The following sections provide a complete list of my publications to date. Copies of select publications, including drafts of some of my working papers, are available here.

Articles in Refereed Journals


Bonner, S.J. and Schwarz, C.J. (2011).
Smoothing population size estimates for time-stratified mark-recapture experiments using Bayesian p-splines. Biometrics. Accepted for publication.

Bonner, S.J., Morgan, B.J.T., and King, R. (2010).
Continuous, time-varying covariates in mark-recapture-recovery analyses: A comparison of methods. Biometrics, 65(4):1256--1265.

Calvert, A., Bonner, S.J., Jonsen, I., Flemming, J., Walde, S., and Taylor, P. (2009).
A hierarchical Bayesian approach to multi-state mark-recapture: Simulations and applications. Journal of Applied Ecology, 46:610--620.

Lampinen, T.M., Bonner, S.J., Rusch, M., and Hogg, R.S. (2007).
High prevalence of smoking among urban-dwelling Canadian men who have sex with men. Journal of Urban Health, 83(6):1143--1150.

Bonner, S.J. and Schwarz, C.J. (2006).
An extension of the Cormack-Jolly-Seber model for continuous covariates with application to Microtus pennsylvanicus. Biometrics, 62(1):142--149.

Hogg, R.S., Bangsberg, D.R., Lima, V.D., Alexander, C., Bonner, S., Yip, B., Wood, E., Dong, W.W., Montaner, J.S.G., and Harrigan, P.R. (2006).
Emergence of drug resistance is associated with an increased risk of death among patients first starting HAART. PLoS Medicine, 3(9):e356.

Wood, E., Hogg, R.S., Bonner, S., Kerr, T., Li, K., Palepu, A., Guillemi, S., Schechter, M.T., and Montaner, J.S.G. (2004).
Staging for anti-retroviral therapy among HIV-infected drug users. Journal of the American Medical Association, 292:1175a--1177a.

Non-Refereed Journal Articles


Zala, C., Alexander, C.S., Ochoa, C., Guillemi, S., Ting, L.S., Bonner, S., Cahn, P., Harrigan, P.R., and Montaner, J.S.G. (2005).
Comparable pharmacokinetics of generic Indinavir (Inhibisam) versus brand Indinavir (Crixivan) when boosted with Ritonavir. Journal of Acquired Immune Deficiency Syndromes, 38(1):363--364. Letter to the Editor.

Articles in Refereed Conference Proceedings


Bonner, S.J., Thomson, D.L., and Schwarz, C.J. (2008).
Time-varying covariates and semi-parametric regression in capture-recapture: An adaptive spline approach. In D.L. Thomson, E.G. Cooch, and M.J. Conroy (eds.), Modelling Demographic Processes in Marked Populations, vol. 3 of Environmental and Ecological Statistics, pp. 657--676. Springer, New York. Proceedings of the 8th EURING Technical Meeting.

Gimenez, O., Bonner, S.J., King, R., Parker, R.A., Brooks, S.P., Jamieson, L.E., Grosbois, V., Morgan, B.J.T., and Thomas, L. (2008).
WinBUGS for population ecologists: Bayesian modeling using Markov chain Monte Carlo methods. In D.L. Thomson, E.G. Cooch, and M.J. Conroy (eds.), Modelling Demographic Processes in Marked Populations, vol. 3 of Environmental and Ecological Statistics, pp. 883--916. Springer, New York. Proceedings of the 8th EURING Technical Meeting.

Bonner, S.J. and Schwarz, C.J. (2004).
Continuous time-dependent individual covariates and the Cormack-Jolly-Seber model. In J.C. Senar, A. Dhont, and M.J. Conroy (eds.), Animal Biodiversity and Conservation, vol. 27. Proceedings of the 7th EURING Technical Meeting.

Invited Presentations


Bonner, S.J. and Schwarz, C. (2011).
Advances in modelling time-stratified mark-recapture data from salmon outmigrations via bayesian p-splines. 39th Annual Meeting of the Statistical Society of Canada. Wolfville, NS.

Bonner, S., Newlands, N., and Heckman, N. (2010).
Functional data modelling of climate trends in British Columbia. Functional Data Analysis: Future Directions. Banff, AB.

Schwarz, C. and Bonner, S. (2010).
Bayesian time-stratified Petersen estimators for abundance. UBC Fisheries Quantitative Seminar. UBC Fisheries Centre, Vancouver, BC (Presented by C Schwarz).

Bonner, S.J. (2009).
Bayesian estimation of abundance for open populations with covariate dependent capture and survival probabilities. University of Victoria. Victoria, BC.

Bonner, S.J. (2008).
Application of Bayesian p-splines to the stratified two-stage capture-recapture study. University of British Columbia. Vancouver, BC.

Conference Presentations

Bonner, S., Newlands, N., Qian, B., and Heckman, N. (2010).
Functional data analysis of the trends and predictors of climate in British Columbia. Joint Statistical Meetings. Vancouver, British Columbia.

Bonner, S., Newlands, N., Qian, B., and Heckman, N. (2010).
Functional data analysis of the trends and predictors of climate in British Columbia. IMS New Researchers Conference. Vancouver, British Columbia.

Bonner, S.J. and Schwarz, C.J. (2010).
Bayesian time-stratified Petersen estimators for abundance. International Statistical Ecology Conference. St Andrews, Scotland (Presented by C Schwarz).

Bonner, S.J. and Schwarz, C.J. (2009).
Bayesian estimation of abundance for open populations with covariate dependent capture and survival probabilities. 9th EURING Technical Meeting. Pescara, Italy.

Bonner, S.J. and Schwarz, C.J. (2008).
Hierarchical Bayesian modelling of two-stage capture-recapture experiments. Joint Meeting of the Statistical Society of Canada and the Soci\'et\'e Francaise de Statistique. Ottawa, Ontario.

Bonner, S.J. and Schwarz, C.J. (2007).
Bayesian smoothing of the stratified-Petersen model. WNAR/IMS Annual Meeting. Irvine, California.

Bonner, S.J., Thomson, D.T., and Schwarz, C.J. (2007).
Time-varying covariates and semi-parametric regression in capture-recapture: an adaptive spline approach. 8th EURING Technical Meeting. Dunedin, New Zealand.

Bonner, S.J. (2006).
Time-dependent covariates in mark-recapture. 3rd SFU/UBC Joint Student Statistics Workshop. University of British Columbia, Vancouver.

Bonner, S.J. (2005).
An introduction to capture-recapture. 1st SFU/UBC Joint Student Statistics Workshop. University of British Columbia,Vancouver.

Hogg, R.S., Bonner, S.J., Daniel, M., Harrigan, P.R., Yip, B., Braistein, P., Wood, E., and Montaner, J.S.G. (2004).
Impact of depression on all cause mortality among men and women initiating HAART. 15th International AIDS Conference. Bangkok, Thailand. Presented by R. Hogg.

Bonner, S.J. and Schwarz, C.J. (2003).
Continuous individual time-dependent covariates in the Cormack-Jolly-Seber model. 7th EURING Technical Meeting. Radolfzell, Germany.

Technical Reports


Bonner, S.J. and Schwarz, C.J. (2011).
A spline-based capture-mark-recapture model applied to estimating the number of Steelhead within the Bulkley River passing the Moricetown canyon in 2001-2010. Technical report, BC Ministry of Environment.

Bonner, S.J. (2010).
Functional data analysis of the trends and predictors of climate in british columbia. Technical report, Agriculture and Agri-Food Canada.

Bonner, S.J. (2008).
The stratified-Petersen experiment: Effects of heterogeneity by strata on the estimate of run size and its variance. Technical report, BC Hydro.

Bonner, S.J. and Schwarz, C.J. (2008).
Analysis of variability in water quality, sediment quality, and abundance of benthic organisms in two lakes of the Koala watershed. Technical report, Rescan Environmental Services Ltd.

Bonner, S.J. (2006).
Analysis of the effects of 11 chemicals on wireworm mortality. Technical report, Pacific Agri-Food Research Centre.

Posters


Bonner, S.J., King, R., and Morgan, B.J.T. (2007).
Comparison of methods for incorporating covariates in mark-recapture-recovery analysis. 8th EURING Technical Meeting. Dunedin, New Zealand.

Bonner, S., Rusch, M., Lampinen, T.M., Miller, M.L., Devlin, B., and Hogg, R.S. (2004).
Smoking behaviour among men who have sex with men. 13th Annual Canadian AIDS/HIV Research Conference. Montreal, Quebec.

Bonner, S.J., Hogg, R.S., Geller, J., Yip, B., Gataric, N., and Montaner, J.S. (2004).
Concordance between two measures of adherence to anti-retroviral therapy. 13th Annual Canadian AIDS/HIV Research Conference. Montreal, Quebec.

Guillemi, S., Alexander, C.S., Bonner, S., Ting, L., Harris, M., Harrigan, P.R., and Montaner, J.S. (2004).
Lopinavir through concentration remains consistent for adult patients regardless of age. 13th Annual Canadian AIDS/HIV Research Conference. Montreal, Quebec.

Harris, M., Alexander, C., Bonner, S., Ting, L., McNabb, K., Harrigan, P.R., and Montaner, J.S.G. (2004).
Soft gel and hard gel formulations offer similar exposure to Saquinavir in Ritonavir-boosted regimens. 5th International Workshop on Clinical Pharmacology of HIV Therapy. Rome, Italy.

Harris, M., Zalunardo, N., Bonner, S., Werb, R., Valyi, M., and Montaner, J.S. (2004).
Use of estimated glomerular filtration rate (GFR) to predict renal toxicity in patients receiving Tenofovir DF (TDF). 11th Conference on Retroviruses and Opportunistic Infections. San Francisco, California.