DDR-Yihui-Xie.bib

@article{knuth1984,
  title={Literate programming},
  author={Knuth, Donald E.},
  journal={The Computer Journal},
  volume={27},
  number={2},
  pages={97--111},
  year={1984},
  publisher={British Computer Society}
}
@article{rossini2004,
  title={Emacs speaks statistics: A multiplatform, multipackage development environment for statistical analysis},
  author={Rossini, A.J. and Heiberger, R.M. and Sparapani, R.A. and Maechler, M. and Hornik, K.},
  journal={Journal of Computational and Graphical Statistics},
  volume={13},
  number={1},
  pages={247--261},
  year={2004},
  publisher={Taylor \& Francis}
}
@article{buckheit1995,
  title={WaveLab and Reproducible Research},
  author={Buckheit, J.B. and Donoho, D.L.},
  journal={Wavelets and statistics},
  volume={103},
  pages={55},
  year={1995},
  publisher={Springer Verlag}
}
@article{fomel2009,
  title={Guest Editors' Introduction: Reproducible Research},
  author={Fomel, S. and Claerbout, J.F.},
  journal={Computing in Science \& Engineering},
  volume={11},
  number={1},
  pages={5--7},
  year={2009},
  publisher={IEEE}
}
@article{peng2009,
  title={Reproducible research and Biostatistics},
  author={Peng, R.D.},
  journal={Biostatistics},
  volume={10},
  number={3},
  pages={405--408},
  year={2009},
  publisher={Biometrika Trust}
}
@techreport{knuth1983,
  title={The {WEB} system of structured documentation},
  author={Knuth, Donald E.},
  year={1983},
  institution={Department of Computer Science, Stanford University}
}

@inproceedings{leisch2002,
  title={Sweave: Dynamic Generation of Statistical Reports Using Literate Data Analysis},
  author={Leisch, Friedrich},
  booktitle={COMPSTAT 2002 Proceedings in Computational Statistics},
  number={69},
  pages={575--580},
  year={2002},
  organization={Heidelberg: Physica Verlag}
}

@article{baggerly2004,
  title={Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments},
  author={Keith A. Baggerly and Jeffrey S. Morris and Kevin R. Coombes},
  journal={Bioinformatics},
  volume={20},
  number={5},
  pages={777--785},
  year={2004},
  publisher={Oxford Univ Press}
}

@article{gentleman2004,
  title={Statistical analyses and reproducible research},
  author={Gentleman, Robert and {Temple Lang}, Duncan},
  year={2004},
  journal={Bioconductor Project Working Papers},
  publisher={Berkeley Electronic Press},
  note={URL: \url{http://biostats.bepress.com/bioconductor/paper2}}
}

@article{gentleman2005,
  title={Reproducible research: A bioinformatics case study},
  author={Gentleman, Robert},
  journal={Statistical Applications in Genetics and Molecular Biology},
  volume={4},
  number={1},
  pages={1034},
  year={2005}
}


@article{ramsey1994,
  title={Literate programming simplified},
  author={Ramsey, Norman},
  journal={Software, IEEE},
  volume={11},
  number={5},
  pages={97--105},
  year={1994},
  publisher={IEEE}
}

@inproceedings{rossini2002,
  title={Literate Statistical Analysis},
  author={Rossini, Anthony},
  booktitle={Proceedings of the 2nd International Workshop on Distributed Statistical Computing},
  pages={15--17},
  address={Vienna, Austria},
  year={2002}
}

@article{ihaka1996,
  title={R: A language for data analysis and graphics},
  author={Ihaka, Ross and Gentleman, Robert},
  journal={Journal of computational and graphical statistics},
  volume={5},
  number={3},
  pages={299--314},
  year={1996},
  publisher={Taylor \& Francis}
}

@Manual{R-langdef,
  title = {R Language Definition},
  author = {{R Core Team}},
  organization = {R Foundation for Statistical Computing},
  address = {Vienna, Austria},
  year = {2013},
  url = {http://www.R-project.org/},
}

@Manual{markdown,
  title = {The Markdown Project},
  author = {John Gruber},
  year = {2004},
  note = {URL: \url{http://daringfireball.net/projects/markdown/}},
}

@misc{heesch2008,
  title={Doxygen: Source code documentation generator tool},
  author={{van Heesch}, Dimitri},
  year={2008},
  note={URL: \url{http://www.doxygen.org/}},
}

@Manual{tantau2008,
  title={The TikZ and PGF Packages},
  author={Tantau, Till},
  year={2008},
  note={URL: \url{http://sourceforge.net/projects/pgf/}}
}

@book{murrell2011,
  title={R Graphics, Second Edition},
  author={Murrell, Paul},
  year={2011},
  publisher={Chapman \& Hall/CRC}
}
@Manual{oetiker1995,
  title={The not so short introduction to LATEX2$\varepsilon$},
  author={Oetiker, T. and Partl, H. and Hyna, I. and Schlegl, E.},
  note={URL: \url{http://www.ctan.org/tex-archive/info/lshort/}},
  year={1995}
}
@inproceedings{graphviz,
  title={Graphviz --- Open Source Graph Drawing Tools},
  author={Ellson, J. and Gansner, E. and Koutsofios, L. and North, S. and Woodhull, G.},
  booktitle={Graph Drawing},
  pages={483--484},
  year={2002},
  organization={Springer-Verlag}
}
@Manual{beamer,
  title={User's Guide to the Beamer Class},
  author={Till Tantau and Joseph Wright and Vedran Miletic},
  year={2012},
  note={URL: \url{http://bitbucket.org/rivanvx/beamer}}
}
@article{org-mode,
  author =	"Eric Schulte and Dan Davison and Thomas Dye and Carsten Dominik",
  title =	"A Multi-Language Computing Environment for Literate Programming and Reproducible Research",
  journal =	"Journal of Statistical Software",
  volume =	"46",
  number =	"3",
  pages =	"1--24",
  day =  	"25",
  month =	"1",
  year = 	"2012",
  CODEN =	"JSSOBK",
  ISSN = 	"1548-7660",
  bibdate =	"2011-10-03",
  URL =  	"http://www.jstatsoft.org/v46/i03",
  accepted =	"2011-10-03",
  acknowledgement = "",
  keywords =	"",
  submitted =	"2010-12-22",
}
@article{sasweave,
  author =	"Russell  V.  Lenth and S\o{}ren  H\o{}jsgaard",
  title =	"SASWeave: Literate Programming Using SAS",
  journal =	"Journal of Statistical Software",
  volume =	"19",
  number =	"8",
  pages =	"1--20",
  day =  	"27",
  month =	"5",
  year = 	"2007",
  CODEN =	"JSSOBK",
  ISSN = 	"1548-7660",
  bibdate =	"2007-05-27",
  URL =  	"http://www.jstatsoft.org/v19/i08",
  accepted =	"2007-05-27",
  acknowledgement = "",
  keywords =	"",
  submitted =	"2007-02-14",
}
@article{huang2012,
  title={Comparability and reproducibility of biomedical data},
  author={Huang, Y. and Gottardo, R.},
  journal={Briefings in Bioinformatics},
  doi = {10.1093/bib/bbs078},
  year={2012},
  publisher={Oxford University Press}
}
@article{murrell2006,
  author = {Paul Murrell and Brian Ripley},
  title = {Non-Standard Fonts in {PostScript} and {PDF} graphics},
  journal = {R News},
  year = 2006,
  volume = 6,
  number = 2,
  pages = {41--47},
  month = {May},
  url = {http://CRAN.R-project.org/doc/Rnews/},
  pdf = {http://CRAN.R-project.org/doc/Rnews/Rnews_2006-2.pdf}
}
@book{lebanon2012,
  author = {Guy Lebanon},
  title  = {Probability: The Analysis of Data},
  volume = 1,
  year   = 2012,
  month  = October,
  publisher={CreateSpace Independent Publishing Platform},
}
@BOOK{MASS02,
  AUTHOR =       {William N. Venables and Brian D. Ripley},
  TITLE =        {Modern Applied Statistics with S},
  PUBLISHER =    {Springer-Verlag},
  YEAR =         {2002},
  edition =      {4th},
  isbn =         {0-387-95457-0},
}
@book{harrell2001,
  title={Regression modeling strategies: with applications to linear models, logistic regression, and survival analysis},
  author={Harrell, Jr., Frank E},
  year={2001},
  publisher={Springer New York}
}
@book{ramsey2002,
  title={The Statistical Sleuth: A Course in Methods of Data Analysis, Second Edition},
  author={Ramsey, F.L. and Schafer, D.W.},
  year={2002},
  publisher={Duxbury Press}
}
@Article{ggbio,
    title = {ggbio: an {R} package for extending the grammar of graphics for genomic data},
    author = {Tengfei Yin and Dianne Cook and Michael Lawrence},
    journal = {Genome Biology},
    volume = {13},
    number = {8},
    pages = {R77},
    year = {2012},
    publisher = {BioMed Central Ltd},
}
@book{friedl2006,
  title={Mastering regular expressions},
  author={Friedl, Jeffrey},
  year={2006},
  publisher={O'Reilly Media, Incorporated}
}
@misc{murphy2012,
  title={Changes and Additions to \textbf{ggplot2} 0.9.0},
  author={Dennis Murphy},
  year={2012},
  note={URL: \url{https://github.com/djmurphy420/ggplot2-transition-guide}},
}
@misc{horton2012,
  title={The Statistical Sleuth (2nd Edition) In {R}},
  author={Nicholas Horton and Kate Aloisio and Ruobing Zhang and Linda Loi},
  year={2012},
  note={URL: \url{http://www.math.smith.edu/~nhorton/sleuth/}},
}