To cite the 'knitr' package in publications use:

Yihui Xie (2014). knitr: A general-purpose package for dynamic report generation in R. R package version 1.6.

Yihui Xie (2013) Dynamic Documents with R and knitr. Chapman and Hall/CRC. ISBN 978-1482203530

Yihui Xie (2014) knitr: A Comprehensive Tool for Reproducible Research in R. In Victoria Stodden, Friedrich Leisch and Roger D. Peng, editors, Implementing Reproducible Computational Research. Chapman and Hall/CRC. ISBN 978-1466561595

Corresponding BibTeX entries:

  @Manual{,
    title = {knitr: A general-purpose package for dynamic report
      generation in R},
    author = {Yihui Xie},
    year = {2014},
    note = {R package version 1.6},
    url = {http://yihui.name/knitr/},
  }

  @Book{,
    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/},
  }

  @InCollection{,
    booktitle = {Implementing Reproducible Computational Research},
    editor = {Victoria Stodden and Friedrich Leisch and Roger D. Peng},
    title = {knitr: A Comprehensive Tool for Reproducible Research in
      {R}},
    author = {Yihui Xie},
    publisher = {Chapman and Hall/CRC},
    year = {2014},
    note = {ISBN 978-1466561595},
    url = {http://www.crcpress.com/product/isbn/9781466561595},
  }