To cite the windex package please use the following (but see also references to the Wheatsheaf index method in help files of relevant functions):

Arbuckle, K., Minter, A. (2015). “windex: Analyzing convergent evolution using the Wheatsheaf index in R.” Evolutionary Bioinformatics, 11, 11-14.

Corresponding BibTeX entry:

  @Article{,
    title = {windex: Analyzing convergent evolution using the
      Wheatsheaf index in R.},
    author = {{Arbuckle} and {K.} and {Minter} and {A.}},
    journal = {Evolutionary Bioinformatics},
    year = {2015},
    volume = {11},
    pages = {11-14},
  }