To cite package 'Claddis' in a publication use:

  Lloyd, Graeme T. (2016). Estimating morphological diversity and tempo
  with discrete character-taxon matrices: implementation, challenges,
  progress, and future directions. Biological Journal of the Linnean
  Society, 118, 131-151.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Estimating morphological diversity and tempo with discrete character-taxon matrices: implementation, challenges, progress, and future directions},
    author = {Graeme T. Lloyd},
    journal = {Biological Journal of the Linnean Society},
    year = {2016},
    volume = {118},
    pages = {131-151},
    doi = {10.1111/bij.12746},
  }

  Lloyd, Graeme T. (2018). Journeys through discrete-character
  morphospace: synthesizing phylogeny, tempo, and disparity.
  Palaeontology, 61, 637-645.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Journeys through discrete-character morphospace: synthesizing phylogeny, tempo, and disparity},
    author = {Graeme T. Lloyd},
    journal = {Palaeontology},
    year = {2018},
    volume = {61},
    pages = {637-645},
    doi = {10.1111/pala.12380},
  }

  Lehmann, Oscar E. R., Ezcurra, Martin D., Butler, Richard J. and
  Lloyd, Graeme T. (2019). Biases with the Generalized Euclidean
  Distance measure in disparity analyses with high levels of missing
  data. Palaeontology, 62, 837-849.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Biases with the Generalized Euclidean Distance measure in disparity analyses with high levels of missing data},
    author = {Oscar E. R. Lehmann and Martin D. Ezcurra and Richard J. Butler and Graeme T. Lloyd},
    journal = {Palaeontology},
    year = {2019},
    volume = {62},
    pages = {837-849},
    doi = {10.1111/pala.12430},
  }

As Claddis is evolving rapidly, you may want to also cite its version
number (found with 'library(help = Claddis)').