To cite package 'nlme' in publications use:

Jose Pinheiro, Douglas Bates, Saikat DebRoy, Deepayan Sarkar and the R Development Core Team (2012). nlme: Linear and Nonlinear Mixed Effects Models. R package version 3.1-104.

Corresponding BibTeX entry:

  @Manual{,
    title = {nlme: Linear and Nonlinear Mixed Effects Models},
    author = {Jose Pinheiro and Douglas Bates and Saikat DebRoy and
      Deepayan Sarkar and {R Core Team}},
    year = {2012},
    note = {R package version 3.1-104},
  }