To cite rotl in publications use:

Michonneau F, Brown JW, Winter DJ (2016). “rotl: an R package to interact with the Open Tree of Life data.” Methods in Ecology and Evolution, 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 CE, Smith SA, Allman JF, Burleigh JG, Chaudhary R, Coghill LM, Crandall KA, Deng J, Drew BT, Gazis R, Gude K, Hibbett DS, Katz LA, IV HDL, McTavish EJ, Midford PE, Owen CL, Ree RH, Rees JA, Soltis DE, Williams T, Cranston KA (2015). “Synthesis of phylogeny and taxonomy into a comprehensive tree of life.” Proceedings of the National Academy of Sciences, 112(41), 12764-12769. doi: 10.1073/pnas.1423041112.

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},
  }