scholarly journals Assessment of Substitution Model Adequacy Using Frequentist and Bayesian Methods

2010 ◽  
Vol 27 (12) ◽  
pp. 2790-2803 ◽  
Author(s):  
Jennifer Ripplinger ◽  
Jack Sullivan
2015 ◽  
Vol 33 (1) ◽  
pp. 255-267 ◽  
Author(s):  
Sebastián Duchêne ◽  
Francesca Di Giallonardo ◽  
Edward C. Holmes

2019 ◽  
Vol 62 (3) ◽  
pp. 577-586 ◽  
Author(s):  
Garnett P. McMillan ◽  
John B. Cannon

Purpose This article presents a basic exploration of Bayesian inference to inform researchers unfamiliar to this type of analysis of the many advantages this readily available approach provides. Method First, we demonstrate the development of Bayes' theorem, the cornerstone of Bayesian statistics, into an iterative process of updating priors. Working with a few assumptions, including normalcy and conjugacy of prior distribution, we express how one would calculate the posterior distribution using the prior distribution and the likelihood of the parameter. Next, we move to an example in auditory research by considering the effect of sound therapy for reducing the perceived loudness of tinnitus. In this case, as well as most real-world settings, we turn to Markov chain simulations because the assumptions allowing for easy calculations no longer hold. Using Markov chain Monte Carlo methods, we can illustrate several analysis solutions given by a straightforward Bayesian approach. Conclusion Bayesian methods are widely applicable and can help scientists overcome analysis problems, including how to include existing information, run interim analysis, achieve consensus through measurement, and, most importantly, interpret results correctly. Supplemental Material https://doi.org/10.23641/asha.7822592


2005 ◽  
Vol 25 (1_suppl) ◽  
pp. S627-S627
Author(s):  
Mary E Spilker ◽  
Gjermund Henriksen ◽  
Till Sprenger ◽  
Michael Valet ◽  
Isabelle Stangier ◽  
...  
Keyword(s):  

1982 ◽  
Vol 21 (1) ◽  
pp. 83-84
Author(s):  
Karol J. Krotki

The publication reviewed is number 9 in the series" Applied Statistics and Econometrics" edited by Gerhard Tintner, Pierre Desire Truonet, and Heinrich Strecker. The purpose of the series is to publish papers " too long for ordinary journal articles, but not long enough for books . ... . . Upon acceptance, speedy publication can be promised". The abstracts in English, French, and German, usual in this series, are missing from the copy reviewed. The book consists of ten chapters: sampling theory; multi -stage sampling and other fundamental problems; optimum stratification; variances; sampling with replacement and other theoretical issues; experimental design; information theory; a posteriori raising factors ; order statistics; Bayesian methods. Such an ambitious content within 130 pages requires parsimonious presentation. One chapter has been squeezed into hardly more than four pages. The chapter on a posteriori raising factors will be useful in developing countries and particularly when samples do not work out as designed. It will also be refreshing to those limited to the literature in the English language.


Author(s):  
Timothy McGrew

One of the central complaints about Bayesian probability is that it places no constraints on individual subjectivity in one’s initial probability assignments. Those sympathetic to Bayesian methods have responded by adding restrictions motivated by broader epistemic concerns about the possibility of changing one’s mind. This chapter explores some cases where, intuitively, a straightforward Bayesian model yields unreasonable results. Problems arise in these cases not because there is something wrong with the Bayesian formalism per se but because standard textbook illustrations teach us to represent our inferences in simplified ways that break down in extreme cases. It also explores some interesting limitations on the extent to which successive items of evidence ought to induce us to change our minds when certain screening conditions obtain.


2019 ◽  
Vol 23 (10) ◽  
pp. 4323-4331 ◽  
Author(s):  
Wouter J. M. Knoben ◽  
Jim E. Freer ◽  
Ross A. Woods

Abstract. A traditional metric used in hydrology to summarize model performance is the Nash–Sutcliffe efficiency (NSE). Increasingly an alternative metric, the Kling–Gupta efficiency (KGE), is used instead. When NSE is used, NSE = 0 corresponds to using the mean flow as a benchmark predictor. The same reasoning is applied in various studies that use KGE as a metric: negative KGE values are viewed as bad model performance, and only positive values are seen as good model performance. Here we show that using the mean flow as a predictor does not result in KGE = 0, but instead KGE =1-√2≈-0.41. Thus, KGE values greater than −0.41 indicate that a model improves upon the mean flow benchmark – even if the model's KGE value is negative. NSE and KGE values cannot be directly compared, because their relationship is non-unique and depends in part on the coefficient of variation of the observed time series. Therefore, modellers who use the KGE metric should not let their understanding of NSE values guide them in interpreting KGE values and instead develop new understanding based on the constitutive parts of the KGE metric and the explicit use of benchmark values to compare KGE scores against. More generally, a strong case can be made for moving away from ad hoc use of aggregated efficiency metrics and towards a framework based on purpose-dependent evaluation metrics and benchmarks that allows for more robust model adequacy assessment.


2017 ◽  
Vol 14 (134) ◽  
pp. 20170340 ◽  
Author(s):  
Aidan C. Daly ◽  
Jonathan Cooper ◽  
David J. Gavaghan ◽  
Chris Holmes

Bayesian methods are advantageous for biological modelling studies due to their ability to quantify and characterize posterior variability in model parameters. When Bayesian methods cannot be applied, due either to non-determinism in the model or limitations on system observability, approximate Bayesian computation (ABC) methods can be used to similar effect, despite producing inflated estimates of the true posterior variance. Owing to generally differing application domains, there are few studies comparing Bayesian and ABC methods, and thus there is little understanding of the properties and magnitude of this uncertainty inflation. To address this problem, we present two popular strategies for ABC sampling that we have adapted to perform exact Bayesian inference, and compare them on several model problems. We find that one sampler was impractical for exact inference due to its sensitivity to a key normalizing constant, and additionally highlight sensitivities of both samplers to various algorithmic parameters and model conditions. We conclude with a study of the O'Hara–Rudy cardiac action potential model to quantify the uncertainty amplification resulting from employing ABC using a set of clinically relevant biomarkers. We hope that this work serves to guide the implementation and comparative assessment of Bayesian and ABC sampling techniques in biological models.


Author(s):  
Saheb Foroutaifar

AbstractThe main objectives of this study were to compare the prediction accuracy of different Bayesian methods for traits with a wide range of genetic architecture using simulation and real data and to assess the sensitivity of these methods to the violation of their assumptions. For the simulation study, different scenarios were implemented based on two traits with low or high heritability and different numbers of QTL and the distribution of their effects. For real data analysis, a German Holstein dataset for milk fat percentage, milk yield, and somatic cell score was used. The simulation results showed that, with the exception of the Bayes R, the other methods were sensitive to changes in the number of QTLs and distribution of QTL effects. Having a distribution of QTL effects, similar to what different Bayesian methods assume for estimating marker effects, did not improve their prediction accuracy. The Bayes B method gave higher or equal accuracy rather than the rest. The real data analysis showed that similar to scenarios with a large number of QTLs in the simulation, there was no difference between the accuracies of the different methods for any of the traits.


Sign in / Sign up

Export Citation Format

Share Document