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 should also cite the source data from the Open Tree of Life

OpenTreeOfLife, Redelings B, Reyes LLS, Cranston KA, Allman J, Holder MT, McTavish EJ (2019). “Open Tree of Life Synthetic Tree.” doi:10.5281/zenodo.3937741, https://doi.org/10.5281/zenodo.3937741.

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},
  }

  @Misc{,
    title = {Open Tree of Life Synthetic Tree},
    author = {{OpenTreeOfLife} and Benjamin Redelings and Luna Luisa
      Sanchez Reyes and Karen A. Cranston and Jim Allman and Mark T.
      Holder and Emily Jane McTavish},
    year = {2019},
    version = {12.3},
    publisher = {Zenodo},
    doi = {10.5281/zenodo.3937741},
    url = {https://doi.org/10.5281/zenodo.3937741},
  }