To cite the pomp package in publications use:

Aaron A. King, E. L. Ionides, C. M. Bret\'o, S. P. Ellner, B. E. Kendall, Helen Wearing, Matthew J. Ferrari, Michael Lavine, and Daniel C. Reuman 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 and Helen Wearing and
      Matthew J. Ferrari and Michael Lavine and Daniel C. Reuman},
    year = {2010},
    url = {http://pomp.r-forge.r-rproject.org},
  }