Bayesian computation via empirical likelihood

Proceedings of the National Academy of Sciences of the United States of America

Volumn 110, Issue 4, 2013, Pages 1321-1326

  Mengersen, Kerrie L ^a   Pudlo, Pierre ^b,c,d   Robert, Christian P ^e,f,g  

^a QUEENSLAND UNIVERSITY OF TECHNOLOGY   (Australia)

^b CENTRE DE BIOLOGIE ET DE GESTION DES POPULATIONS   (France)

^c UNIV MONTPELLIER   (France)

^d LIRMM   (France)

^e UNIVERSITÉ PARIS DAUPHINE   (France)

^f INSTITUT UNIVERSITAIRE DE FRANCE   (France)

^g Centre de Rechercheen Statistique et Economie   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BAYES THEOREM; PRIORITY JOURNAL; SIMULATION; STOCHASTIC MODEL;

ALGORITHMS; BAYES THEOREM; BIOPHYSICAL PHENOMENA; BIOSTATISTICS; GENETICS, POPULATION; LIKELIHOOD FUNCTIONS; MODELS, STATISTICAL; STOCHASTIC PROCESSES;

EID: 84872858974     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1208827110     Document Type: Article

References (42)

1. Tavaré S, Balding DJ, Griffiths RC, Donnelly P (1997) Inferring coalescence times from DNA sequence data. Genetics 145(2):505-518.
2. Beaumont MA, Zhang W, Balding DJ (2002) Approximate Bayesian computation in population genetics. Genetics 162(4):2025-2035.
3. Cornuet JM, et al. (2008) Inferring population history with DIY ABC: A user-friendly approach to approximate Bayesian computation. Bioinformatics 24(23):2713-2719.
4. Cappé O, Moulines E, Rydén T (2004) Hidden Markov Models (Springer, New York).
5. Robert C, Casella G (2004) Monte Carlo Statistical Methods (Springer, New York), 2nd Ed.
6. Pritchard JK, Seielstad MT, Perez-Lezaun A, Feldman MW (1999) Population growth of human Y chromosomes: A study of Y chromosome microsatellites. Mol Biol Evol 16(12):1791-1798.
7. Beaumont M (2010) Approximate Bayesian computation in evolution and ecology. Annu Rev Ecol Evol Syst 41:379-406.
8. Lopes JS, Beaumont MA (2010) ABC: A useful Bayesian tool for the analysis of population data. Infect Genet Evol 10(6):826-833.
9. Bazin E, Dawson KJ, Beaumont MA (2010) Likelihood-free inference of population structure and local adaptation in a Bayesian hierarchical model. Genetics 185(2): 587-602.
10. Marjoram P, Molitor J, Plagnol V, Tavaré S (2003) Markov chain Monte Carlo without likelihoods. Proc Natl Acad Sci USA 100(26):15324-15328.
11. Templeton AR (2010) Coherent and incoherent inference in phylogeography and human evolution. Proc Natl Acad Sci USA 107(14):6376-6381.
12. Berger JO, Fienberg SE, Raftery AE, Robert CP (2010) Incoherent phylogeographic inference. Proc Natl Acad Sci USA 107(41):E157-author reply E158.
13. Robert CP, Cornuet JM, Marin JM, Pillai NS (2011) Lack of confidence in approximate Bayesian computation model choice. Proc Natl Acad Sci USA 108(37):15112-15117.
14. Owen AB (1988) Empirical likelihood ratio confidence intervals for a single functional. Biometrika 75(2):237-249.
15. Marin J, Pudlo P, Robert C, Ryder R (2012) Approximate Bayesian computational methods. Stat Comput 22(6):1167-1180.
16. Biau G, Cérou F, Guyader A (2012) New Insights into Approximate Bayesian Computation. Tech Rep HAL 00721164. Available at http://hal.inria.fr/ hal-00721164/en.
17. Zhou M (2012) emplik: Empirical likelihood ratio for censored/truncated data. R package version 0.9-8-2.
18. Owen AB (2001) Empirical Likelihood (Chapman & Hall, London).
19. Lazar NA (2003) Bayesian empirical likelihood. Biometrika 90:319-326.
20. Schennach SM (2005) Bayesian exponentially tilted empirical likelihood. Biometrika 92(1):31-46.
21. Liu J (2001) Monte Carlo Strategies in Scientific Computing (Springer, New York).
22. Cornuet JM, Marin JM, Mira A, Robert C (2012) Adaptive multiple importance sampling. Scand J Stat 39(4):798-812.
23. Estoup A, Beaumont M, Sennedot F, Moritz C, Cornuet JM (2004) Genetic analysis of complex demographic scenarios: Spatially expanding populations of the cane toad, Bufo marinus. Evolution 58(9):2021-2036.
24. Estoup A, Clegg SM (2003) Bayesian inferences on the recent island colonization history by the bird Zosterops lateralis lateralis. Mol Ecol 12(3):657-674.
25. Fagundes NJ, et al. (2007) Statistical evaluation of alternative models of human evolution. Proc Natl Acad Sci USA 104(45):17614-17619.
26. Lombaert E, et al. (2010) Bridgehead effect in the worldwide invasion of the biocontrol harlequin ladybird. PLoS ONE 5(3):e9743.
27. Ohta H, Kimura M (1973) A model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a finite population. Genet Res 22(2): 201-204, and reprinted in (2007) 89(5-6):367-370.
28. Hudson RR (2001) Two-locus sampling distributions and their application. Genetics 159(4):1805-1817.
29. Kim Y, Stephan W (2002) Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics 160(2):765-777.
30. McVean G, Awadalla P, Fearnhead P (2002) A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics 160(3):1231-1241.
31. Fearnhead P (2003) Consistency of estimators of the population-scaled recombination rate. Theor Popul Biol 64(1):67-79.
32. Barthelmé S, Chopin N (2012) Expectation-propagation for likelihood-free inference. Tech Rep arXiv:1107.5959v2. Available at http://arxiv.org/pdf/1107.5959.
33. Wilson IJ, Balding DJ (1998) Genealogical inference from microsatellite data. Genetics 150(1):499-510.
34. Haynes M, MacGillivray H, Mengersen K (1997) Robustness of ranking and selection rules using generalized g-and k distributions. J Stat Plann Inference 65(1):45-66.
35. GilchristW(2000) StatisticalModelling withQuantile Functions (Chapman&Hall,London).
36. Allingham D, King R, Mengersen K (2009) Bayesian estimation of quantile distributions. Stat Comput 19(2):189-201.
37. Drovandi C, Pettitt A (2011) Likelihood-free Bayesian estimation of multivariate quantile distributions. Comput Stat Data Anal 55(9):2541-2556.
38. Fearnhead P, Prangle D (2012) Semi-automatic approximate Bayesian computation. J R Stat Soc, B 74(3):419-474.
39. Bollerslev T (1986) Generalized autoregressive conditional heteroskedasticity. J Econom 31(3):307-327.
40. Chan N, Ling S (2006) Empirical likelihood for GARCH models. Econometric Theory 22 (3):403-428.
41. Cox D, Kartsonaki C (2012) The fitting of complex parametric models. Biometrika 99 (3):741-747.
42. Cornuet JM, Ravigné V, Estoup A (2010) Inference on population history and model checking using DNA sequence and microsatellite data with the software DIYABC (v1.0). BMC Bioinf 11:401.