An outline of my current research at University of Washington and NOAA is listed below. My Google Scholar page also lists publications from my time at the Fred Hutchinson Cancer Research Center.

Locally-adaptive nonparametric smoothing

I am working with Vladimir Minin on developing locally-adaptive smoothing methods based on Markov random fields and shrinkage priors. This approach offers a flexible and fully Bayesian method for fitting trends or surfaces with locally sharp features or varying smoothness. We have developed methods for one-dimensional problems and are applying them to phylodynamics and mark-recapture. We are also currently extending the method for spatial applications. I have developed an R package titled spmrf for fitting nonparametric models using our method, which is located on this GitHub repository.


  • Faulkner, J.R., and V.N. Minin. 2017. Locally adaptive smoothing with Markov random fields and shrinkage priors. Bayesian Analysis -- advanced publication [PDF]


  • Faulkner, J.R., and V.N. Minin. Adaptive nonparametric smoothing for capture-recapture models. Presented at the International Biometrics Conference, Victoria, B.C., July 2016. [SLIDES]
  • Faulkner, J.R., and V.N. Minin. Locally-adaptive Bayesian nonparametric inference for phylodynamics. Presented at the Joint Statistical Meetings, Chicago, August 2016. [SLIDES]

Latent Variable Methods for Mark-Recapture

We work with mark-recapture data on massive numbers of individually-tagged fish, but the data suffer from very low detection probabilities. We need to model the survival and migration of these fish as functions of time-dependent covariates which are only measured at detection sites. We are working on Bayesian methods to jointly model the migration, survival, and detection processes while accounting for latent passage times of undetected fish. We are also working to find solutions to the computational challenges presented by the massive data sets.

Ecological Modeling of Salmon

Much of my research has focused on finding better ways to model the migrational process of threatened and endangered stocks of juvenile salmon passing through the system of dams and reservoirs on the Snake and Columbia Rivers. These include models for survival, migration timing, travel time, passage routing at dams, and smolt-to-adult returns. Many of these models are used to inform the Comprehensive Passage (COMPASS) model, which was developed through collaboration between NOAA, University of Washington, and other state, federal, and tribal interests, and is mainly used for evalution of potential management decisions. Some related publications and presentations are:

  • Zabel, R.W., J.R. Faulkner, S.G. Smith, J.J. Anderson, C. Van Holmes, N. Beer, S. Iltis, J. Krinke, G. Fredericks, B. Bellerud, J. Sweet, and A.E. Giorgi. 2008. Comprehensive passage (COMPASS) model: a model of downstream migration and survival of juvenile salmonids through a hydrowpoer system. Hydrobiologia 609:289-300. [PDF]
  • Faulkner, J.R. 2012. Modeling route-specific passage probabilities of migrating juvenile salmonids at hydroelectric dams using detections of PIT tags in juvenile bypass systems. Poster presented at the Northwest Fisheries Science Center Science Symposium. [PDF]
  • Faulkner, J.R., E. Buhle, and M. Scheuerell. 2015. Accounting for density-dependent predation in the survival of juvenile salmon and steelhead during their seaward migration. Presentation at the American Fisheries Society Meetings, August 2015. [SLIDES]

Statistics Applied to Genetics

I collaborate with Robin Waples on a number of his projects involving genetics and try to provide statistical solutions to his problems. Here are some of our relevent publications:

  • Waples, R.S., A. Elz, B.D. Arnsberg, J.R. Faulkner, J.J. Hard, E. Timmins-Schiffmann, L.K. Park. In press. Human-mediated evolution in a threatened species? Juvenile life-history changes in Snake River salmon. Evolutionary Applications. [LINK]
  • Waples, R.S., G. Luikart, J.R. Faulkner, and D.A. Tallmon. 2013. Simple life history traits explain key effective population size ratios across diverse taxa. Proceedings of the Royal Societ of London. Series B 280:2013339 [LINK]
  • Waples, R.S., and J.R. Faulkner. 2009. Modeling evolutionary processes in small populations: not as ideal as you think. Molecular Ecology 18(9):1834-1847. [LINK]

Time Series Analysis

I am working with Don Percival on a novel test for detection of white noise in time series. This started as my student project in Percival's time series course and is working its way into a paper which is close to submission. The following are slides from an electronic poster presentation at JSM in 2014:

  • Faulkner, J.R., and D.B. Percival. A new goodness-of-fit test for time series models based on correlation between the sample autocorrelation and partial autocorrelation sequences. Presented at the Joint Statistical Meetings, Boston, MA, August 2014. [SLIDES]