To cite the pomp package in publications use:

Aaron A. King, E. L. Ionides, C. M. Bret\'o, S. P. Ellner, and B. E. Kendall pomp: Statistical inference for partially observed Markov processes (R package) http://pomp.r-forge.r-project.org

As pomp is continually evolving, you may want to cite its version number. Find it with 'help(package=pomp)'.

Corresponding BibTeX entry:

  @Manual{,
    title = {pomp: Statistical inference for partially observed Markov
      processes (R package)},
    author = {Aaron A. King and Edward L. Ionides and Carles Martinez
      Bret\'o and Steve Ellner and Bruce Kendall},
    year = {2009},
    url = {http://pomp.r-forge.r-rproject.org},
  }