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. and Minter, A. 2015. windex: Analyzing convergent
  evolution using the Wheatsheaf index in R. Evolutionary
  Bioinformatics 11:11-14. doi:10.4137/EBO.S20968

A BibTeX entry for LaTeX users is

  @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},
  }