To cite ss3sim in publications use:

Anderson, SC, Monnahan, CC, Johnson, KF, Ono, K, Valero, JL, Cunningham, CJ, Hurtado-Ferro, F, Licandeo, R, McGilliard, CR, Szuwalski, CS, Vert-pre, KA, and Whitten, AR (2014). ss3sim: Fisheries stock assessment simulation testing with Stock Synthesis. R package version 0.8.2.

Anderson, SC, Monnahan, CC, Johnson, KF, Ono, K, and Valero, JL (2014). ss3sim: An R package for fisheries stock assessment simulation with Stock Synthesis. PLOS ONE. In press. doi:10.1371/journal.pone.0092725.

Corresponding BibTeX entries:

  @Manual{,
    title = {ss3sim: Fisheries stock assessment simulation with Stock
      Synthesis},
    author = {Sean C. Anderson and Cole C. Monnahan and Kelli F.
      Johnson and Kotaro Ono and Juan L. Valero and Curry J. Cunningham
      and Felipe Hurtado-Ferro and Roberto Licandeo and Carey R.
      McGilliard and Cody S. Szuwalski and Katyana A. Vert-pre and
      Athol R. Whitten},
    year = {2014},
    note = {R package version 0.8.2},
  }

  @Article{,
    title = {ss3sim: An R package for fisheries stock assessment
      simulation with Stock Synthesis},
    author = {Sean C. Anderson and Cole C. Monnahan and Kelli F.
      Johnson and Kotaro Ono and Juan L. Valero},
    year = {2014},
    journal = {PLOS ONE},
    doi = {10.1371/journal.pone.0092725},
  }