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Equivalence of variance components between standard and recursive genetic models using LDL′ transformations release_avlld34lrfe5vk3tnacuekaz6u

by Luis Varona, David López-Carbonell, Houssemeddine Srihi, Carlos Hervás-Rivero, Óscar González-Recio, Juan Altarriba

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refs[] {'index': 0, 'target_release_id': None, 'extra': {'authors': ['J Pearl'], 'doi': '10.1017/cbo9780511803161', 'edition': '2', 'unstructured': 'Pearl J. Causality: models, reasoning, and inference. 2nd ed. Cambridge: Cambridge University Press; 2009.', 'volume-title': 'Causality: models, reasoning, and inference'}, 'key': '901_CR1', 'year': 2009, 'container_name': 'Causality: models, reasoning, and inference', 'title': None, 'locator': None}
{'index': 1, 'target_release_id': None, 'extra': {'authors': ['D Gianola'], 'doi': '10.1534/genetics.103.025734', 'unstructured': 'Gianola D, Sorensen D. Quantitative genetic models for describing simultaneous and recursive relationships between phenotypes. Genetics. 2004;167:1407–24.', 'volume': '167'}, 'key': '901_CR2', 'year': 2004, 'container_name': 'Genetics', 'title': None, 'locator': '1407'}
{'index': 2, 'target_release_id': None, 'extra': {'authors': ['CG De Los'], 'doi': '10.3168/jds.s0022-0302(06)72493-6', 'unstructured': 'De Los CG, Gianola D, Heringstad B. A structural equation model for describing relationships between somatic cell score and milk yield in first-lactation dairy cows. J Dairy Sci. 2006;89:4445–55.', 'volume': '89'}, 'key': '901_CR3', 'year': 2006, 'container_name': 'J Dairy Sci', 'title': None, 'locator': '4445'}
{'index': 3, 'target_release_id': None, 'extra': {'authors': ['E López De Maturana'], 'doi': '10.3168/jds.2005-442', 'unstructured': 'López De Maturana E, Legarra A, Varona L, Ugarte E. Analysis of fertility and dystocia in holsteins using recursive models to handle censored and categorical data. J Dairy Sci. 2007;90:2012–24.', 'volume': '90'}, 'key': '901_CR4', 'year': 2007, 'container_name': 'J Dairy Sci', 'title': None, 'locator': '2012'}
{'index': 4, 'target_release_id': None, 'extra': {'authors': ['BD Valente'], 'doi': '10.1186/1297-9686-43-37', 'unstructured': 'Valente BD, Rosa GJM, Silva MA, Teixeira RB, Torres RA. Searching for phenotypic causal networks involving complex traits: an application to European quail. Genet Sel Evol. 2011;43:37.', 'volume': '43'}, 'key': '901_CR5', 'year': 2011, 'container_name': 'Genet Sel Evol', 'title': None, 'locator': '37'}
{'index': 5, 'target_release_id': None, 'extra': {'authors': ['CR Henderson'], 'unstructured': 'Henderson CR. Applications of linear models in animal breeding. Guelph: University of Guelph; 1984.', 'volume-title': 'Applications of linear models in animal breeding'}, 'key': '901_CR6', 'year': 1984, 'container_name': 'Applications of linear models in animal breeding', 'title': None, 'locator': None}
{'index': 6, 'target_release_id': None, 'extra': {'authors': ['L Varona'], 'doi': '10.1534/genetics.107.077818', 'unstructured': 'Varona L, Sorensen D, Thompson R. Analysis of litter size and average litter weight in pigs using a recursive model. Genetics. 2007;177:1791–9.', 'volume': '177'}, 'key': '901_CR7', 'year': 2007, 'container_name': 'Genetics', 'title': None, 'locator': '1791'}
{'index': 7, 'target_release_id': None, 'extra': {'authors': ['MA Tanner'], 'doi': '10.1080/01621459.1987.10478458', 'unstructured': 'Tanner MA, Wong WH. The calculation of posterior distributions by data augmentation. J Am Stat Assoc. 1987;82:528–40.', 'volume': '82'}, 'key': '901_CR8', 'year': 1987, 'container_name': 'J Am Stat Assoc', 'title': None, 'locator': '528'}
{'index': 8, 'target_release_id': None, 'extra': {'authors': ['I Misztal'], 'unstructured': 'Misztal I, Tsuruta S, Lourenco D, Aguilar I, Legarra A, Vitezica Z. Manual for BLUPF90 family of programs. Athens: University of Georgia; 2018.', 'volume-title': 'Manual for BLUPF90 family of programs'}, 'key': '901_CR9', 'year': 2018, 'container_name': 'Manual for BLUPF90 family of programs', 'title': None, 'locator': None}
{'index': 9, 'target_release_id': None, 'extra': {'unstructured': 'Madsen P, Jensen J, Labouriau R, Christensen OF, Sahana G. DMU—a package for analyzing multivariate mixed models in quantitative genetics and genomics. In: Proceedings of the 10th world congress on genetics applied to livestock production. 17–22 August 2014; Vancouver. 2014.'}, 'key': '901_CR10', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 10, 'target_release_id': None, 'extra': {'authors': ['K Meyer'], 'doi': '10.1631/jzus.2007.b0815', 'unstructured': 'Meyer K. WOMBAT: a tool for mixed model analyses in quantitative genetics by restricted maximum likelihood (REML). J Zhejiang Univ Sci B. 2007;8:815–21.', 'volume': '8'}, 'key': '901_CR11', 'year': 2007, 'container_name': 'J Zhejiang Univ Sci B', 'title': None, 'locator': '815'}
{'index': 11, 'target_release_id': None, 'extra': {'authors': ['L Varona'], 'doi': '10.3168/jds.2022-22578', 'unstructured': 'Varona L, González-Recio O. Invited review: recursive models in animal breeding: interpretation, limitations, and extensions. J Dairy Sci. 2023;106:2198–212.', 'volume': '106'}, 'key': '901_CR12', 'year': 2023, 'container_name': 'J Dairy Sci', 'title': None, 'locator': '2198'}
{'index': 12, 'target_release_id': None, 'extra': {'authors': ['J Altarriba'], 'doi': '10.1016/j.livsci.2009.03.013', 'unstructured': 'Altarriba J, Yagüe G, Moreno C, Varona L. Exploring the possibilities of genetic improvement from traceability data. An example in the Pirenaica beef cattle. Livest Sci. 2009;125:115–20.', 'volume': '125'}, 'key': '901_CR13', 'year': 2009, 'container_name': 'Livest Sci', 'title': None, 'locator': '115'}
{'index': 13, 'target_release_id': None, 'extra': {'authors': ['AE Gelfand'], 'doi': '10.1080/01621459.1990.10476213', 'unstructured': 'Gelfand AE, Smith AFM. Sampling-based approaches to calculating marginal densities. J Am Stat Assoc. 1990;85:398–409.', 'volume': '85'}, 'key': '901_CR14', 'year': 1990, 'container_name': 'J Am Stat Assoc', 'title': None, 'locator': '398'}
{'index': 14, 'target_release_id': None, 'extra': {'authors': ['CP Van Tassell'], 'doi': '10.2527/1996.74112586x', 'unstructured': 'Van Tassell CP, Van Vleck LD. Multiple-trait Gibbs sampler for animal models: flexible programs for Bayesian and likelihood-based (co)variance component inference. J Anim Sci. 1996;74:2586–97.', 'volume': '74'}, 'key': '901_CR15', 'year': 1996, 'container_name': 'J Anim Sci', 'title': None, 'locator': '2586'}
{'index': 15, 'target_release_id': None, 'extra': {'authors': ['M Plummer'], 'unstructured': 'Plummer M, Best N, Cowles K, Vines K. CODA: convergence diagnosis and output analysis for MCMC. R News. 2006;6:7–11.', 'volume': '6'}, 'key': '901_CR16', 'year': 2006, 'container_name': 'R News', 'title': None, 'locator': '7'}
{'index': 16, 'target_release_id': None, 'extra': {'authors': ['AR Utrera'], 'unstructured': 'Utrera AR, Van Vleck LD. Heritability estimates for carcass traits of cattle: a review. Genet Mol Res. 2004;3:380–94.', 'volume': '3'}, 'key': '901_CR17', 'year': 2004, 'container_name': 'Genet Mol Res', 'title': None, 'locator': '380'}
{'index': 17, 'target_release_id': None, 'extra': {'authors': ['BD Valente'], 'doi': '10.1534/genetics.113.151209', 'unstructured': 'Valente BD, Rosa GJM, Gianola D, Wu X-L, Weigel K. Is structural equation modeling advantageous for the genetic improvement of multiple traits? Genetics. 2013;194:561–72.', 'volume': '194'}, 'key': '901_CR18', 'year': 2013, 'container_name': 'Genetics', 'title': None, 'locator': '561'}
{'index': 18, 'target_release_id': None, 'extra': {'authors': ['GJM Rosa'], 'doi': '10.2527/jas.2012-5840', 'unstructured': 'Rosa GJM, Valente BD. BREEDING AND GENETICS SYMPOSIUM: Inferring causal effects from observational data in livestock. J Anim Sci. 2013;91:553–64.', 'volume': '91'}, 'key': '901_CR19', 'year': 2013, 'container_name': 'J Anim Sci', 'title': None, 'locator': '553'}
release_date 2024-05-02
release_stage published
release_type article-journal
release_year 2024
subtitle
title Equivalence of variance components between standard and recursive genetic models using LDL′ transformations
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volume 56
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