To cite rotl in publications use:

Michonneau, F., Brown, J. W. and Winter, D. J. (2016), rotl: an R package to interact with the Open Tree of Life data. Methods Ecol Evol. 7(12):1476-1481.<doi:10.1111/2041-210X.12593>

You may also want to cite the paper for the Open Tree of Life

Hinchliff, C. E., et al. (2015). Synthesis of phylogeny and taxonomy into a comprehensive tree of life. Proceedings of the National Academy of Sciences 112.41 (2015): 12764-12769

Corresponding BibTeX entries:

  @Article{,
    title = {{rotl}: an R package to interact with the Open Tree of
      Life data},
    author = {Francois Michonneau and Joseph W. Brown and David J.
      Winter},
    journal = {Methods in Ecology and Evolution},
    year = {2016},
    volume = {7},
    number = {12},
    pages = {1476-1481},
    doi = {10.1111/2041-210X.12593},
  }

  @Article{,
    title = {Synthesis of phylogeny and taxonomy into a comprehensive
      tree of life},
    author = {Cody E. Hinchliff and Stephen A. Smith and James F.
      Allman and J. Gordon Burleigh and Ruchi Chaudhary and Lyndon M.
      Coghill and Keith A. Crandall and Jiabin Deng and Bryan T. Drew
      and Romina Gazis and Karl Gude and David S. Hibbett and Laura A.
      Katz and H. Dail Laughinghouse IV and Emily Jane McTavish and
      Peter E. Midford and Christopher L. Owen and Richard H. Ree and
      Jonathan A. Rees and Douglas E. Soltis and Tiffani Williams and
      Karen A. Cranston},
    journal = {Proceedings of the National Academy of Sciences},
    year = {2015},
    volume = {112},
    number = {41},
    pages = {12764-12769},
    doi = {10.1073/pnas.1423041112},
  }