To cite the package 'MonoPhy' in publications use:

  Schwery, O. & O'Meara, B.C. (2016), MonoPhy: a simple R package to
  find and visualize monophyly issues. PeerJ Computer Science 2:e56.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {MonoPhy: a simple R package to find and visualize monophyly issues},
    author = {Orlando Schwery and Brian C. O'Meara},
    year = {2016},
    volume = {2},
    pages = {e56},
    journal = {PeerJ Computer Science},
    issn = {2376-5992},
    url = {https://doi.org/10.7717/peerj-cs.56},
    doi = {10.7717/peerj-cs.56},
  }

You may also want to cite the version number you used (found via
'library(help=MonoPhy)').