To cite diversitree in a publication, please use:

  FitzJohn, R.G. 2012. Diversitree: Comparative Phylogenetic Analyses
  of Diversification in R.  Methods in Ecology and Evolution 3:
  1084-1092 doi:10.1111/j.2041-210X.2012.00234.x

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Diversitree: Comparative Phylogenetic Analyses of Diversification in R},
    author = {Richard G FitzJohn},
    journal = {Methods in Ecology and Evolution},
    year = {2012},
    volume = {3},
    pages = {1084-1092},
    doi = {10.1111/j.2041-210X.2012.00234.x},
  }