To cite ss3sim in publications use:

Anderson, SC, Monnahan, CC, Johnson, KF, Ono, K, Valero, JL, Cunningham, CJ, Hurtado-Ferro, F, Kuriyama, P, Licandeo, R, McGilliard, CR, Rudd, M, Stawitz, CC, Szuwalski, CS, Taylor, IG, Vert-pre, KA, and Whitten, AR (2016). ss3sim: Fisheries Stock Assessment Simulation Testing with Stock Synthesis. R package version 0.9.3.

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. 9(4): e92725. http://doi.org/10.1371/journal.pone.0092725.

Corresponding BibTeX entries:

  @Manual{,
    title = {ss3sim: Fisheries Stock Assessment Simulation Testing 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 Peter Kuriyama and Roberto Licandeo
      and Carey R. McGilliard and Merrill Rudd and Christine C. Stawitz
      and Cody S. Szuwalski and Ian G. Taylor and Katyana A. Vert-pre
      and Athol R. Whitten},
    year = {2016},
    note = {R package version 0.9.3},
  }
  @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},
    volume = {9},
    number = {4},
    pages = {e92725},
    doi = {10.1371/journal.pone.0092725},
  }