Bayesian Hypothesis Testing: An Alternative to Null Hypothesis Significance Testing (NHST) in Psychology and Social Sciences

Ortega, Alonso; Navarrete, Gorka

doi:10.5772/intechopen.70230

Cited by 31 publications

(26 citation statements)

References 79 publications

(118 reference statements)

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…When the alternative hypotheis refers to a specific point, the LR may also be referred to as the Bayes factor, BF (e.g., Lee & Wagenmakers, 2005;Ortega & Navarrete, 2017). Many authors recommend the LR (or the posterior odds) as alternatives to ST and its p value (Goodman & Royall, 1988;Kruschke & Lidell, 2017;Lindley, 1975).…”

Section: Is the Variability Of The P Value Related To Its Inductive Vmentioning

confidence: 99%

Testing Significance Testing

Krueger

Heck

2018

Collabra: Psychology

View full text Add to dashboard Cite

The practice of Significance Testing (ST) remains widespread in psychological science despite continual criticism of its flaws and abuses. Using simulation experiments, we address four concerns about ST and for two of these we compare ST's performance with prominent alternatives. We find the following: First, the p values delivered by ST predict the posterior probability of the tested hypothesis well under many research conditions. Second, low p values support inductive inferences because they are most likely to occur when the tested hypothesis is false. Third, p values track likelihood ratios without raising the uncertainties of relative inference. Fourth, p values predict the replicability of research findings better than confidence intervals do. Given these results, we conclude that p values may be used judiciously as a heuristic tool for inductive inference. Yet, p values cannot bear the full burden of inference. We encourage researchers to be flexible in their selection and use of statistical methods.

show abstract

Section: Is the Variability Of The P Value Related To Its Inductive Vmentioning

confidence: 99%

Testing Significance Testing

Krueger

Heck

2018

Collabra: Psychology

View full text Add to dashboard Cite

show abstract

“…Bayesian hypothesis tests are a method to determine whether a given dataset better matches one hypothesis or another (Ortega & Navarrete, 2017). Given that there we could not find software to help determine if mitochondrial URFs were protein coding or not, we developed a Bayesian hypothesis test.…”

Section: Bayesian Protein Coding Likelihood Testmentioning

confidence: 99%

“…The test statistic then consisted of the Bayes factor that the ORF was drawn from the coding distribution (See a more detailed exposition in the Supplemental Methods). The Bayes factor allowed us to assess if factors such as sequence length limited the amount of evidence that the hypothesis had to classify that specific locus (Ortega & Navarrete, 2017).…”

Section: Bayesian Protein Coding Likelihood Testmentioning

confidence: 99%

Conserved novel ORFs in the mitochondrial genome of the ctenophore Beroe forskalii

Schultz

Eizenga

Corbett-Detig

et al. 2020

PeerJ

View full text Add to dashboard Cite

To date, five ctenophore species’ mitochondrial genomes have been sequenced, and each contains open reading frames (ORFs) that if translated have no identifiable orthologs. ORFs with no identifiable orthologs are called unidentified reading frames (URFs). If truly protein-coding, ctenophore mitochondrial URFs represent a little understood path in early-diverging metazoan mitochondrial evolution and metabolism. We sequenced and annotated the mitochondrial genomes of three individuals of the beroid ctenophore Beroe forskalii and found that in addition to sharing the same canonical mitochondrial genes as other ctenophores, the B. forskalii mitochondrial genome contains two URFs. These URFs are conserved among the three individuals but not found in other sequenced species. We developed computational tools called pauvre and cuttlery to determine the likelihood that URFs are protein coding. There is evidence that the two URFs are under negative selection, and a novel Bayesian hypothesis test of trinucleotide frequency shows that the URFs are more similar to known coding genes than noncoding intergenic sequence. Protein structure and function prediction of all ctenophore URFs suggests that they all code for transmembrane transport proteins. These findings, along with the presence of URFs in other sequenced ctenophore mitochondrial genomes, suggest that ctenophores may have uncharacterized transmembrane proteins present in their mitochondria.

show abstract

“…Hence, Bayesians are interested in posterior probability distributions. If they select two discrete hypotheses, H and ∼H, from these distributions, they can compute odds ratios p(H|D)/p(∼H|D) or ratios of posterior over the prior odds (Ortega and Navarrete 2017). If they consider an entire distribution of hypotheses (i.e., where the hypothesis is a random variable), an infinite number of odds ratios awaits contemplation.…”

Section: The Bayesian Alternativementioning

confidence: 99%

Putting the P -Value in its Place

Krueger

Heck

2019

The American Statistician

View full text Add to dashboard Cite

As the debate over best statistical practices continues in academic journals, conferences, and the blogosphere, working researchers (e.g., psychologists) need to figure out how much time and effort to invest in attending to experts' arguments, how to design their next project, and how to craft a sustainable longterm strategy for data analysis and inference. The present special issue of The American Statistician promises help. In this article, we offer a modest proposal for a continued and informed use of the conventional p-value without the pitfalls of statistical rituals. Other statistical indices should complement reporting, and extra-statistical (e.g., theoretical) judgments ought to be made with care and clarity.

show abstract

Bayesian Hypothesis Testing: An Alternative to Null Hypothesis Significance Testing (NHST) in Psychology and Social Sciences

Cited by 31 publications

References 79 publications

Testing Significance Testing

Testing Significance Testing

Conserved novel ORFs in the mitochondrial genome of the ctenophore Beroe forskalii

Putting the P -Value in its Place

Contact Info

Product

Resources

About