To cite the pomp package in publications use:

A. A. King, E. L. Ionides, C. M. Bret\'o, S. P. Ellner, M. J. Ferrari, B. E. Kendall, M. Lavine, D. Nguyen, D. C. Reuman, H. Wearing, and S. N. Wood 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 Stephen P. Ellner and Matthew J. Ferrari and Bruce E.
      Kendall and Michael Lavine and Dao Nguyen and Daniel C. Reuman
      and Helen Wearing and Simon N. Wood},
    year = {2014},
    url = {http://pomp.r-forge.r-rproject.org},
  }