015},
note = {R package version 2.17.0},
url = {http://CRAN.R-project.org/package=gplots},
}
@Article{,
title = {The ade4 package: implementing the duality diagram for ecologists},
author = {S. Dray and A.B. Dufour},
journal = {Journal of Statistical Software},
year = {2007},
volume = {22},
pages = {1-20},
number = {4},
}
@Article{,
title = {The ade4 package-{I}- {O}ne-table methods},
author = {D. Chessel and A.B. Dufour and J. Thioulouse},
journal = {R News},
year = {2004},
volume = {4},
pages = {5-10},
}
@Article{,
title = {The ade4 package-{II}: {T}wo-table and {K}-table methods.},
author = {S. Dray and A.B. Dufour and D. Chessel},
journal = {R News},
year = {2007},
volume = {7},
number = {2},
pages = {47-52},
}
@Book{,
author = {Hadley Wickham},
title = {ggplot2: elegant graphics for data analysis},
publisher = {Springer New York},
year = {2009},
isbn = {978-0-387-98140-6},
url = {http://had.co.nz/ggplot2/book},
}
@Article{,
title = {Reshaping Data with the {reshape} Package},
author = {Hadley Wickham},
journal = {Journal of Statistical Software},
year = {2007},
volume = {21},
number = {12},
pages = {1--20},
url = {http://www.jstatsoft.org/v21/i12/},
}
@Manual{,
title = {gridExtra: Miscellaneous Functions for "Grid" Graphics},
author = {Baptiste Auguie},
year = {2015},
note = {R package version 2.0.0},
url = {http://CRAN.R-project.org/package=gridExtra},
}
@Manual{,
title = {foreach: Foreach looping construct for R},
author = {Revolution Analytics and Steve Weston},
year = {2014},
note = {R package version 1.4.2},
url = {http://CRAN.R-project.org/package=foreach},
}
@Manual{,
title = {irr: Various Coefficients of Interrater Reliability and Agreement},
author = {Matthias Gamer and Jim Lemon and Ian Fellows Puspendra Singh <[email protected]>},
year = {2012},
note = {R package version 0.84},
url = {http://CRAN.R-project.org/package=irr},
}
@Article{,
author = {Paul J. McMurdie and Susan Holmes},
journal = {PLoS ONE},
pages = {e61217},
title = {phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data},
volume = {8},
number = {4},
year = {2013},
url = {http://dx.plos.org/10.1371/journal.pone.0061217},
}
@Manual{,
title = {biom: An interface package (beta) for the BIOM file format.},
author = {Paul J. McMurdie and the biom-format team http://biom-format.org/},
year = {2014},
note = {R package version 0.3.12},
url = {http://CRAN.R-project.org/package=biom},
}
@Article{,
title = {The Split-Apply-Combine Strategy for Data Analysis},
author = {Hadley Wickham},
journal = {Journal of Statistical Software},
year = {2011},
volume = {40},
number = {1},
pages = {1--29},
url = {http://www.jstatsoft.org/v40/i01/},
}
@Manual{,
title = {dplyr: A Grammar of Data Manipulation},
author = {Hadley Wickham and Romain Francois},
year = {2015},
note = {R package version 0.4.2},
url = {http://CRAN.R-project.org/package=dplyr},
}
@Manual{,
title = {vegan: Community Ecology Package},
author = {Jari Oksanen and F. Guillaume Blanchet and Roeland Kindt and Pierre Legendre and Peter R. Minchin and R. B. O'Hara and Gavin L. Simpson and Peter Solymos and M. Henry H. Stevens and Helene Wagner},
year = {2015},
note = {R package version 2.3-0},
url = {http://CRAN.R-project.org/package=vegan},
}
@Manual{,
title = {gplots: Various R Programming Tools for Plotting Data},
author = {Gregory R. Warnes and Ben Bolker and Lodewijk Bonebakker and Robert Gentleman and Wolfgang Huber Andy Liaw and Thomas Lumley and Martin Maechler and Arni Magnusson and Steffen Moeller and Marc Schwartz and Bill Venables},
year = {2015},
note = {R package version 2.17.0},
url = {http://CRAN.R-project.org/package=gplots},
}
@Article{,
title = {The ade4 package: implementing the duality diagram for ecologists},
author = {S. Dray and A.B. Dufour},
journal = {Journal of Statistical Software},
year = {2007},
volume = {22},
pages = {1-20},
number = {4},
}
@Article{,
title = {The ade4 package-{I}- {O}ne-table methods},
author = {D. Chessel and A.B. Dufour and J. Thioulouse},
journal = {R News},
year = {2004},
volume = {4},
pages = {5-10},
}
@Article{,
title = {The ade4 package-{II}: {T}wo-table and {K}-table methods.},
author = {S. Dray and A.B. Dufour and D. Chessel},
journal = {R News},
year = {2007},
volume = {7},
number = {2},
pages = {47-52},
}
@Book{,
author = {Hadley Wickham},
title = {ggplot2: elegant graphics for data analysis},
publisher = {Springer New York},
year = {2009},
isbn = {978-0-387-98140-6},
url = {http://had.co.nz/ggplot2/book},
}
@Article{,
title = {Reshaping Data with the {reshape} Package},
author = {Hadley Wickham},
journal = {Journal of Statistical Software},
year = {2007},
volume = {21},
number = {12},
pages = {1--20},
url = {http://www.jstatsoft.org/v21/i12/},
}
@Manual{,
title = {gridExtra: Miscellaneous Functions for "Grid" Graphics},
author = {Baptiste Auguie},
year = {2015},
note = {R package version 2.0.0},
url = {http://CRAN.R-project.org/package=gridExtra},
}
@Manual{,
title = {foreach: Foreach looping construct for R},
author = {Revolution Analytics and Steve Weston},
year = {2014},
note = {R package version 1.4.2},
url = {http://CRAN.R-project.org/package=foreach},
}
@Manual{,
title = {irr: Various Coefficients of Interrater Reliability and Agreement},
author = {Matthias Gamer and Jim Lemon and Ian Fellows Puspendra Singh <[email protected]>},
year = {2012},
note = {R package version 0.84},
url = {http://CRAN.R-project.org/package=irr},
}
@Article{,
author = {Paul J. McMurdie and Susan Holmes},
journal = {PLoS ONE},
pages = {e61217},
title = {phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data},
volume = {8},
number = {4},
year = {2013},
url = {http://dx.plos.org/10.1371/journal.pone.0061217},
}
@Manual{,
title = {biom: An interface package (beta) for the BIOM file format.},
author = {Paul J. McMurdie and the biom-format team http://biom-format.org/},
year = {2014},
note = {R package version 0.3.12},
url = {http://CRAN.R-project.org/package=biom},
}
@Article{,
title = {The Split-Apply-Combine Strategy for Data Analysis},
author = {Hadley Wickham},
journal = {Journal of Statistical Software},
year = {2011},
volume = {40},
number = {1},
pages = {1--29},
url = {http://www.jstatsoft.org/v40/i01/},
}
@Manual{,
title = {dplyr: A Grammar of Data Manipulation},
author = {Hadley Wickham and Romain Francois},
year = {2015},
note = {R package version 0.4.2},
url = {http://CRAN.R-project.org/package=dplyr},
}
@Manual{,
title = {vegan: Community Ecology Package},
author = {Jari Oksanen and F. Guillaume Blanchet and Roeland Kindt and Pierre Legendre and Peter R. Minchin and R. B. O'Hara and Gavin L. Simpson and Peter Solymos and M. Henry H. Stevens and Helene Wagner},
year = {2015},
note = {R package version 2.3-0},
url = {http://CRAN.R-project.org/package=vegan},
}
@Manual{,
title = {gplots: Various R Programming Tools for Plotting Data},
author = {Gregory R. Warnes and Ben Bolker and Lodewijk Bonebakker and Robert Gentleman and Wolfgang Huber Andy Liaw and Thomas Lumley and Martin Maechler and Arni Magnusson and Steffen Moeller and Marc Schwartz and Bill Venables},
year = {2015},
note = {R package version 2.17.0},
url = {http://CRAN.R-project.org/package=gplots},
}
@Article{,
title = {The ade4 package: implementing the duality diagram for ecologists},
author = {S. Dray and A.B. Dufour},
journal = {Journal of Statistical Software},
year = {2007},
volume = {22},
pages = {1-20},
number = {4},
}
@Article{,
title = {The ade4 package-{I}- {O}ne-table methods},
author = {D. Chessel and A.B. Dufour and J. Thioulouse},
journal = {R News},
year = {2004},
volume = {4},
pages = {5-10},
}
@Article{,
title = {The ade4 package-{II}: {T}wo-table and {K}-table methods.},
author = {S. Dray and A.B. Dufour and D. Chessel},
journal = {R News},
year = {2007},
volume = {7},
number = {2},
pages = {47-52},
}
@Book{,
author = {Hadley Wickham},
title = {ggplot2: elegant graphics for data analysis},
publisher = {Springer New York},
year = {2009},
isbn = {978-0-387-98140-6},
url = {http://had.co.nz/ggplot2/book},
}
@Article{,
title = {Reshaping Data with the {reshape} Package},
author = {Hadley Wickham},
journal = {Journal of Statistical Software},
year = {2007},
volume = {21},
number = {12},
pages = {1--20},
url = {http://www.jstatsoft.org/v21/i12/},
}
@Manual{,
title = {gridExtra: Miscellaneous Functions for "Grid" Graphics},
author = {Baptiste Auguie},
year = {2015},
note = {R package version 2.0.0},
url = {http://CRAN.R-project.org/package=gridExtra},
}
@Manual{,
title = {foreach: Foreach looping construct for R},
author = {Revolution Analytics and Steve Weston},
year = {2014},
note = {R package version 1.4.2},
url = {http://CRAN.R-project.org/package=foreach},
}
@Manual{,
title = {irr: Various Coefficients of Interrater Reliability and Agreement},
author = {Matthias Gamer and Jim Lemon and Ian Fellows Puspendra Singh <[email protected]>},
year = {2012},
note = {R package version 0.84},
url = {http://CRAN.R-project.org/package=irr},
}
@Article{,
author = {Paul J. McMurdie and Susan Holmes},
journal = {PLoS ONE},
pages = {e61217},
title = {phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data},
volume = {8},
number = {4},
year = {2013},
url = {http://dx.plos.org/10.1371/journal.pone.0061217},
}
@Manual{,
title = {biom: An interface package (beta) for the BIOM file format.},
author = {Paul J. McMurdie and the biom-format team http://biom-format.org/},
year = {2014},
note = {R package version 0.3.12},
url = {http://CRAN.R-project.org/package=biom},
}
@Article{,
title = {The Split-Apply-Combine Strategy for Data Analysis},
author = {Hadley Wickham},
journal = {Journal of Statistical Software},
year = {2011},
volume = {40},
number = {1},
pages = {1--29},
url = {http://www.jstatsoft.org/v40/i01/},
}
@Manual{,
title = {dplyr: A Grammar of Data Manipulation},
author = {Hadley Wickham and Romain Francois},
year = {2015},
note = {R package version 0.4.2},
url = {http://CRAN.R-project.org/package=dplyr},
}
@Manual{,
title = {vegan: Community Ecology Package},
author = {Jari Oksanen and F. Guillaume Blanchet and Roeland Kindt and Pierre Legendre and Peter R. Minchin and R. B. O'Hara and Gavin L. Simpson and Peter Solymos and M. Henry H. Stevens and Helene Wagner},
year = {2015},
note = {R package version 2.3-0},
url = {http://CRAN.R-project.org/package=vegan},
}
@Manual{,
title = {gplots: Various R Programming Tools for Plotting Data},
author = {Gregory R. Warnes and Ben Bolker and Lodewijk Bonebakker and Robert Gentleman and Wolfgang Huber Andy Liaw and Thomas Lumley and Martin Maechler and Arni Magnusson and Steffen Moeller and Marc Schwartz and Bill Venables},
year = {2015},
note = {R package version 2.17.0},
url = {http://CRAN.R-project.org/package=gplots},
}
@Article{,
title = {The ade4 package: implementing the duality diagram for ecologists},
author = {S. Dray and A.B. Dufour},
journal = {Journal of Statistical Software},
year = {2007},
volume = {22},
pages = {1-20},
number = {4},
}
@Article{,
title = {The ade4 package-{I}- {O}ne-table methods},
author = {D. Chessel and A.B. Dufour and J. Thioulouse},
journal = {R News},
year = {2004},
volume = {4},
pages = {5-10},
}
@Article{,
title = {The ade4 package-{II}: {T}wo-table and {K}-table methods.},
author = {S. Dray and A.B. Dufour and D. Chessel},
journal = {R News},
year = {2007},
volume = {7},
number = {2},
pages = {47-52},
}
@Book{,
author = {Hadley Wickham},
title = {ggplot2: elegant graphics for data analysis},
publisher = {Springer New York},
year = {2009},
isbn = {978-0-387-98140-6},
url = {http://had.co.nz/ggplot2/book},
}
@Article{,
title = {Reshaping Data with the {reshape} Package},
author = {Hadley Wickham},
journal = {Journal of Statistical Software},
year = {2007},
volume = {21},
number = {12},
pages = {1--20},
url = {http://www.jstatsoft.org/v21/i12/},
}
@Manual{,
title = {gridExtra: Miscellaneous Functions for "Grid" Graphics},
author = {Baptiste Auguie},
year = {2015},
note = {R package version 2.0.0},
url = {http://CRAN.R-project.org/package=gridExtra},
}
@Manual{,
title = {foreach: Foreach looping construct for R},
author = {Revolution Analytics and Steve Weston},
year = {2014},
note = {R package version 1.4.2},
url = {http://CRAN.R-project.org/package=foreach},
}
@Manual{,
title = {irr: Various Coefficients of Interrater Reliability and Agreement},
author = {Matthias Gamer and Jim Lemon and Ian Fellows Puspendra Singh <[email protected]>},
year = {2012},
note = {R package version 0.84},
url = {http://CRAN.R-project.org/package=irr},
}
@Article{,
author = {Paul J. McMurdie and Susan Holmes},
journal = {PLoS ONE},
pages = {e61217},
title = {phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data},
volume = {8},
number = {4},
year = {2013},
url = {http://dx.plos.org/10.1371/journal.pone.0061217},
}
@Manual{,
title = {biom: An interface package (beta) for the BIOM file format.},
author = {Paul J. McMurdie and the biom-format team http://biom-format.org/},
year = {2014},
note = {R package version 0.3.12},
url = {http://CRAN.R-project.org/package=biom},
}
@Article{,
title = {The Split-Apply-Combine Strategy for Data Analysis},
author = {Hadley Wickham},
journal = {Journal of Statistical Software},
year = {2011},
volume = {40},
number = {1},
pages = {1--29},
url = {http://www.jstatsoft.org/v40/i01/},
}
@Manual{,
title = {dplyr: A Grammar of Data Manipulation},
author = {Hadley Wickham and Romain Francois},
year = {2015},
note = {R package version 0.4.2},
url = {http://CRAN.R-project.org/package=dplyr},
}
@Manual{,
title = {vegan: Community Ecology Package},
author = {Jari Oksanen and F. Guillaume Blanchet and Roeland Kindt and Pierre Legendre and Peter R. Minchin and R. B. O'Hara and Gavin L. Simpson and Peter Solymos and M. Henry H. Stevens and Helene Wagner},
year = {2015},
note = {R package version 2.3-0},
url = {http://CRAN.R-project.org/package=vegan},
}
@Manual{,
title = {gplots: Various R Programming Tools for Plotting Data},
author = {Gregory R. Warnes and Ben Bolker and Lodewijk Bonebakker and Robert Gentleman and Wolfgang Huber Andy Liaw and Thomas Lumley and Martin Maechler and Arni Magnusson and Steffen Moeller and Marc Schwartz and Bill Venables},
year = {2015},
note = {R package version 2.17.0},
url = {http://CRAN.R-project.org/package=gplots},
}
@Article{,
title = {The ade4 package: implementing the duality diagram for ecologists},
author = {S. Dray and A.B. Dufour},
journal = {Journal of Statistical Software},
year = {2007},
volume = {22},
pages = {1-20},
number = {4},
}
@Article{,
title = {The ade4 package-{I}- {O}ne-table methods},
author = {D. Chessel and A.B. Dufour and J. Thioulouse},
journal = {R News},
year = {2004},
volume = {4},
pages = {5-10},
}
@Article{,
title = {The ade4 package-{II}: {T}wo-table and {K}-table methods.},
author = {S. Dray and A.B. Dufour and D. Chessel},
journal = {R News},
year = {2007},
volume = {7},
number = {2},
pages = {47-52},
}
@Book{,
author = {Hadley Wickham},
title = {ggplot2: elegant graphics for data analysis},
publisher = {Springer New York},
year = {2009},
isbn = {978-0-387-98140-6},
url = {http://had.co.nz/ggplot2/book},
}
@Article{,
title = {Reshaping Data with the {reshape} Package},
author = {Hadley Wickham},
journal = {Journal of Statistical Software},
year = {2007},
volume = {21},
number = {12},
pages = {1--20},
url = {http://www.jstatsoft.org/v21/i12/},
}
@Manual{,
title = {gridExtra: Miscellaneous Functions for "Grid" Graphics},
author = {Baptiste Auguie},
year = {2015},
note = {R package version 2.0.0},
url = {http://CRAN.R-project.org/package=gridExtra},
}
@Manual{,
title = {foreach: Foreach looping construct for R},
author = {Revolution Analytics and Steve Weston},
year = {2014},
note = {R package version 1.4.2},
url = {http://CRAN.R-project.org/package=foreach},
}
@Manual{,
title = {irr: Various Coefficients of Interrater Reliability and Agreement},
author = {Matthias Gamer and Jim Lemon and Ian Fellows Puspendra Singh <[email protected]>},
year = {2012},
note = {R package version 0.84},
url = {http://CRAN.R-project.org/package=irr},
}
@Article{,
author = {Paul J. McMurdie and Susan Holmes},
journal = {PLoS ONE},
pages = {e61217},
title = {phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data},
volume = {8},
number = {4},
year = {2013},
url = {http://dx.plos.org/10.1371/journal.pone.0061217},
}
@Manual{,
title = {biom: An interface package (beta) for the BIOM file format.},
author = {Paul J. McMurdie and the biom-format team http://biom-format.org/},
year = {2014},
note = {R package version 0.3.12},
url = {http://CRAN.R-project.org/package=biom},
}
@Article{,
title = {The Split-Apply-Combine Strategy for Data Analysis},
author = {Hadley Wickham},
journal = {Journal of Statistical Software},
year = {2011},
volume = {40},
number = {1},
pages = {1--29},
url = {http://www.jstatsoft.org/v40/i01/},
}
@Manual{,
title = {dplyr: A Grammar of Data Manipulation},
author = {Hadley Wickham and Romain Francois},
year = {2015},
note = {R package version 0.4.2},
url = {http://CRAN.R-project.org/package=dplyr},
}
@Manual{,
title = {vegan: Community Ecology Package},
author = {Jari Oksanen and F. Guillaume Blanchet and Roeland Kindt and Pierre Legendre and Peter R. Minchin and R. B. O'Hara and Gavin L. Simpson and Peter Solymos and M. Henry H. Stevens and Helene Wagner},
year = {2015},
note = {R package version 2.3-0},
url = {http://CRAN.R-project.org/package=vegan},
}
@Manual{,
title = {gplots: Various R Programming Tools for Plotting Data},
author = {Gregory R. Warnes and Ben Bolker and Lodewijk Bonebakker and Robert Gentleman and Wolfgang Huber Andy Liaw and Thomas Lumley and Martin Maechler and Arni Magnusson and Steffen Moeller and Marc Schwartz and Bill Venables},
year = {2015},
note = {R package version 2.17.0},
url = {http://CRAN.R-project.org/package=gplots},
}
@Article{,
title = {The ade4 package: implementing the duality diagram for ecologists},
author = {S. Dray and A.B. Dufour},
journal = {Journal of Statistical Software},
year = {2007},
volume = {22},
pages = {1-20},
number = {4},
}
@Article{,
title = {The ade4 package-{I}- {O}ne-table methods},
author = {D. Chessel and A.B. Dufour and J. Thioulouse},
journal = {R News},
year = {2004},
volume = {4},
pages = {5-10},
}
@Article{,
title = {The ade4 package-{II}: {T}wo-table and {K}-table methods.},
author = {S. Dray and A.B. Dufour and D. Chessel},
journal = {R News},
year = {2007},
volume = {7},
number = {2},
pages = {47-52},
}
@Book{,
author = {Hadley Wickham},
title = {ggplot2: elegant graphics for data analysis},
publisher = {Springer New York},
year = {2009},
isbn = {978-0-387-98140-6},
url = {http://had.co.nz/ggplot2/book},
}
@Article{,
title = {Reshaping Data with the {reshape} Package},
author = {Hadley Wickham},
journal = {Journal of Statistical Software},
year = {2007},
volume = {21},
number = {12},
pages = {1--20},
url = {http://www.jstatsoft.org/v21/i12/},
}
@Manual{,
title = {gridExtra: Miscellaneous Functions for "Grid" Graphics},
author = {Baptiste Auguie},
year = {2015},
note = {R package version 2.0.0},
url = {http://CRAN.R-project.org/package=gridExtra},
}
@Manual{,
title = {foreach: Foreach looping construct for R},
author = {Revolution Analytics and Steve Weston},
year = {2014},
note = {R package version 1.4.2},
url = {http://CRAN.R-project.org/package=foreach},
}
@Manual{,
title = {irr: Various Coefficients of Interrater Reliability and Agreement},
author = {Matthias Gamer and Jim Lemon and Ian Fellows Puspendra Singh <[email protected]>},
year = {2012},
note = {R package version 0.84},
url = {http://CRAN.R-project.org/package=irr},
}
@Article{,
author = {Paul J. McMurdie and Susan Holmes},
journal = {PLoS ONE},
pages = {e61217},
title = {phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data},
volume = {8},
number = {4},
year = {2013},
url = {http://dx.plos.org/10.1371/journal.pone.0061217},
}
@Manual{,
title = {biom: An interface package (beta) for the BIOM file format.},
author = {Paul J. McMurdie and the biom-format team http://biom-format.org/},
year = {2014},
note = {R package version 0.3.12},
url = {http://CRAN.R-project.org/package=biom},
}
@Article{,
title = {The Split-Apply-Combine Strategy for Data Analysis},
author = {Hadley Wickham},
journal = {Journal of Statistical Software},
year = {2011},
volume = {40},
number = {1},
pages = {1--29},
url = {http://www.jstatsoft.org/v40/i01/},
}
@Manual{,
title = {dplyr: A Grammar of Data Manipulation},
author = {Hadley Wickham and Romain Francois},
year = {2015},
note = {R package version 0.4.2},
url = {http://CRAN.R-project.org/package=dplyr},
}
@Manual{,
title = {vegan: Community Ecology Package},
author = {Jari Oksanen and F. Guillaume Blanchet and Roeland Kindt and Pierre Legendre and Peter R. Minchin and R. B. O'Hara and Gavin L. Simpson and Peter Solymos and M. Henry H. Stevens and Helene Wagner},
year = {2015},
note = {R package version 2.3-0},
url = {http://CRAN.R-project.org/package=vegan},
}
@Manual{,
title = {gplots: Various R Programming Tools for Plotting Data},
author = {Gregory R. Warnes and Ben Bolker and Lodewijk Bonebakker and Robert Gentleman and Wolfgang Huber Andy Liaw and Thomas Lumley and Martin Maechler and Arni Magnusson and Steffen Moeller and Marc Schwartz and Bill Venables},
year = {2015},
note = {R package version 2.17.0},
url = {http://CRAN.R-project.org/package=gplots},
}
@Article{,
title = {The ade4 package: implementing the duality diagram for ecologists},
author = {S. Dray and A.B. Dufour},
journal = {Journal of Statistical Software},
year = {2007},
volume = {22},
pages = {1-20},
number = {4},
}
@Article{,
title = {The ade4 package-{I}- {O}ne-table methods},
author = {D. Chessel and A.B. Dufour and J. Thioulouse},
journal = {R News},
year = {2004},
volume = {4},
pages = {5-10},
}
@Article{,
title = {The ade4 package-{II}: {T}wo-table and {K}-table methods.},
author = {S. Dray and A.B. Dufour and D. Chessel},
journal = {R News},
year = {2007},
volume = {7},
number = {2},
pages = {47-52},
}
@Book{,
author = {Hadley Wickham},
title = {ggplot2: elegant graphics for data analysis},
publisher = {Springer New York},
year = {2009},
isbn = {978-0-387-98140-6},
url = {http://had.co.nz/ggplot2/book},
}
@Article{,
title = {Reshaping Data with the {reshape} Package},
author = {Hadley Wickham},
journal = {Journal of Statistical Software},
year = {2007},
volume = {21},
number = {12},
pages = {1--20},
url = {http://www.jstatsoft.org/v21/i12/},
}
@Manual{,
title = {gridExtra: Miscellaneous Functions for "Grid" Graphics},
author = {Baptiste Auguie},
year = {2015},
note = {R package version 2.0.0},
url = {http://CRAN.R-project.org/package=gridExtra},
}
@Manual{,
title = {foreach: Foreach looping construct for R},
author = {Revolution Analytics and Steve Weston},
year = {2014},
note = {R package version 1.4.2},
url = {http://CRAN.R-project.org/package=foreach},
}
@Manual{,
title = {irr: Various Coefficients of Interrater Reliability and Agreement},
author = {Matthias Gamer and Jim Lemon and Ian Fellows Puspendra Singh <[email protected]>},
year = {2012},
note = {R package version 0.84},
url = {http://CRAN.R-project.org/package=irr},
}
@Article{,
author = {Paul J. McMurdie and Susan Holmes},
journal = {PLoS ONE},
pages = {e61217},
title = {phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data},
volume = {8},
number = {4},
year = {2013},
url = {http://dx.plos.org/10.1371/journal.pone.0061217},
}
@Manual{,
title = {biom: An interface package (beta) for the BIOM file format.},
author = {Paul J. McMurdie and the biom-format team http://biom-format.org/},
year = {2014},
note = {R package version 0.3.12},
url = {http://CRAN.R-project.org/package=biom},
}
@Article{,
title = {The Split-Apply-Combine Strategy for Data Analysis},
author = {Hadley Wickham},
journal = {Journal of Statistical Software},
year = {2011},
volume = {40},
number = {1},
pages = {1--29},
url = {http://www.jstatsoft.org/v40/i01/},
}
@Manual{,
title = {dplyr: A Grammar of Data Manipulation},
author = {Hadley Wickham and Romain Francois},
year = {2015},
note = {R package version 0.4.2},
url = {http://CRAN.R-project.org/package=dplyr},
}
@Manual{,
title = {vegan: Community Ecology Package},
author = {Jari Oksanen and F. Guillaume Blanchet and Roeland Kindt and Pierre Legendre and Peter R. Minchin and R. B. O'Hara and Gavin L. Simpson and Peter Solymos and M. Henry H. Stevens and Helene Wagner},
year = {2015},
note = {R package version 2.3-0},
url = {http://CRAN.R-project.org/package=vegan},
}
@Manual{,
title = {gplots: Various R Programming Tools for Plotting Data},
author = {Gregory R. Warnes and Ben Bolker and Lodewijk Bonebakker and Robert Gentleman and Wolfgang Huber Andy Liaw and Thomas Lumley and Martin Maechler and Arni Magnusson and Steffen Moeller and Marc Schwartz and Bill Venables},
year = {2015},
note = {R package version 2.17.0},
url = {http://CRAN.R-project.org/package=gplots},
}
@Article{,
title = {The ade4 package: implementing the duality diagram for ecologists},
author = {S. Dray and A.B. Dufour},
journal = {Journal of Statistical Software},
year = {2007},
volume = {22},
pages = {1-20},
number = {4},
}
@Article{,
title = {The ade4 package-{I}- {O}ne-table methods},
author = {D. Chessel and A.B. Dufour and J. Thioulouse},
journal = {R News},
year = {2004},
volume = {4},
pages = {5-10},
}
@Article{,
title = {The ade4 package-{II}: {T}wo-table and {K}-table methods.},
author = {S. Dray and A.B. Dufour and D. Chessel},
journal = {R News},
year = {2007},
volume = {7},
number = {2},
pages = {47-52},
}
@Book{,
author = {Hadley Wickham},
title = {ggplot2: elegant graphics for data analysis},
publisher = {Springer New York},
year = {2009},
isbn = {978-0-387-98140-6},
url = {http://had.co.nz/ggplot2/book},
}
@Article{,
title = {Reshaping Data with the {reshape} Package},
author = {Hadley Wickham},
journal = {Journal of Statistical Software},
year = {2007},
volume = {21},
number = {12},
pages = {1--20},
url = {http://www.jstatsoft.org/v21/i12/},
}
@Manual{,
title = {gridExtra: Miscellaneous Functions for "Grid" Graphics},
author = {Baptiste Auguie},
year = {2015},
note = {R package version 2.0.0},
url = {http://CRAN.R-project.org/package=gridExtra},
}
@Manual{,
title = {foreach: Foreach looping construct for R},
author = {Revolution Analytics and Steve Weston},
year = {2014},
note = {R package version 1.4.2},
url = {http://CRAN.R-project.org/package=foreach},
}
@Manual{,
title = {irr: Various Coefficients of Interrater Reliability and Agreement},
author = {Matthias Gamer and Jim Lemon and Ian Fellows Puspendra Singh <[email protected]>},
year = {2012},
note = {R package version 0.84},
url = {http://CRAN.R-project.org/package=irr},
}
@Article{,
author = {Paul J. McMurdie and Susan Holmes},
journal = {PLoS ONE},
pages = {e61217},
title = {phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data},
volume = {8},
number = {4},
year = {2013},
url = {http://dx.plos.org/10.1371/journal.pone.0061217},
}
@Manual{,
title = {biom: An interface package (beta) for the BIOM file format.},
author = {Paul J. McMurdie and the biom-format team http://biom-format.org/},
year = {2014},
note = {R package version 0.3.12},
url = {http://CRAN.R-project.org/package=biom},
}
@Article{,
title = {The Split-Apply-Combine Strategy for Data Analysis},
author = {Hadley Wickham},
journal = {Journal of Statistical Software},
year = {2011},
volume = {40},
number = {1},
pages = {1--29},
url = {http://www.jstatsoft.org/v40/i01/},
}
@Manual{,
title = {dplyr: A Grammar of Data Manipulation},
author = {Hadley Wickham and Romain Francois},
year = {2015},
note = {R package version 0.4.2},
url = {http://CRAN.R-project.org/package=dplyr},
}
@Manual{,
title = {vegan: Community Ecology Package},
author = {Jari Oksanen and F. Guillaume Blanchet and Roeland Kindt and Pierre Legendre and Peter R. Minchin and R. B. O'Hara and Gavin L. Simpson and Peter Solymos and M. Henry H. Stevens and Helene Wagner},
year = {2015},
note = {R package version 2.3-0},
url = {http://CRAN.R-project.org/package=vegan},
}
@Manual{,
title = {gplots: Various R Programming Tools for Plotting Data},
author = {Gregory R. Warnes and Ben Bolker and Lodewijk Bonebakker and Robert Gentleman and Wolfgang Huber Andy Liaw and Thomas Lumley and Martin Maechler and Arni Magnusson and Steffen Moeller and Marc Schwartz and Bill Venables},
year = {2015},
note = {R package version 2.17.0},
url = {http://CRAN.R-project.org/package=gplots},
}
@Article{,
title = {The ade4 package: implementing the duality diagram for ecologists},
author = {S. Dray and A.B. Dufour},
journal = {Journal of Statistical Software},
year = {2007},
volume = {22},
pages = {1-20},
number = {4},
}
@Article{,
title = {The ade4 package-{I}- {O}ne-table methods},
author = {D. Chessel and A.B. Dufour and J. Thioulouse},
journal = {R News},
year = {2004},
volume = {4},
pages = {5-10},
}
@Article{,
title = {The ade4 package-{II}: {T}wo-table and {K}-table methods.},
author = {S. Dray and A.B. Dufour and D. Chessel},
journal = {R News},
year = {2007},
volume = {7},
number = {2},
pages = {47-52},
}
@Book{,
author = {Hadley Wickham},
title = {ggplot2: elegant graphics for data analysis},
publisher = {Springer New York},