Home
  • E-mailHans.Skaug@uib.no
  • Phone+47 55 58 48 61+47 469 45 448
  • Visitor Address
    Realfagbygget, Allegaten 41, 4 etg. sør.
    Bergen
    Room 
    4A17d
  • Postal Address
    Postboks 7803
    5020 Bergen

Biostatistics

I am interested in applications of statistics and probability to biology, especially to marine ecology. I have developed methods for line transect surveys and CKMR (close-kin mark recapture) methods in particular. Key reference for CKMR:

  1. Bravington, MV, Skaug, HJ, Anderson, EC (2016). Close-kin Mark-Recapture. Statistical Science.

Computational statistics

My opinion for a long time has been that Statisticians should have Automatic Differentiation (AD) in their toolbox. AD is the same type of technology as "back-propagation" used in Deep Learning. My conjecture has been that a combination of AD and the Laplace approximation is a powerful platform for fitting models with continuous latent variables. Software projects in which this idea is implemented are:

 

Key references for the AD-Laplace:

  1. Skaug, H.J., Fournier D.A. (2006) Automatic Approximation of the Marginal Likelihood in non-Gaussian Hierarchical Models. Computational Statistics and Data Analysis.
  2. Kristensen, K., Nielsen, A., Berg, C. W., Skaug, H., & Bell, B. (2016). TMB: automatic differentiation and Laplace approximation. Journal of Statistical Software.

Editorial services

co-Editor in chief of Scandinavian Journal of Statistics (2018–2021)

Short courses / workshops (last 5 years)

  • CKMR (Close-kin mark recapture) course (co-thought) Dalhousie University, Halifax, July 2019.
  • TMB (Template Model Builder) course (co-thought) at IMR Bergen, June 2019.
  • Modelling in TMB (Template Model Builder). Course (co-thought) at IMR Bergen,  June 2018.
  • An introduction to fish stock assessment in TMB (Template Model Builder). Course given Oct. 2017 in La Jolla

 

Teaching at UiB (last 5 years)

  • Spring 2018: STAT202 Biostatistics
  • Fall     2017: STAT110 Introduction to statistics
  • Spring 2017: STAT111 Statistical Methods
  • Fall     2016: STAT110 Introduction to statistics
  • Spring 2016: STAT202 BiostatisticsFall     
  • 2015: STAT110 Introduction to statistics
  • Spring 2015: STAT211 Time series

Google Scholar profile: https://scholar.google.com/citations?user=RTHIfAUAAAAJ&hl=no&oi=ao 

From CRIStin (Current research information system in Norway):

  • 2020. Experimental design for parameter estimation in steady-state linear models of metabolic networks. Mathematical Biosciences.
  • 2020. Estimation and identifiability of kinetic parameters in dynamical models of biochemical reaction networks.
  • 2019. dCOD 1.0: DECODING THE SYSTEMS TOXICOLOGY OF ATLANTIC COD (GADUS MORHUA) – HIGHLIGHTS SO FAR.
  • 2019. dCOD 1.0: DECODING THE SYSTEMS TOXICOLOGY OF ATLANTIC COD (GADUS MORHUA) – HIGHLIGHTS SO FAR.
  • 2019. Validation of close‐kin mark–recapture (CKMR) methods for estimating population abundance. Methods in Ecology and Evolution. 1445-1453.
  • 2019. Stochastic data assimilation of observations with a detection limit.
  • 2019. Integration by differentiation; almost a free lunch.
  • 2019. Efficient Computation of Hessian Matrices in TensorFlow . arXiv.org.
  • 2019. Editorial. Scandinavian Journal of Statistics. 1-1.
  • 2019. Drivers of the summer-distribution of Northeast Atlantic mackerel (Scomber scombrus) in the Nordic Seas from 2011 to 2017; a Bayesian hierarchical modelling approach. ICES Journal of Marine Science. 530-548.
  • 2019. Contaminant accumulation and biological responses in Atlantic cod (Gadus morhua) caged at a capped waste disposal site in Kollevåg, Western Norway. Marine Environmental Research. 39-51.
  • 2019. Close-Kin Mark-Recapture (CKMR).
  • 2019. Close-Kin Mark-Recapture (CKMR).
  • 2019. Close kin mark recapture in fisheries .
  • 2019. Bayesian flux balance analysis of metabolic pathways.
  • 2019. Bayesian and frequentist computation with application to data from the Medical Birth Registry of Norway.
  • 2018. dCOD 1.0: DECODING THE SYSTEMS TOXICOLOGY OF ATLANTIC COD (GADUS MORHUA).
  • 2018. Model Reduction for Tracer Transport and Applications.
  • 2018. Mathematical methods for detection and localization of CO2 leaks.
  • 2018. Machine Learning in CO2 leak detection.
  • 2018. Experimental design for estimation of first order kinetic parameters in steady-state metabolic networks.
  • 2018. Ecotoxicological responses in Atlantic cod (Gadus morhua) after caging at a capped waste disposal site in Kollevåg, Western Norway .
  • 2018. Ecotoxicological responses in Atlantic cod (Gadus morhua) after caging at a capped waste disposal site in Kollevåg, Western Norway .
  • 2018. Combining Models and Machine Learning Techniques to Design Leak Detection Monitoring .
  • 2018. Bayesian flux balance analysis; concepts and computation.
  • 2017. glmmTMB balances speed and flexibility among packages for zero-inflated generalized linear mixed modeling. The R Journal. 378-400.
  • 2017. dCod 1.0: decoding the systems toxicology of Atlantic cod (Gadus morhua).
  • 2017. dCod 1.0 decoding the systems toxicology of Atlantic cod.
  • 2017. Whole genome resequencing reveals diagnostic markers for investigating global migration and hybridization between minke whale species. BMC Genomics. 1-11.
  • 2017. The parent-offspring probability when sampling age-structured populations. Theoretical Population Biology. 20-26.
  • 2017. TMB: a flexible framework for developing mixed model software in R.
  • 2017. Structural identifiability of kinetic parameters.
  • 2017. Structural identifiability of kinetic parameters.
  • 2017. PRECISION-CUT LIVER SLICES (PCLS) FOR TOXICOGENOMIC STUDIES IN ATLANTIC COD (Gadus morhua): THE dCOD 1.0 PROJECT.
  • 2017. On the application of improved symplectic integrators in Hamiltonian Monte Carlo. Communications in Statistics - Simulation and Computation. 500-509.
  • 2017. Mathematical modeling of regulatory interactions in the fatty acid synthesis pathway.
  • 2017. Mathematical modeling of regulatory interactions in the fatty acid synthesis pathway.
  • 2017. Mathematical modeling of regulatory interactions in the fatty acid synthesis pathway.
  • 2017. Bayes’ theorem as the fundament to design monitoring programs.
  • 2017. Assessment of machine learning methods as a tool in detecting leakages.
  • 2017. Assessment of Topological Data Analysis and Machine Learning Technologies as Tools for Seep Detection.
  • 2016. Trade-offs between accuracy and interpretability in von Bertalanffy random-effects models of growth. Ecological Applications. 1535-1552.
  • 2016. TMB: Automatic differentiation and laplace approximation. Journal of Statistical Software. 1-21.
  • 2016. Likelihood Estimation of Jump-Diffusions: Extensions from Diffusions to Jump-Diffusions, Implementation with Automatic Differentiation, and Applications.
  • 2016. Close-kin mark-recapture. Statistical Science. 259-274.
  • 2016. Bayes’ theorem as the fundament to design monitoring programs.
  • 2015. The importance of spatial models for estimating the strength of density dependence. Ecology. 1202-1212.
  • 2015. Spatial factor analysis: A new tool for estimating joint species distributions and correlations in species range. Methods in Ecology and Evolution. 627-637.
  • 2015. Panel data model with mixed frequency – an application to producers' pricing behaviour.
  • 2015. Measurement error model for the Norwegian minke whale surveys 2008-2013.
  • 2015. Geostatistical delta-generalized linear mixed models improve precision for estimated abundance indices for West Coast groundfishes. ICES Journal of Marine Science. 1297-1310.
  • 2015. Fitting state-space models to seal populations with scarce data. ICES Journal of Marine Science. 1462-1469.
  • 2015. Distance sampling with a random scale detection function. Environmental and Ecological Statistics. 725-737.
  • 2015. Data assimilation by use of the iterative ensemble smoother for 2D facies models. SPE Journal. 169-185.
  • 2015. DNA-register for vågehval: en skattekiste for studier av hvalbiologi. Fisken og Havet, Særnummer. 108-109.
  • 2015. Bandwidth selection in pre-smoothed particle filters. Statistics and computing. 16 pages.
  • 2015. Abundance estimates of common minke whales in the Northeast Atlantic base don survey data collected over the period 2008-2013.
  • 2014. Unødvendig med fem fangstområder for vågehval. Forskning.no.
  • 2014. Preliminary abundance estimates of common minke whales in the Northeast Atlantic based on survey data collected over the period 2008-2013.
  • 2014. Next-generation sequencing for molecular ecology: a caveat regarding pooled samples. 502-512.
  • 2014. Maximum likelihood estimation of partially observed diffusion models. Journal of Econometrics. 73-80.
  • 2014. Investigating population genetic structure in a highly mobile marine organism: The minke whale balaenoptera acutorostrata acutorostrata in the north east atlantic. PLOS ONE.
  • 2014. Estimation of production rates with transient well-flow modeling and the auxiliary particle filter. SPE Journal. 172-180.
  • 2014. Determining individual variation in growth and its implication for life-history and population processes using the Empirical Bayes Method. PLoS Computational Biology.
  • 2014. Bandwidth Selection In Pre-Smoothed Particle Filters.
  • 2014. A flexible and automated likelihood based framework for inference in stochastic volatility models. Computational Statistics & Data Analysis. 642-654.
  • 2013. Strategies for fitting nonlinear ecological models in R, AD Model Builder, and BUGS. Methods in Ecology and Evolution. 501-512.
  • 2013. Markov-modulated nonhomogeneous poisson processes for modeling detections in surveys of marine mammal abundance. Journal of the American Statistical Association. 840-851.
  • 2013. Hybrids between common and Antarctic minke whales are fertile and can back-cross. BMC Genetics. 11 pages.
  • 2013. Estimating genotyping error rates from parent-offspring dyads. Statistics and Probability Letters. 812-819.
  • 2012. The Norwegian minke whale DNA register: a data base monitoring commercial harvest and trade of whale products. Fish and Fisheries. 313-332.
  • 2012. Numerical comparison of Ensemble Kalman Filter and Randomized maximum Likelihood.
  • 2012. Good ethics or political and cultural censoring in science? ICES Journal of Marine Science. 493-497.
  • 2012. Fitting general stochastic volatility models using Laplace accelerated sequential importance sampling. Computational Statistics & Data Analysis. 3105-3119.
  • 2012. Filtering with state space localized Kalman gain. Physica D : Non-linear phenomena. 1123-1135.
  • 2012. Data Assimilation Using the Iterative Ensemble Smoother for 2-D Categorical Models.
  • 2012. Comparing the adaptive Gaussian mixture filter with the ensemble Kalman filter on synthetic reservoir models. Computational Geosciences. 467-482.
  • 2012. Abundance estimation of long-diving animals using line transect methods. Biometrics. 504-513.
  • 2012. AD Model Builder: using automatic differentiation for statistical inference of highly parameterized complex nonlinear models. Optimization Methods and Software. 233-249.
  • 2011. Quantifying Monte Carlo Uncertainty in the Ensemble Kalman Filter. SPE Journal. 172-182.
  • 2011. Genotyping errors in a calibrated DNA register: implications for identification of individuals. BMC Genetics. 10 pages.
  • 2011. Bridging the ensemble Kalman filter and particle filters: the adaptive Gaussian mixture filter. Computational Geosciences. 293-305.
  • 2010. Simulated maximum likelihood estimation of continuous time stochastic volatility models. 25 pages.
  • 2010. Migration of Antarctic Minke Whales to the Arctic. PLOS ONE.
  • 2010. Maximum Simulated Likelihood Methods and Applications. Emerald Group Publishing Limited.
  • 2010. Hva kan et register over vågehvalens DNA fortelle om adferd og biologi? Ottar. 10-15.
  • 2010. Global occurrence trajectories of microfossils: environmental volatility and the rise and fall of individual species. Paleobiology. 224-252.
  • 2010. Estimating genetic architectures from artificial-selection responses: A random-effect framework. Theoretical Population Biology. 119-130.
  • 2010. Detecting dyads of related individuals in large collections of DNA-profiles by controlling the false discovery rate. Molecular Ecology Resources. 693-700.
  • 2010. Asymptotic bias of the hazard probability model under model mis-specification. Journal of Cetacean Research and Management. 249-252.
  • 2010. A method for defining management units based on genetically determined close relatives. ICES Journal of Marine Science. 551-558.
  • 2008. Genetic analyses reveal promiscuous mating in female minke whales, Balaenoptera acutorostrata. Journal of Cetacean Research and Management. 249-251.
  • 2008. Fitting mixed-effects models when data are left truncated. Insurance, Mathematics & Economics. 121-133.
  • 2008. Estimating distributions of correlated individual life-history traits from mark-recapture data.
  • 2008. Building and Fitting Non-Gaussian Latent Variable Models via the Moment-Generating Function. Scandinavian Journal of Statistics. 664-676.
  • 2007. Historical population assessment of Barents Sea harp sea's (Pagophilus groenlandicus). ICES Journal of Marine Science. 1356-1365.
  • 2006. On Curvature and Separability in Unconstrained Optimisation.
  • 2006. Markov modulated Poisson processes for clustered line transect data. Environmental and Ecological Statistics. 199-211.
  • 2006. DNA registers of legally obtained wildlife and derived products as means to identify illegal takes. Conservation Biology. 1284-1293.
  • 2006. Automatic Approximation of the Marginal Likelihood in non-Gaussian Hierarchical Models. Computational Statistics & Data Analysis. 699-709.
  • 2006. An integrated-likelihood method for estimating genetic differentiation between populations. Genetics. 2073-2082.
  • 2005. Genetic tagging of males in North Atlantic minke whales through comparison of mother and fetus DNA-profiles. Journal of Cetacean Research and Management. 113-117.
  • 2005. Genetic tagging of male North Atlantic minke whales through comparison of maternal and foetal DNA-profiles. Journal of Cetacean Research and Management. 113-117.
  • 2005. Disentangling the effects of capture efficiency and population abundance on catch data using random effects models. ICES Journal of Marine Science. 1543-1555.
  • 2004. Abundance of minke whales (Balaenoptera acutorostrata) in the Northeastern Atlantic. Canadian Journal of Fisheries and Aquatic Sciences. 870-886.
  • 2002. Automatic differentiation to facilitate maximum likelihood estimation in nonlinear random effects models. Journal of Computational And Graphical Statistics. 458-470.
  • 2001. Allele-sharing methods for estimation of population size. Biometrics. 750-756.
  • 2000. Towards a statistical model for the uncertainty in fisheries data for stock asssessment in the Barents Sea. SAMBA/06/00. SAMBA/06/00. .
  • 1999. Simulated likelihood methods for complex double-platform line transect surveys. Biometrics. 678-687.
  • 1999. Hazard models for line transect surveys with independent observers. Biometrics. 29-36.
  • 1997. Do Minke Whales (Balaenoptera acutorostrara) Exhibit Particular Prey Preferences? Journal of Northwest Atlantic Fishery Science. 91-104.
  • 1997. Abundance of northeastern Atlantic minke whales, estimates for 1989 and 1995. Rep. int. Whal. Commn. 453-483.
  • 1996. Perpendicular distance line transect methods based on integrated spatial hazard probability models. Ukjent.
  • 1996. NAILS-96, System Design and Program Documentation. Ukjent.
  • 1996. NAILS-96 Specification document.
  • 1996. Diet and food avaliability for Northeastern Atlantic minke whales, Balaenoptera Acutorostrata. Reports of the International Whaling Commission. 371-382.
  • 1996. Abundance of northeastern Atlantic minke whales, estimates for 1989 and 1995. Ukjent.
  • 1995. Methods for simulation of stochastic vector-fields in NSPACE. STAT/18/95. STAT/18/95. .
  • 1994. Nonparametric tests of serial indepence.
  • 1994. Nonparametric functional estimation with application to hypothesis testing.
  • 1994. Ikkeparametriske tester for seriell uavhengighet.
  • 1993. The limit distribution of the Hoeffding statistic for test of serial independence. Report No.22 Jan. 1993. .
  • 1993. A nonparametric test of serial independence based on the empirical distribution function. Biometrika. 591-602.
  • 1991. Edgeworth utvikling og bootstrapping i tidsrekke analyse.

More information in national current research information system (CRIStin)