Bayesian parameter estimation and Bayesian hypothesis testing present attractive alternatives to classical inference using confidence intervals and p values. In part I of this series we outline ten prominent advantages of the Bayesian approach. Many of these advantages translate to concrete opportunities for pragmatic researchers. For instance, Bayesian hypothesis testing allows researchers to quantify evidence and monitor its progression as data come in, without needing to know the intention with which the data were collected. We end by countering several objections to Bayesian hypothesis testing. Part II of this series discusses JASP, a free and open source software program that makes it easy to conduct Bayesian estimation and testing for a range of popular statistical scenarios (Wagenmakers et al. this issue).
- MeSH
- Bayes Theorem * MeSH
- Humans MeSH
- Psychology * MeSH
- Research Design MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Bayesian hypothesis testing presents an attractive alternative to p value hypothesis testing. Part I of this series outlined several advantages of Bayesian hypothesis testing, including the ability to quantify evidence and the ability to monitor and update this evidence as data come in, without the need to know the intention with which the data were collected. Despite these and other practical advantages, Bayesian hypothesis tests are still reported relatively rarely. An important impediment to the widespread adoption of Bayesian tests is arguably the lack of user-friendly software for the run-of-the-mill statistical problems that confront psychologists for the analysis of almost every experiment: the t-test, ANOVA, correlation, regression, and contingency tables. In Part II of this series we introduce JASP ( http://www.jasp-stats.org ), an open-source, cross-platform, user-friendly graphical software package that allows users to carry out Bayesian hypothesis tests for standard statistical problems. JASP is based in part on the Bayesian analyses implemented in Morey and Rouder's BayesFactor package for R. Armed with JASP, the practical advantages of Bayesian hypothesis testing are only a mouse click away.
- MeSH
- Bayes Theorem * MeSH
- Humans MeSH
- Psychology * MeSH
- Software * MeSH
- Research Design MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
The Iowa Gambling Task (IGT) is one of the most popular experimental paradigms for comparing complex decision-making across groups. Most commonly, IGT behavior is analyzed using frequentist tests to compare performance across groups, and to compare inferred parameters of cognitive models developed for the IGT. Here, we present a Bayesian alternative based on Bayesian repeated-measures ANOVA for comparing performance, and a suite of three complementary model-based methods for assessing the cognitive processes underlying IGT performance. The three model-based methods involve Bayesian hierarchical parameter estimation, Bayes factor model comparison, and Bayesian latent-mixture modeling. We illustrate these Bayesian methods by applying them to test the extent to which differences in intuitive versus deliberate decision style are associated with differences in IGT performance. The results show that intuitive and deliberate decision-makers behave similarly on the IGT, and the modeling analyses consistently suggest that both groups of decision-makers rely on similar cognitive processes. Our results challenge the notion that individual differences in intuitive and deliberate decision styles have a broad impact on decision-making. They also highlight the advantages of Bayesian methods, especially their ability to quantify evidence in favor of the null hypothesis, and that they allow model-based analyses to incorporate hierarchical and latent-mixture structures.
- MeSH
- Bayes Theorem * MeSH
- Executive Function physiology MeSH
- Data Interpretation, Statistical * MeSH
- Humans MeSH
- Neuropsychological Tests * MeSH
- Reinforcement, Psychology * MeSH
- Models, Psychological * MeSH
- Decision Making physiology MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Review MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
Networks 13 -- 1.2.3 The úr-Separation Criterion 16 -- 1.2.4 Inference with Bayesian Networks 20 -- 1.3 Causal Bayesian Networks 21 -- 1.3.1 Causal Networks as Oracles for Interventions 22 -- 1.3.2 Causal Rules 85 -- 3.4.3 Symbolic Derivation of Causal Effects: An Example 86 -- 3.4.4 Causal Inference by 180 -- 6.2 Why There Is No Statistical Test for Confounding, Why Many -- Think There Is, and Why They , and Graphical Vocabulary 331 -- 11.1.1 Is the Causal-Statistical Dichotomy Necessary?
1st ed. xii, 384 s.
- MeSH
- Causality MeSH
- Probability MeSH
- Conspectus
- Přírodní vědy. Matematické vědy
- NML Fields
- přírodní vědy
- statistika, zdravotnická statistika
Models based on ordinary differential equations (ODE) are widespread tools for describing dynamical systems. In biomedical sciences, data from each subject can be sparse making difficult to precisely estimate individual parameters by standard non-linear regression but information can often be gained from between-subjects variability. This makes natural the use of mixed-effects models to estimate population parameters. Although the maximum likelihood approach is a valuable option, identifiability issues favour Bayesian approaches which can incorporate prior knowledge in a flexible way. However, the combination of difficulties coming from the ODE system and from the presence of random effects raises a major numerical challenge. Computations can be simplified by making a normal approximation of the posterior to find the maximum of the posterior distribution (MAP). Here we present the NIMROD program (normal approximation inference in models with random effects based on ordinary differential equations) devoted to the MAP estimation in ODE models. We describe the specific implemented features such as convergence criteria and an approximation of the leave-one-out cross-validation to assess the model quality of fit. In pharmacokinetics models, first, we evaluate the properties of this algorithm and compare it with FOCE and MCMC algorithms in simulations. Then, we illustrate NIMROD use on Amprenavir pharmacokinetics data from the PUZZLE clinical trial in HIV infected patients.
- MeSH
- Algorithms MeSH
- Bayes Theorem MeSH
- HIV Infections drug therapy MeSH
- Carbamates pharmacokinetics MeSH
- Clinical Trials as Topic MeSH
- Anti-HIV Agents pharmacokinetics MeSH
- Humans MeSH
- Drug Monitoring instrumentation methods MeSH
- Likelihood Functions MeSH
- Reproducibility of Results MeSH
- Software * MeSH
- Models, Statistical MeSH
- Sulfonamides pharmacokinetics MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
Monte Carlo statistical methods, particularly those based on Markov chains, are now an essential component He has written three other books, including The Bayesian Choice, Second Edition, Springer 2001. He has served as the Theory and Methods Editor of the Journal of the American Statistical Association and Executive Editor of Statistical Science. He has authored three other textbooks: Statistical Inference, Second Edition, 2001, with Roger L.
Springer texts in statistics
2nd ed. xxx, 645 s., grafy
- Conspectus
- Statistika
- NML Fields
- statistika, zdravotnická statistika
The ciliate genus Spirostomum comprises eight morphospecies, inhabiting diverse aquatic environments worldwide, where they can be used as water quality indicators. Although Spirostomum species are relatively easily identified using morphological methods, the previous nuclear rDNA-based phylogenies indicated several conflicts in morphospecies delineation. Moreover, the single locus phylogenies and previous analytical approaches could not unambiguously resolve phylogenetic relationships among Spirostomum morphospecies. Here, we attempt to investigate species boundaries and evolutionary history of Spirostomum taxa, using 166 new sequences from multiple populations employing one mitochondrial locus (CO1 gene) and two nuclear loci (rRNA operon and alpha-tubulin gene). In accordance with previous studies, relationships among the eight Spirostomum morphospecies were poorly supported statistically in individual gene trees. To overcome this problem, we utilised for the first time in ciliates the Bayesian coalescent approach, which accounts for ancestral polymorphisms, incomplete lineage sorting, and recombination. This strategy enabled us to robustly resolve deep relationships between Spirostomum species and to support the hypothesis that taxa with compact macronucleus and taxa with moniliform macronucleus each form a distinct lineage. Bayesian coalescent-based delimitation analyses strongly statistically supported the traditional morphospecies concept but also indicated that there are two S. minus-like cryptic species and S. teres is non-monophyletic. Spirostomum teres was very likely defined by a set of ancestral features of lineages that also gave rise to S. yagiui and S. dharwarensis. However, molecular data from type populations of the morphospecies S. minus and S. teres are required to unambiguously resolve the taxonomic problems.
- MeSH
- Bayes Theorem MeSH
- Ciliophora classification genetics MeSH
- Species Specificity MeSH
- Phylogeny * MeSH
- Macronucleus genetics MeSH
- DNA, Ribosomal analysis MeSH
- RNA, Protozoan analysis MeSH
- RNA, Ribosomal, 18S analysis MeSH
- Sequence Analysis, DNA MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
branch and bound -- Ancestral states and branch lengths -- Variants of parsimony -- Compatibility -- Statistical evolution -- Restriction sites, RAPDS, and microsatellites -- Likelihood methods -- Hadamard methods -- Bayesian inference of phylogenies
xx, 664 stran : grafy 23 cm
- Conspectus
- Obecná botanika
- NML Fields
- botanika
- NML Publication type
- učebnice vysokých škol
completely revised and updated -- In the twenty years since publication of the first edition of The Statistical update their classic text with these and other current developments in the second edition of The Statistical Other chapters include: -- Inference in Parametric Models and Related Topics Relative Risk (Cox) Regression Data -- With its comprehensive survey of the field and resources tor students and researchers, The Statistical Inference in Parametric Models and Related Topics -- 3.1 Introduction, 52 -- 3.2 Censoring Mechanisms
Wiley series in probability and statistics
2nd ed. xiii, 439 s.
- Keywords
- Analýza dat, Analýza statistická, Regrese,
- Conspectus
- Statistika
- NML Fields
- statistika, zdravotnická statistika
In order to clarify the phylogenetic relationships among the main marine myxosporean clades including newly established Ceratonova clade and scrutinizing their evolutionary origins, we performed large-scale phylogenetic analysis of all myxosporean species from the marine myxosporean lineage based on three gene analyses and statistical topology tests. Furthermore, we obtained new molecular data for Ceratonova shasta, C. gasterostea, eight Ceratomyxa species and one Myxodavisia species. We described five new species: Ceratomyxa ayami n. sp., C. leatherjacketi n. sp., C. synaphobranchi n. sp., C. verudaensis n. sp. and Myxodavisia bulani n. sp.; two of these formed a new, basal Ceratomyxa subclade. We identified that the Ceratomyxa clade is basal to all other marine myxosporean lineages, and Kudoa with Enteromyxum are the most recently branching clades. Topologies were least stable at the nodes connecting the marine urinary clade, the marine gall bladder clade and the Ceratonova clade. Bayesian inference analysis of SSU rDNA and the statistical tree topology tests suggested that Ceratonova is closely related to the Enteromyxum and Kudoa clades, which represent a large group of histozoic species. A close relationship between Ceratomyxa and Ceratonova was not supported, despite their similar myxospore morphologies. Overall, the site of sporulation in the vertebrate host is a more accurate predictor of phylogenetic relationships than the morphology of the myxospore.
- MeSH
- Bayes Theorem MeSH
- Biological Evolution * MeSH
- Phylogeny * MeSH
- Models, Genetic MeSH
- Myxozoa classification MeSH
- Likelihood Functions MeSH
- DNA, Ribosomal genetics MeSH
- Sequence Analysis, DNA MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
