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This is an introduction to Bayesian inference with a focus on hierarchical models and hyper-parameters. We write primarily for an audience of Bayesian novices, but we hope to provide useful insights for seasoned veterans as well. Examples are drawn from gravitational-wave astronomy, though we endeavor for the presentation to be understandable to a broader audience. We begin with a review of the fundamentals: likelihoods, priors, and posteriors. Next, we discuss Bayesian evidence, Bayes factors, odds ratios, and model selection. From there, we describe how posteriors are estimated using samplers such as Markov Chain Monte Carlo algorithms and nested sampling. Finally, we generalize the formalism to discuss hyper-parameters and hierarchical models. We include extensive appendices discussing the creation of credible intervals, Gaussian noise, explicit marginalization, posterior predictive distributions, and selection effects.
Gravitational wave (GW) detection is now commonplace and as the sensitivity of the global network of GW detectors improves, we will observe $mathcal{O}(100)$s of transient GW events per year. The current methods used to estimate their source paramete
The analysis of gravitational wave data involves many model selection problems. The most important example is the detection problem of selecting between the data being consistent with instrument noise alone, or instrument noise and a gravitational wa
Model fitting is possibly the most extended problem in science. Classical approaches include the use of least-squares fitting procedures and maximum likelihood methods to estimate the value of the parameters in the model. However, in recent years, Ba
To support and guide an extensive experimental research into systems biology of signaling pathways, increasingly more mechanistic models are being developed with hopes of gaining further insight into biological processes. In order to analyse these mo
The label switching problem arises in the Bayesian analysis of models containing multiple indistinguishable parameters with arbitrary ordering. Any permutation of these parameters is equivalent, therefore models with many such parameters have extreme