Estimation of Y haplotype frequencies with lower order dependencies

Purps, 2014, A global analysis of Y-chromosomal haplotype diversity for 23 STR loci, Forensic Sci. Int.: Genet., 12, 12, 10.1016/j.fsigen.2014.04.008 Egeland, 2008, Estimating haplotype frequency and coverage of databases, PLOS ONE, 3, 1, 10.1371/journal.pone.0003988 Brenner, 2010, Fundamental problem of forensic mathematics – the evidential value of a rare haplotype, Forensic Sci. Int.: Genet., 4, 281, 10.1016/j.fsigen.2009.10.013 Willuweit, 2011, Y-STR frequency surveying method: a critical reappraisal, Forensic Sci. Int.: Genet., 5, 84, 10.1016/j.fsigen.2010.10.014 Andersen, 2013, Estimating trace-suspect match probabilities for singleton Y-STR haplotypes using coalescent theory, Forensic Sci. Int.: Genet., 7, 264, 10.1016/j.fsigen.2012.11.004 Andersen, 2013, The discrete Laplace exponential family and estimation of Y-STR haplotype frequencies, J. Theoret. Biol., 329, 39, 10.1016/j.jtbi.2013.03.009 Cereda, 2017, Impact of model choice on LR assessment in case of rare haplotype match (frequentist approach), Scand. J. Stat., 44, 230, 10.1111/sjos.12250 Cereda, 2017, Bayesian approach to LR assessment in case of rare type match, Stat. Neerland., 71, 141, 10.1111/stan.12104 Andersen, 2018, Modelling the dependence structure of Y-STR haplotypes using graphical models, Forensic Sci. Int.: Genet., 37, 29, 10.1016/j.fsigen.2018.07.014 Taylor, 2018, Likelihood ratio development for mixed Y-STR profiles, Forensic Sci. Int.: Genet., 35, 82, 10.1016/j.fsigen.2018.03.006 Caliebe, 2018, Match probabilities for Y-chromosomal profiles: a paradigm shift, Forensic Sci. Int.: Genet., 37, 200, 10.1016/j.fsigen.2018.08.009 Caliebe, 2015, No shortcut solution to the problem of Y-STR match probability calculation, Forensic Sci. Int.: Genet., 15, 69, 10.1016/j.fsigen.2014.10.016 Hall, 2016 Andersen, 2018, Discrete Laplace mixture model with applications in forensic genetics, J. Open Source Softw., 3 Lauritzen, 1996 Cowell, 1999 Kovács, 2010, On the approximation of a discrete multivariate probability distribution using the new concept of t-cherry junction tree, 39 Malvestuto, 1991, Approximating discrete probability distributions with decomposable models, IEEE Trans. Syst. Man Cybern., 21, 1287, 10.1109/21.120082 Malvestuto, 2012, A backward selection procedure for approximating a discrete probability distribution by decomposable models, Kybernetika, 48, 825 Beineke, 1969, The number of labeled k-dimensional trees, J. Combin. Theory, 6, 200, 10.1016/S0021-9800(69)80120-1 Siegert, 2015, Shannon's equivocation for forensic Y-STR marker selection, Forensic Sci. Int.: Genet., 16, 216, 10.1016/j.fsigen.2015.02.001 Szántai, 2012, Hypergraphs as a mean of discovering the dependence structure of a discrete multivariate probability distribution, Ann. Oper. Res., 193, 71, 10.1007/s10479-010-0814-y Karger, 2001, Learning markov networks: maximum bounded tree-width graphs, 392 Dagum, 1993, Approximating probabilistic inference in bayesian belief networks is np-hard, Artif. Intell., 60, 141, 10.1016/0004-3702(93)90036-B Kirkeby, 2019, tcherry: Learning the structure of tcherry trees, J. Open Source Softw., 4, 1480, 10.21105/joss.01480 Szántai, 2013, Discovering a junction tree behind a Markov network by a greedy algorithm, Optim. Eng., 14, 503, 10.1007/s11081-013-9232-8 Hallenberg, 2005, Y-chromosome STR haplotypes in Danes, Forensic Sci. Int., 155, 205, 10.1016/j.forsciint.2004.12.019 R Core Team, 2018 Andersen, 2018, malan. MAle Lineage Analysis, J. Open Source Softw., 3 Willuweit, 2015, The new Y chromosome haplotype reference database, Forensic Sci. Int.: Genet., 15, 43, 10.1016/j.fsigen.2014.11.024 Chow, 1968, Approximating discrete probability distributions with dependence trees, IEEE Trans. Inform. Theory, 14, 462, 10.1109/TIT.1968.1054142 Scutari, 2010, Learning Bayesian networks with the bnlearn R package, J. Stat. Softw., 35, 1, 10.18637/jss.v035.i03 Højsgaard, 2012, Graphical independence networks with the gRain package for R, J. Stat. Softw., 46, 1 Andersen, 2015 Proulx, 2014, Modeling social network relationships via t-cherry junction trees, IEEE INFOCOM 2014 – IEEE Conference on Computer Communications, 2229, 10.1109/INFOCOM.2014.6848166 Brenner, 2014, Understanding Y haplotype matching probability, Forensic Sci. Int.: Genet., 8, 233, 10.1016/j.fsigen.2013.10.007 Andersen, 2017, How convincing is a matching Y-chromosome profile?, PLOS Genet., 13, e1007028, 10.1371/journal.pgen.1007028 Andersen, 2019, Y-profile evidence: close paternal relatives and mixtures, Forensic Sci. Int.: Genet., 38, 48, 10.1016/j.fsigen.2018.10.004 Sainudiin, 2004, Microsatellite mutation models, Genetics, 168, 383, 10.1534/genetics.103.022665 Jochens, 2011, Empirical evaluation reveals best fit of a logistic mutation model for human y-chromosomal microsatellites, Genetics, 189, 1403, 10.1534/genetics.111.132308 Simonsson, 2016, Stationary mutation models, Forensic Sci. Int.: Genet., 23, 217, 10.1016/j.fsigen.2016.04.005