Hans J. Skaug's picture

Hans J. Skaug

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

Biostatistics and computational statistics

I am interested in applications of statistics and probability to biology, especially to marine ecology. I have developed methods for line transect surveys and population genetics, close-kin methods in particular. A second field of research is computational statistics. My conjecture about the future is that a combination of the Laplace approximation and Automatic Differentiation (AD) will enable the statistician to build and fit (almost) all the latent variable models he/she would like.

I have been contributing to the following software projects that both use AD and Laplace approximation:


Spring 2015: STAT211 Time series

Fall     2014: STAT101 Elementary statistics

Spring 2014: STAT202 Biostatistics

Fall     2013: STAT101 Elementary statistics

  • Malde, Ketil; Seliussen, Bjørghild Breistein; Sanchez, Maria Quintela; Dahle, Geir; Besnier, Francois; Skaug, Hans J.; Øien, Nils Inge; Solvang, Hiroko Kato; Haug, Tore; Skern-Mauritzen, Rasmus; Kanda, Naohisa; Pastene, Luis A.; Jonassen, Inge; Glover, Kevin. 2017. Whole genome resequencing reveals diagnostic markers for investigating global migration and hybridization between minke whale species. BMC Genomics. 18:76: 1-11. doi: 10.1186/s12864-016-3416-5
  • Mannseth, Janne; Kleppe, Tore Selland; Skaug, Hans J. 2017. On the application of improved symplectic integrators in Hamiltonian Monte Carlo. Communications in statistics. Simulation and computation. 10 pages. doi: 10.1080/03610918.2017.1283703
  • Skaug, Hans J. 2017. The parent-offspring probability when sampling age-structured populations. Theoretical Population Biology. 118: 20-26. doi: 10.1016/j.tpb.2017.09.001
  • Bravington, Mark V.; Skaug, Hans J.; Anderson, Eric C. 2016. Close-kin mark-recapture. Statistical Science. 31: 259-274. doi: 10.1214/16-STS552
  • Kristensen, Kasper; Nielsen, Anders; Berg, Casper W.; Skaug, Hans J.; Bell, Bradley M. 2016. TMB: Automatic differentiation and laplace approximation. Journal of Statistical Software. 70: 1-21. doi: 10.18637/jss.v070.i05
  • Vincenzi, Simone; Crivelli, Alain J.; Munch, Stephan; Skaug, Hans J.; Mangel, Marc. 2016. Trade-offs between accuracy and interpretability in von Bertalanffy random-effects models of growth. Ecological Applications. 26: 1535-1552. doi: 10.1890/15-1177
  • Haug, Tore; Øien, Nils Inge; Skaug, Hans J.; Glover, Kevin A. 2015. DNA-register for vågehval: en skattekiste for studier av hvalbiologi. Fisken og Havet, Særnummer. 1-2015: 108-109.
  • Kleppe, Tore Selland; Skaug, Hans J. 2015. Bandwidth selection in pre-smoothed particle filters. Statistics and computing. Published ahead of print. 16 pages. doi: 10.1007/s11222-015-9591-4
  • Oedekoven, Cornelia S; Laake, Jeffrey L; Skaug, Hans J. 2015. Distance sampling with a random scale detection function. Environmental and Ecological Statistics. 22: 725-737. doi: 10.1007/s10651-015-0316-9
  • Thorson, James T.; Scheuerell, Mark D.; Shelton, Andrew O.; See, Kevin E.; Skaug, Hans J.; Kristensen, Kasper. 2015. Spatial factor analysis: A new tool for estimating joint species distributions and correlations in species range. Methods in Ecology and Evolution. 6: 627-637. doi: 10.1111/2041-210X.12359
  • Thorson, James T.; Shelton, Andrew O.; Ward, Eric J.; Skaug, Hans J. 2015. Geostatistical delta-generalized linear mixed models improve precision for estimated abundance indices for West Coast groundfishes. ICES Journal of Marine Science. 72: 1297-1310. doi: 10.1093/icesjms/fsu243
  • Thorson, James T.; Skaug, Hans J.; Kristensen, Kasper; Shelton, Andrew O.; Ward, Eric J.; Harms, John H.; Benante, James A. 2015. The importance of spatial models for estimating the strength of density dependence. Ecology. 96: 1202-1212. doi: 10.1890/14-0739.1.sm
  • Zhang, Yanhui; Oliver, Dean; Chen, Yan; Skaug, Hans J. 2015. Data assimilation by use of the iterative ensemble smoother for 2D facies models. SPE Journal. 20: 169-185. doi: 10.2118/170248-PA
  • Øigård, Tor Arne; Skaug, Hans J. 2015. Fitting state-space models to seal populations with scarce data. ICES Journal of Marine Science. 72: 1462-1469. doi: 10.1093/icesjms/fsu195
  • Anderson, Eric C.; Skaug, Hans J.; Barshis, David J. 2014. Next-generation sequencing for molecular ecology: a caveat regarding pooled samples. Molecular Ecology. 23: 502-512. doi: 10.1111/mec.12609
  • Haug, Tore; Øien, Nils Inge; Skaug, Hans J.; Glover, Kevin. 2014. Unødvendig med fem fangstområder for vågehval. Forskning.no : nettavis med nyheter fra norsk og internasjonal forskning. Published 2014-11-10.
  • Kleppe, Tore Selland; Yu, Jun; Skaug, Hans J. 2014. Maximum likelihood estimation of partially observed diffusion models. Journal of Econometrics. 180: 73-80. doi: 10.1016/j.jeconom.2014.02.002
  • Lorentzen, Rolf; Stordal, Andreas S.; Nævdal, Geir; Karlsen, Hans A; Skaug, Hans J. 2014. Estimation of production rates with transient well-flow modeling and the auxiliary particle filter. SPE Journal. 19: 172-180. doi: 10.2118/165582-PA
  • Sanchez, Maria Quintela; Skaug, Hans J.; Øien, Nils Inge; Haug, Tore; Seliussen, Bjørghild Breistein; Solvang, Hiroko Kato; Pampoulie, Christophe; Kanda, Naohisa; Pastene, Luis A.; Glover, Kevin. 2014. Investigating population genetic structure in a highly mobile marine organism: The minke whale balaenoptera acutorostrata acutorostrata in the north east atlantic. PLoS ONE. 9. doi: 10.1371/journal.pone.0108640
  • Skaug, Hans J.; Yu, Jun. 2014. A flexible and automated likelihood based framework for inference in stochastic volatility models. Computational Statistics & Data Analysis. 76: 642-654. doi: 10.1016/j.csda.2013.10.005
  • Vincenzi, Simone; Mangel, Marc; Crivelli, Alain J.; Munch, Stephan; Skaug, Hans J. 2014. Determining individual variation in growth and its implication for life-history and population processes using the Empirical Bayes Method. PloS Computational Biology. 10. doi: 10.1371/journal.pcbi.1003828
  • Bolker, Benjamin M.; Gardner, Beth; Maunder, Mark; Berg, Casper W.; Brooks, Molly; Comita, Liza; Crone, Elizabeth; Cubaynes, Sarah; Davies, Trevor; de Valpine, Perry; Ford, Jessica; Gimenez, Olivier; Kéry, Marc; Kim, Eun Jung; Lennert-Cody, Cleridy; Magnusson, Amy; Martell, Steve; Nash, John; Nielsen, Anders; Regetz, Jim; Skaug, Hans J.; Zipkin, Elise. 2013. Strategies for fitting nonlinear ecological models in R, AD Model Builder, and BUGS. Methods in Ecology and Evolution. 4: 501-512. doi: 10.1111/2041-210X.12044
  • Glover, Kevin; Kanda, Naohisa; Haug, tore; Pastene, Luis A.; Øien, Nils Inge; Seliussen, Bjørghild Breistein; Sørvik, Anne Grete Eide; Skaug, Hans J. 2013. Hybrids between common and Antarctic minke whales are fertile and can back-cross. BMC Genetics. 14. 11 pages. doi: 10.1186/1471-2156-14-25
  • Haaland, Øystein Ariansen; Skaug, Hans J. 2013. Estimating genotyping error rates from parent-offspring dyads. Statistics and Probability Letters. 83: 812-819. doi: 10.1016/j.spl.2012.11.009
  • Langrock, Roland; Borchers, David L.; Skaug, Hans J. 2013. Markov-modulated nonhomogeneous poisson processes for modeling detections in surveys of marine mammal abundance. Journal of the American Statistical Association. 108: 840-851. doi: 10.1080/01621459.2013.797356
  • Fournier, David A.; Skaug, Hans J.; Ancheta, Johnoel; Ianelli, James; Magnusson, Arni; Maunder, Mark N.; Nielsen, Anders; Sibert, John. 2012. AD Model Builder: using automatic differentiation for statistical inference of highly parameterized complex nonlinear models. Optimization Methods and Software. 27: 233-249. doi: 10.1080/10556788.2011.597854
  • Glover, Kevin Alan; Haug, tore; Øien, Nils Inge; Walløe, Lars; Lindblom, Lotta; Seliussen, Bjørghild Breistein; Skaug, Hans J. 2012. The Norwegian minke whale DNA register: a data base monitoring commercial harvest and trade of whale products. Fish and Fisheries. 13: 313-332. doi: 10.1111/j.1467-2979.2011.00447.x
  • Kleppe, Tore Selland; Skaug, Hans J. 2012. Fitting general stochastic volatility models using Laplace accelerated sequential importance sampling. Computational Statistics & Data Analysis. 56: 3105-3119. doi: 10.1016/j.csda.2011.05.007
  • Okamura, Hiroshi; Minamikawa, Shingo; Skaug, Hans J.; Kishiro, Toshiya. 2012. Abundance estimation of long-diving animals using line transect methods. Biometrics. 68: 504-513. doi: 10.1111/j.1541-0420.2011.01689.x
  • Stordal, Andreas S.; Karlsen, Hans A; Nævdal, Geir; Oliver, Dean; Skaug, Hans J. 2012. Filtering with state space localized Kalman gain. Physica D : Non-linear Phenomena. 241: 1123-1135. doi: 10.1016/j.physd.2012.03.006
  • Stordal, Andreas S.; Valestrand, Randi; Karlsen, Hans A; Nævdal, Geir; Skaug, Hans J. 2012. Comparing the adaptive Gaussian mixture filter with the ensemble Kalman filter on synthetic reservoir models. Computational Geosciences. 16: 467-482. Published 2012-11-23. doi: 10.1007/s10596-011-9262-2
  • Torrissen, Ole; Glover, Kevin; Haug, tore; Misund, Ole Arve; Skaug, Hans J.; Kaiser, Matthias. 2012. Good ethics or political and cultural censoring in science? ICES Journal of Marine Science. 69: 493-497. doi: 10.1093/icesjms/fss016
  • Haaland, Øystein; Glover, Kevin A.; Seliussen, Bjørghild Breistein; Skaug, Hans Julius. 2011. Genotyping errors in a calibrated DNA register: implications for identification of individuals. BMC Genetics. 12. 10 pages. doi: 10.1186/1471-2156-12-36
  • Stordal, Andreas S.; Karlsen, Hans A; Nævdal, Geir; Skaug, Hans Julius; Vallès, Brice. 2011. Bridging the ensemble Kalman filter and particle filters: the adaptive Gaussian mixture filter. Computational Geosciences. 15: 293-305. doi: 10.1007/s10596-010-9207-1
  • Thulin, Kristian; Nævdal, Geir; Skaug, Hans Julius; Aanonsen, Sigurd Ivar. 2011. Quantifying Monte Carlo Uncertainty in the Ensemble Kalman Filter. SPE Journal. 16: 172-182.
  • Glover, Kevin; Kanda, Naohisa; Haug, Tore; Pastene, Luis A.; Øien, Nils Inge; Goto, Mutsuo; Seliussen, Bjørghild B; Skaug, Hans Julius. 2010. Migration of Antarctic Minke Whales to the Arctic. PLoS ONE. 5. doi: 10.1371/journal.pone.0015197
  • Kleppe, Tore Selland; Green, William; Yu, Jun; Hill, R. Carter; Skaug, Hans Julius. 2010. Maximum Simulated Likelihood Methods and Applications. Emerald Group Publishing Limited. ISBN: 978-0-85724-149-8.
  • Kleppe, Tore Selland; Skaug, Hans J.; hiroshi, okamura. 2010. Asymptotic bias of the hazard probability model under model mis-specification. Journal of Cetacean Research and Management. 11: 249-252.
  • Kleppe, Tore Selland; Yu, Jun; Skaug, Hans Julius. 2010. Simulated maximum likelihood estimation of continuous time stochastic volatility models. -, pages 137-161. In:
    • Kleppe, Tore Selland; Green, William; Yu, Jun; Hill, R. Carter; Skaug, Hans Julius. 2010. Maximum Simulated Likelihood Methods and Applications. Emerald Group Publishing Limited. ISBN: 978-0-85724-149-8.
  • Le Rouzic, Arnaud; Skaug, Hans Julius; Hansen, Thomas F. 2010. Estimating genetic architectures from artificial-selection responses: A random-effect framework. Theoretical Population Biology. 77: 119-130. doi: 10.1016/j.tpb.2009.12.003
  • Liow, Lee Hsiang; Skaug, Hans Julius; Ergon, Torbjørn H.; Schweder, Tore. 2010. Global occurrence trajectories of microfossils: environmental volatility and the rise and fall of individual species. Paleobiology. 36: 224-252. doi: 10.1666/08080.1
  • Skaug, Hans Julius; Berube, Martine; Palsbøll, Per. 2010. Detecting dyads of related individuals in large collections of DNA-profiles by controlling the false discovery rate. Molecular Ecology Resources. 10: 693-700. doi: 10.1111/j.1755-0998.2010.02833.x
  • Skaug, Hans Julius; Øien, Nils Inge; Haug, Tore. 2010. Hva kan et register over vågehvalens DNA fortelle om adferd og biologi? Ottar. 280: 10-15.
  • Økland, Jan-Magnus; Haaland, Øystein; Skaug, Hans Julius. 2010. A method for defining management units based on genetically determined close relatives. ICES Journal of Marine Science. 67: 551-558. doi: 10.1093/icesjms/fsp260
  • Kleppe, Tore Selland; Skaug, Hans Julius. 2008. Building and Fitting Non-Gaussian Latent Variable Models via the Moment-Generating Function. Scandinavian Journal of Statistics. 35: 664-676. doi: 10.1111/j.1467-9469.2008.00611.x
  • Paulsen, Jostein; Lunde, Astrid; Skaug, Hans Julius. 2008. Fitting mixed-effects models when data are left truncated. Insurance, Mathematics & Economics. 43: 121-133. doi: 10.1016/j.insmatheco.2008.03.010
  • Skaug, Hans Julius; Berube, Martine; Rew, Mary Beth; Palsbøll, Per. 2008. Genetic analyses reveal promiscuous mating in female minke whales, Balaenoptera acutorostrata. Journal of Cetacean Research and Management. 9: 249-251.
  • Skaug, Hans Julius; Frimannslund, Lennart; Øien, Nils Inge. 2007. Historical population assessment of Barents Sea harp sea's (Pagophilus groenlandicus). ICES Journal of Marine Science. 64: 1356-1365.
  • Kitakado, T; Kitada, S; Kishino, H; Skaug, Hans Julius. 2006. An integrated-likelihood method for estimating genetic differentiation between populations. Genetics. 173: 2073-2082.
  • Palsbøll, Per; Berube, Martine; Skaug, Hans Julius; Raymakers, Caroline. 2006. DNA registers of legally obtained wildlife and derived products as means to identify illegal takes. Conservation Biology. 4: 1284-1293.
  • Skaug, Hans Julius. 2006. Markov modulated Poisson processes for clustered line transect data. Environmental and Ecological Statistics. 13: 199-211.
  • Skaug, Hans Julius; Fournier, David. 2006. Automatic Approximation of the Marginal Likelihood in non-Gaussian Hierarchical Models. Computational Statistics & Data Analysis. 51: 699-709.
  • Skaug, Hans Julius; Øien, Nils. 2005. Genetic tagging of males in North Atlantic minke whales through comparison of mother and fetus DNA-profiles. Journal of Cetacean Research and Management. 7: 113-117.
  • Skaug, Hans Julius; Øien, Nils. 2005. Genetic tagging of male North Atlantic minke whales through comparison of maternal and foetal DNA-profiles. Journal of Cetacean Research and Management. 7: 113-117.
  • Trenkel, Verena; Skaug, Hans Julius. 2005. Disentangling the effects of capture efficiency and population abundance on catch data using random effects models. ICES Journal of Marine Science. 62: 1543-1555.
  • Skaug, Hans Julius; Øien, Nils; Schweder, Tore; Bøthun, Gjermund. 2004. Abundance of minke whales (Balaenoptera acutorostrata) in the Northeastern Atlantic. Canadian Journal of Fisheries and Aquatic Sciences. 61: 870-886.
  • Skaug, Hans Julius. 2002. Automatic differentiation to facilitate maximum likelihood estimation in nonlinear random effects models. Journal of Computational And Graphical Statistics. 458-470.
  • Skaug, Hans Julius. 2001. Allele-sharing methods for estimation of population size. Biometrics. 55: 750-756.
  • Hirst, David; Høst, Gudmund; Schweder, Tore; Fotland, Åge; Jakobsen, Tore; Skaug, Hans Julius; Mehl, Sigbjørn; Bogstad, Bjarte. 2000. Towards a statistical model for the uncertainty in fisheries data for stock asssessment in the Barents Sea. NR-notat. SAMBA/06/00. Norsk Regnesentral, Oslo. 19 pages.
  • Schweder, Tore; Skaug, Hans J.; Langaas, Mette; Dimakos, Xeni Kristine. 1999. Simulated likelihood methods for complex double-platform line transect surveys. Biometrics. 55: 678-687.
  • Skaug, Hans Julius; Schweder, T. 1999. Hazard models for line transect surveys with independent observers. Biometrics. 55: 29-36.
  • Schweder, Tore; Skaug, Hans J.; Dimakos, Xeni Kristine; Langaas, Mette; Øien, N. 1997. Abundance of northeastern Atlantic minke whales, estimates for 1989 and 1995. Rep. int. Whal. Commn. 47: 453-483.
  • Skaug, Hans J.; Gjøsæter, Harald; Haug, tore; Nilssen, Kjell Tormod; Lindstrøm, Ulf. 1997. Do Minke Whales (Balaenoptera acutorostrara) Exhibit Particular Prey Preferences? Journal of Northwest Atlantic Fishery Science. 22: 91-104.
  • Belsnes, Dag; Bergan, Marius; Dimakos, Xeni Kristine; Hagen, Gro; Hatlebakk, Einar; Hauksson, Brynjulv; Koppervik, Ingvar; Langaas, Mette; Skaug, Hans Julius; Soelberg, Knut. 1996. NAILS-96, System Design and Program Documentation. Ukjent. Published 1996-01-01.
  • Haug, Tore; Lindstrøm, Ulf; Nilssen, Kjell T.; Røttingen, Ingolf; Skaug, Hans Julius. 1996. Diet and food avaliability for Northeastern Atlantic minke whales, Balaenoptera Acutorostrata. Reports of the International Whaling Commission. 46: 371-382. Published 1996-01-01.
  • Schweder, Tore; Skaug, Hans Julius; Dimakos, Xeni Kristine; Langaas, Mette; Øien, Nils. 1996. Abundance of northeastern Atlantic minke whales, estimates for 1989 and 1995. Ukjent. Published 1996-01-01.
  • Skaug, Hans Julius. 1996. Perpendicular distance line transect methods based on integrated spatial hazard probability models. Ukjent. Published 1996-01-01.
  • Follestad, Turid; Høst, Gudmund; Skaug, Hans Julius. 1995. Methods for simulation of stochastic vector-fields in NSPACE. NR-notat. STAT/18/95. Norsk Regnesentral, Oslo. 26 pages.
  • Skaug, Hans Julius. 1994. Nonparametric functional estimation with application to hypothesis testing. Department of Mathematics, University of Bergen, Bergen. 1 pages.
  • Skaug, Hans Julius. 1993. The limit distribution of the Hoeffding statistic for test of serial independence. Report No.22 Jan. 1993. Reports publ.by the Inst.of Mathematics, Dept.of Statistics. Universitetet i Bergen, matematisk institutt.
  • Skaug, Hans Julius; Tjøstheim, Dag Bjarne. 1993. A nonparametric test of serial independence based on the empirical distribution function. Biometrika. 80: 591-602.
  • Skaug, Hans Julius. 1991. Edgeworth utvikling og bootstrapping i tidsrekke analyse.

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