To cite package 'AFLPsim' in publications use:

Balao, F. and García-Castaño, J.L. AFLPsim: an R package to simulate and detect dominant markers under selection in hybridizing populations. Plant Methods 10:40

Corresponding BibTeX entry:

    title = {AFLPsim: an R package for dominant markers simulation,
      hybridization and genome scan},
    author = {F. Balao and J.L. García-Castaño},
    journal = {Plant Methods},
    year = {2014},
    volume = {10},
    pages = {40},