Manuscripts

Stawitz, C.C., Haltuch, M.A., and Johnson, K.F. 2019. How does growth misspecification affect management advice derived from an integrated fisheries stock assessment model? Fisheries Research 213: 12–21. 10.1016/j.fishres.2019.01.004.

Stewart, I.J., Monnahan, C.C. 2017. Implications of process error in selectivity for approaches to weighting compositional data in fisheries stock assessments. Fisheries Research, 192: 126-134. 10.1016/j.fishres.2016.06.018 (code repository).

Johnson, K.F., Councill, E., Thorson, J.T., Brooks, E., Methot, R.D., Punt, A.E. 2016. Can autocorrelated recruitment be estimated using integrated assessment models and how does it affect population forecasts? Fisheries Research, 183: 222–232. 10.1016/j.fishres.2016.06.004 (code repository).

Kuriyama, P.T., Ono, K., Hurtado-Ferro, F., Hicks, A.C., Taylor, I.G., Licandeo, R.R., Johnson, K.F., Anderson, S.C., Monnahan, C.C., Rudd, M.B., Stawitz, C.C., Valero, J.L. 2016. An empirical weight-at-age approach reduces estimation bias compared to modeling parametric growth in integrated, statistical stock assessment models when growth is time varying. Fisheries Research, 180: 119–127. 10.1016/j.fishres.2015.09.007 (code repository).

Monnahan, C.C., Ono, K., Anderson, S.C. Rudd, M.B., Hicks, A.C., Hurtado-Ferro, F., Johnson, K.F., Kuriyama, P.T., Licandeo, R.R., Stawitz, C.C., Taylor, I.G., Valero, J.L. 2016. The effect of length bin width on growth estimation in integrated age-structured stock assessments. Fisheries Research, 180: 103–112. 10.1016/j.fishres.2015.11.002 (code repository).

Johnson, K.F., Monnahan, C.C., McGilliard, C.R., Vert-pre, K.A., Anderson, S.C., Cunningham, C.J., Hurtado-Ferro, F., Licandeo, R.R., Muradian, M.L., Ono, K., Szuwalski, C.S., Valero, J.L., Whitten, A.R., Punt, A.E. 2015. Time-varying natural mortality in fisheries stock assessment models: identifying a default approach. ICES Journal of Marine Science, 72(1): 137-150. 10.1093/icesjms/fsu055 (code repository).

Hurtado-Ferro, F., Szuwalski, C.S., Valero, J.L., Anderson, S.C., Cunningham, C.J.,Johnson, K.F., Licandeo, R.R., McGilliard, C.R., Monahan, C.C., Muradian, M.L., Ono, K., Vert-pre, K.A., Whitten, A.R., Punt, A.E. 2015. Looking in the rear-view mirror: bias and retrospective patterns in integrated, age-structured stock assessment models. ICES Journal of Marine Science, 72(1): 99-110. 10.1093/icesjms/fsu198.

Ono, K., Licandeo, R.R., Muradian, M.L., Cunningham, C.J., Anderson, S.C., Hurtado-Ferro, F., Johnson, K.F., McGilliard, C.R., Monnahan, C.C., Szuwalski, C.S., Valero, J.L., Vert-pre, K.A., Whitten, A.R., Punt, A.E. 2015. The importance of length and age composition data in statistical catch-at-age models for marine species. ICES Journal of Marine Science, 72(1): 31-43. doi.org/10.1093/icesjms/fsu007.

Anderson, S.C., Monnahan, C.C., Johnson, K.F., Ono, K., Valero, J.L. 2014. ss3sim: An R package for fisheries stock assessment simulation with Stock Synthesis. PLOS ONE, 9(4): e92725. 10.1371/journal.pone.0092725.