Simulation Studies as a Tool to Understand Bayes Factors

When social scientists wish to learn about an empirical phenomenon, they perform an experiment. When they wish to learn about a complex numerical phenomenon, they can perform a simulation study. The goal of this Tutorial is twofold. First, it introduces how to set up a simulation study using the relatively simple example of simulating from the prior. Second, it demonstrates how simulation can be used to learn about the Jeffreys-Zellner-Siow (JZS) Bayes factor, a currently popular implementation of the Bayes factor employed in the BayesFactor R package and freeware program JASP. Many technical expositions on Bayes factors exist, but these may be somewhat inaccessible to researchers who are not specialized in statistics. In a step-by-step approach, this Tutorial shows how a simple simulation script can be used to approximate the calculation of the Bayes factor. We explain how a researcher can write such a sampler to approximate Bayes factors in a few lines of code, what the logic is behind the Savage-Dickey method used to visualize Bayes factors, and what the practical differences are for different choices of the prior distribution used to calculate Bayes factors

Imitation by combination: preschool age children evidence summative imitation in a novel problem-solving task.

Children are exceptional, even \u27super,\u27 imitators but comparatively poor independent problem-solvers or innovators. Yet, imitation and innovation are both necessary components of cumulative cultural evolution. Here, we explored the relationship between imitation and innovation by assessing children\u27s ability to generate a solution to a novel problem by imitating two different action sequences demonstrated by two different models, an example of imitation by combination, which we refer to as summative imitation. Children (N = 181) from 3 to 5 years of age and across three experiments were tested in a baseline condition or in one of six demonstration conditions, varying in the number of models and opening techniques demonstrated. Across experiments, more than 75% of children evidenced summative imitation, opening both compartments of the problem box and retrieving the reward hidden in each. Generally, learning different actions from two different models was as good (and in some cases, better) than learning from 1 model, but the underlying representations appear to be the same in both demonstration conditions. These results show that summative imitation not only facilitates imitation learning but can also result in new solutions to problems, an essential feature of innovation and cumulative culture

Reported self-control is not meaningfully associated with inhibition-related executive function:A Bayesian analysis

Self-control is assessed using a remarkable array of measures. In a series of five data-sets (overall N = 2,641) and a mini meta-analysis, we explored the association between canonical operationalisations of self-control: The Self-Control Scale and two measures of inhibition-related executive functioning (the Stroop and Flanker paradigms). Overall, Bayesian correlational analyses suggested little-to-no relationship between self-reported self-control and performance on the Stroop and Flanker tasks. The Bayesian meta-analytical summary of all five data-sets further favoured a null relationship between both types of measurement. These results suggest that the field’s most widely used measure of self-reported self-control is uncorrelated with two of the most widely adopted executive functioning measures of self-control. Consequently, theoretical and practical conclusions drawn using one measure (e.g., the Self-Control Scale) cannot be generalised to findings using the other (e.g., the Stroop task). The lack of empirical correlation between measures of self-control do not invalidate either measure, but instead suggest that treatments of the construct of self-control need to pay greater attention to convergent validity among the many measures used to operationalize self-control

Replication Bayes factors from evidence updating

We describe a general method that allows experimenters to quantify the evidence from the data of a direct replication attempt given data already acquired from an original study. These so-called replication Bayes factors are a reconceptualization of the ones introduced by Verhagen and Wagenmakers (Journal of Experimental Psychology: General, 143(4), 1457–1475 2014) for the common t test. This reconceptualization is computationally simpler and generalizes easily to most common experimental designs for which Bayes factors are available

Exchange coupling in transition-metal nano-clusters on Cu(001) and Cu(111) surfaces

We present results of density-functional calculations on the magnetic properties of Cr, Mn, Fe and Co nano-clusters (1 to 9 atoms large) supported on Cu(001) and Cu(111). The inter-atomic exchange coupling is found to depend on competing mechanisms, namely ferromagnetic double exchange and antiferromagnetic kinetic exchange. Hybridization-induced broadening of the resonances is shown to be important for the coupling strength. The cluster shape is found to weaken the coupling via a mechanism that comprises the different orientation of the atomic d-orbitals and the strength of nearest-neighbour hopping. Especially in Fe clusters, a correlation of binding energy and exchange coupling is also revealed

Aorto-bronchial and aorto-pulmonary fistulation after thoracic endovascular aortic repair: an analysis from the European Registry of Endovascular Aortic Repair Complications

OBJECTIVES To learn upon incidence, underlying mechanisms and effectiveness of treatment strategies in patients with central airway and pulmonary parenchymal aorto-bronchial fistulation after thoracic endovascular aortic repair (TEVAR). METHODS Analysis of an international multicentre registry (European Registry of Endovascular Aortic Repair Complications) between 2001 and 2012 with a total caseload of 4680 TEVAR procedures (14 centres). RESULTS Twenty-six patients with a median age of 70 years (interquartile range: 60-77) (35% female) were identified. The incidence of either central airway (aorto-bronchial) or pulmonary parenchymal (aorto-pulmonary) fistulation (ABPF) in the entire cohort after TEVAR in the study period was 0.56% (central airway 58%, peripheral parenchymal 42%). Atherosclerotic aneurysm formation was the leading indication for TEVAR in 15 patients (58%). The incidence of primary endoleaks after initial TEVAR was n = 10 (38%), of these 80% were either type I or type III endoleaks. Fourteen patients (54%) developed central left bronchial tree lesions, 11 patients (42%) pulmonary parenchymal lesions and 1 patient (4%) developed a tracheal lesion. The recognized mechanism of ABPF was external compression of the bronchial tree in 13 patients (50%), the majority being due to endoleak formation, further ischaemia due to extensive coverage of bronchial feeding arteries in 3 patients (12%). Inflammation and graft erosion accounted for 4 patients (30%) each. Cumulative survival during the entire study period was 39%. Among deaths, 71% were attributed to ABPF. There was no difference in survival in patients having either central airway or pulmonary parenchymal ABPF (33 vs 45%, log-rank P = 0.55). Survival with a radical surgical approach was significantly better when compared with any other treatment strategy in terms of overall survival (63 vs 32% and 63 vs 21% at 1 and 2 years, respectively), as well as in terms of fistula-related survival (63 vs 43% and 63 vs 43% at 1 and 2 years, respectively). CONCLUSIONS ABPF is a rare but highly lethal complication after TEVAR. The leading mechanism behind ABPF seems to be a continuing external compression of either the bronchial tree or left upper lobe parenchyma. In this setting, persisting or newly developing endoleak formation seems to play a crucial role. Prognosis does not differ in patients with central airway or pulmonary parenchymal fistulation. Radical bronchial or pulmonary parenchymal repair in combination with stent graft removal and aortic reconstruction seems to be the most durable treatment strateg

Facilitating knowledge exchange between health-care sectors, organisations and professions: A longitudinal mixed-methods study of boundary-spanning processes and their impact on health-care quality

Background: Relatively little is known about how people and groups who function in boundary-spanning positions between different sectors, organisations and professions contribute to improved quality of health care and clinical outcomes. Objectives: To explore whether or not boundary-spanning processes stimulate the creation and exchange of knowledge between sectors, organisations and professions and whether or not this leads, through better integration of services, to improvements in the quality of care. Design: A 2-year longitudinal nested case study design using mixed methods. Setting: An inner-city area in England (‘Coxford’) comprising 26 general practices in ‘Westpark’ and a comparative sample of 57 practices. Participants: Health-care and non-health-care practitioners representing the range of staff participating in the Westpark Initiative (WI) and patients. Interventions: The WI sought to improve services through facilitating knowledge exchange and collaboration between general practitioners, community services, voluntary groups and acute specialists during the period late 2009 to early 2012. We investigated the impact of the four WI boundary-spanning teams on services and the processes through which they produced their effects. Main outcome measures: (1) Quality-of-care indicators during the period 2008–11; (2) diabetes admissions data from April 2006 to December 2011, adjusted for deprivation scores; and (3) referrals to psychological therapies from January 2010 to March 2012. Data sources: Data sources included 42 semistructured staff interviews, 361 hours of non-participant observation, 36 online diaries, 103 respondents to a staff survey, two patient focus groups and a secondary analyses of local and national data sets. Results: The four teams varied in their ability to, first, exchange knowledge across boundaries and, second, implement changes to improve the integration of services. The study setting experienced conditions of flux and uncertainty in which known horizontal and vertical structures underwent considerable change and the WI did not run its course as originally planned. Although knowledge exchanges did occur across sectoral, organisational and professional boundaries, in the case of child and family health services, early efforts to improve the integration of services were not sustained. In the case of dementia, team leadership and membership were undermined by external reorganisations. The anxiety and depression in black and minority ethnic populations team succeeded in reaching its self-defined goal of increasing referrals from Westpark practices to the local well-being service. From October to December 2010 onwards, referrals have been generally higher in the six practices with a link worker than in those without, but the performance of Westpark and Coxford practices did not differ significantly on three national quality indicators. General practices in a WI diabetes ‘cluster’ performed better on three of 17 Quality and Outcomes Framework (QOF) indicators than practices in the remainder of Westpark and in the wider Coxford primary care trust. Surprisingly, practices in Westpark, but not in the diabetes cluster, performed better on one indicator. No statistically significant differences were found on the remaining 13 QOF indicators. The time profiles differed significantly between the three groups for elective and emergency admissions and bed-days. Conclusions: Boundary spanning is a potential solution to the challenge of integrating health-care services and we explored how such processes perform in an ‘extreme case’ context of uncertainty. Although the WI may have been a necessary intervention to enable knowledge exchange across a range of boundaries, it was not alone sufficient. Even in the face of substantial challenges, one of the four teams was able to adapt and build resilience. Implications for future boundary-spanning interventions are identified. Future research should evaluate the direct, measurable and sustained impact of boundary-spanning processes on patient care outcomes (and experiences), as well as further empirically based critiques and reconceptualisations of the socialisation→externalisation→combination→internalisation (SECI) model, so that the implications can be translated into practical ideas developed in partnership with NHS managers. Funding: The National Institute for Health Research Health Services and Delivery Research programme

The JASP guidelines for conducting and reporting a Bayesian analysis

Despite the increasing popularity of Bayesian inference in empirical research, few practical guidelines provide detailed recommendations for how to apply Bayesian procedures and interpret the results. Here we offer specific guidelines for four different stages of Bayesian statistical reasoning in a research setting: planning the analysis, executing the analysis, interpreting the results, and reporting the results. The guidelines for each stage are illustrated with a running example. Although the guidelines are geared towards analyses performed with the open-source statistical software JASP, most guidelines extend to Bayesian inference in general