12 References
Albert, James H, and Siddhartha Chib. 1993. “Bayesian Analysis of Binary and Polychotomous Response Data.” Journal of the American Statistical Association 88 (422): 669–79.
Barnard, J., R. McCulloch, and X. L. Meng. 2000. “Modeling Covariance Matrices in Terms of Standard Deviations and Correlations, with Application to Shrinkage.” Statistica Sinica 10 (4): 1281–311.
Bates, Douglas, Martin Mächler, Ben Bolker, and Steve Walker. 2015. “Fitting Linear Mixed-Effects Models Using Lme4.” Journal of Statistical Software 67: 1–48.
Box, G. E. P., and G. C. Tiao. 1973. Bayesian Inference in Statistical Analysis. New York: John Wiley & Sons.
Brooks, Mollie E, Kasper Kristensen, Koen J Van Benthem, Arni Magnusson, Casper W Berg, Anders Nielsen, Hans J Skaug, Martin Mächler, and Benjamin M Bolker. 2017. “glmmTMB Balances Speed and Flexibility Among Packages for Zero-Inflated Generalized Linear Mixed Modeling.”
Browne, W. J., F. Steele, M. Golalizadeh, and M. J. Green. 2009. “The Use of Simple Reparameterizations to Improve the Efficiency of Markov Chain Monte Carlo Estimation for Multilevel Models with Applications to Discrete Time Survival Models.” Journal of the Royal Statistical Society Series A - Statistics in Society 172: 579–98.
Bürkner, Paul-Christian. 2017. “brms: An R Package for Bayesian Multilevel Models Using Stan.” Journal of Statistical Software 80 (1): 1–28.
Butler, DG, BR Cullis, AR Gilmour, BJ Gogel, and Ret al Thompson. 2017. “ASReml-R Reference Manual Version 4.” VSN International Ltd, Hemel Hempstead, HP1 1ES, UK.
Carpenter, Jennifer A, Jarrod D Hadfield, Jenny Bangham, and Francis M Jiggins. 2012. “Specific Interactions Between Host and Parasite Genotypes Do Not Act as a Constraint on the Evolution of Antiviral Resistance in Drosophila.” Evolution 66 (4): 1114–25.
Cowles, M. K. 1996. “Accelerating Monte Carlo Markov Chain Convergence for Cumulative–Link Generalized Linear Models.” Statistics and Computing 6 (2): 101–11.
Davis, T. A. 2006. Direct Methods for Sparse Linear Systems. Fundamentals of Algorithms. Philadelphia: SIAM.
Diggle, P., P. Heagerty, K. Liang, and S. Zeger. 2004. Analysis of Longitudinal Data. II. Oxford University Press.
Dyk, D. A. van, and X. L. Meng. 2001. “The Art of Data Augmentation.” Journal of Computational and Graphical Statistics 10 (1): 1–50.
Garcia-Cortes, L. A., and D. Sorensen. 2001. “Alternative Implementations of Monte Carlo EM Algorithms for Likelihood Inferences.” Genetics Selection Evolution 33 (4): 443–52.
Gelman, A. 2006. “Prior Distributions for Variance Parameters in Hierarchical Models.” Bayesian Analysis 1 (3): 515–33.
Gelman, A., J. B. Carlin, H. S. Stern, and D. B. Rubin. 2004. Bayesian Data Analysis. 2nd ed. Texts in Statistical Science. Chapman & Hall.
Gelman, A., D. A. van Dyk, Z. Y. Huang, and W. J. Boscardin. 2008. “Using Redundant Parameterizations to Fit Hierarchical Models.” Journal of Computational and Graphical Statistics 17 (1): 95–122.
Gelman, A., A. Jakulin, M. G. Pittau, and Y. Su. 2008. “A Weakly Informative Default Prior Distribution for Logistic and Other Regression Models.”
Gianola, D., and D. Sorensen. 2004. “Quantitative Genetic Models for Describing Simultaneous and Recursive Relationships Between Phenotypes.” Genetics 167 (3): 1407–24.
Haario, H., E. Saksman, and J. Tamminen. 2001. “An Adaptive Metropolis Algorithm.” Bernoulli 7 (2): 223–42.
Hadfield, J. D. 2010. “MCMC Methods for Multi–Response Generalised Linear Mixed Models: The MCMCglmm R Package.” Journal of Statistical Software 33 (2): 1–22.
Hadfield, J. D., and S. Nakagawa. 2010. “General Quantitative Genetic Methods for Comparative Biology: Phylogenies, Taxonomies, Meta-Analysis and Multi-Trait Models for Continuous and Categorical Characters.” Journal of Evolutionary Biology 23 (3): 494–508.
Hauck Jr, Walter W, and Allan Donner. 1977. “Wald’s Test as Applied to Hypotheses in Logit Analysis.” Journal of the American Statistical Association 72 (360a): 851–53.
Henderson, C. R. 1976. “Simple Method for Computing Inverse of a Numerator Relationship Matrix Used in Prediction of Breeding Values.” Biometrics 32 (1): 69–83.
Hinde, John. 1982. “Compound Poisson Regression Models.” In Glim 82: Proceedings of the International Conference on Generalised Linear Models, 109–21. Springer.
Korsgaard, I. R., A. H. Andersen, and D. Sorensen. 1999. “A Useful Reparameterisation to Obtain Samples from Conditional Inverse Wishart Distributions.” Genetics Selection Evolution 31 (2): 177–81.
Liu, C. H., D. B. Rubin, and Y. N. Wu. 1998. “Parameter Expansion to Accelerate EM: The PX–EM Algorithm.” Biometrika 85 (4): 755–70.
Liu, J. S., and Y. N. Wu. 1999. “Parameter Expansion for Data Augmentation.” Journal of the American Statistical Association 94 (448): 1264–74.
Liu, X. F., and M. J. Daniels. 2006. “A New Algorithm for Simulating a Correlation Matrix Based on Parameter Expansion and Reparameterization.” Journal of Computational and Graphical Statistics 15 (4): 897–914.
Lynch, M. 1991. “Methods for the Analysis of Comparative Data in Evolutionary Biology.” Evolution 45 (5): 1065–80.
McCulloch, C. E., and S. R. Searle. 2001. Generalized, Linear and Mixed Models. Wiley Series in Probability and Statistics. New York: John Wiley & Sons.
Meuwissen, T. H. E., and Z. Luo. 1992. “Computing Inbreeding Coefficients in Large Populations.” Genetics Selection Evolution 24 (4): 305–13.
Ovaskainen, O., H. Rekola, E. Meyke, and E. Arjas. 2008. “Bayesian Methods for Analyzing Movements in Heterogeneous Landscapes from Mark–Recapture Data.” Ecology 89 (2): 542–54.
Pascall, David J, Matthew C Tinsley, Darren J Obbard, and Lena Wilfert. 2018. “Host Evolutionary History Predicts Virus Prevalence Across Bumblebee Species.” BioRxiv, 498717.
Robert, C. P. 1995. “Simulation of Truncated Normal Variables.” Statistics and Computing 5 (2): 121–25.
Spiegelhalter, D. J., N. G. Best, B. R. Carlin, and A. van der Linde. 2002. “Bayesian Measures of Model Complexity and Fit.” Proceedings of the Royal Society of London Series B - Biological Sciences 64 (4): 583–639.
Tokuda, Tomoki, Ben Goodrich, Iven Van Mechelen, Andrew Gelman, and Francis Tuerlinckx. 2025. “Visualizing Distributions of Covariance Matrices.” Journal of Data Science, Statistics, and Visualisation 5 (7).