Results 11  20
of
325
A site and timeheterogeneous model of aminoacid replacement
, 2007
"... 1 We combined the CAT mixture model (Lartillot and Philippe 2004) and the nonstationary BP model (Blanquart and Lartillot 2006) into a new model, CATBP, accounting for variations of the evolutionary process both along the sequence and across lineages. As in CAT, the model implements a mixture of d ..."
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Cited by 42 (6 self)
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1 We combined the CAT mixture model (Lartillot and Philippe 2004) and the nonstationary BP model (Blanquart and Lartillot 2006) into a new model, CATBP, accounting for variations of the evolutionary process both along the sequence and across lineages. As in CAT, the model implements a mixture of distinct Markovian processes of substitution distributed among sites, thus accommodating sitespecific selective constraints induced by protein structure and function. Furthermore, as in BP, these processes are nonstationary, and their equilibrium frequencies are allowed to change along lineages in a correlated way, through discrete shifts in global amino acid composition distributed along the phylogenetic tree. We implemented the CATBP model in a Bayesian Markov Chain Monte Carlo framework, and compared its predictions with those of three simpler models, BP, CAT, and the site and timehomogeneous GTR model, on a concatenation of four mitochondrial proteins of 20 arthropod species. In contrast to GTR, BP and CAT, which all display a phylogenetic reconstruction artefact positioning the bees Apis m. and Melipona b. among chelicerates, the CATBP model
Exploratory Data Analysis for Complex Models
, 2002
"... Exploratory" and "confirmatory" data analysis can both be viewed as methods for comparing observed data to what would be obtained under an implicit or explicit statistical model. ..."
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Cited by 34 (7 self)
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Exploratory" and "confirmatory" data analysis can both be viewed as methods for comparing observed data to what would be obtained under an implicit or explicit statistical model.
Philosophy and the practice of Bayesian statistics
, 2010
"... A substantial school in the philosophy of science identifies Bayesian inference with inductive inference and even rationality as such, and seems to be strengthened by the rise and practical success of Bayesian statistics. We argue that the most successful forms of Bayesian statistics do not actually ..."
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Cited by 33 (8 self)
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A substantial school in the philosophy of science identifies Bayesian inference with inductive inference and even rationality as such, and seems to be strengthened by the rise and practical success of Bayesian statistics. We argue that the most successful forms of Bayesian statistics do not actually support that particular philosophy but rather accord much better with sophisticated forms of hypotheticodeductivism. We examine the actual role played by prior distributions in Bayesian models, and the crucial aspects of model checking and model revision, which fall outside the scope of Bayesian confirmation theory. We draw on the literature on the consistency of Bayesian updating and also on our experience of applied work in social science. Clarity about these matters should benefit not just philosophy of science, but also statistical practice. At best, the inductivist view has encouraged researchers to fit and compare models without checking them; at worst, theorists have actively discouraged practitioners from performing model checking because it does not fit into their framework.
Deriving Value from Social Commerce Networks
, 2008
"... Social commerce is an emerging trend in which sellers are connected in online social networks, and where sellers are individuals instead of firms. This paper examines the economic value implications of a social network between sellers in a large online social commerce marketplace. In this marketpl ..."
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Cited by 31 (0 self)
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Social commerce is an emerging trend in which sellers are connected in online social networks, and where sellers are individuals instead of firms. This paper examines the economic value implications of a social network between sellers in a large online social commerce marketplace. In this marketplace each seller creates his or her own shop, and network ties between sellers are directed hyperlinks between their shops. Three questions are addressed: (i) Does allowing sellers to connect to one another create value (i.e., increase sales), (ii) what are the mechanisms through which this value is created, (iii) how is this value distributed across sellers in the network and how does the position of a seller in the network (e.g., its centrality) influence how much it benefits or suffers from the network? We find that: (i) allowing sellers to connect generates considerable economic value; (ii) the network’s value lies primarily in making shops more accessible to customers browsing the marketplace (the network creates a “virtual shopping
Validation of software for bayesian models using posterior quantiles
 Journal of Computational and Graphical Statistics
"... We present a simulationbased method designed to establish that software developed to fit a specific Bayesian model works properly, capitalizing on properties of Bayesian posterior distributions. We illustrate the validation technique with two examples. The validation method is shown to find errors ..."
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Cited by 28 (6 self)
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We present a simulationbased method designed to establish that software developed to fit a specific Bayesian model works properly, capitalizing on properties of Bayesian posterior distributions. We illustrate the validation technique with two examples. The validation method is shown to find errors in software when they exist and, moreover, the validation output can be informative about the nature and location of such errors.
Promises and lies: Restoring violated trust
 Organizational Behavior and Human Decision Processes
, 2006
"... Trust is critical for effective negotiations, yet trust violations are common. Prior work has often assumed trust to be fragile—easily broken and difficult to repair. We investigate this proposition in a laboratory study and find that trust harmed by untrustworthy behavior can be effectively restore ..."
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Cited by 26 (3 self)
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Trust is critical for effective negotiations, yet trust violations are common. Prior work has often assumed trust to be fragile—easily broken and difficult to repair. We investigate this proposition in a laboratory study and find that trust harmed by untrustworthy behavior can be effectively restored when individuals observe a consistent series of trustworthy actions. Trust harmed by the same untrustworthy actions and deception, however, never fully recovers—even when deceived participants receive a promise, an apology, and observe a consistent series of trustworthy actions. We also find that a promise to change behavior can significantly speed the trust recovery process, but prior deception harms the effectiveness of a promise in accelerating trust recovery.
Modern statistics for spatial point processes
, 2006
"... We summarize and discuss the current state of spatial point process theory and directions for future research, making an analogy with generalized linear models and random effect models, and illustrating the theory with various examples of applications. In particular, we consider Poisson, Gibbs, and ..."
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Cited by 25 (3 self)
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We summarize and discuss the current state of spatial point process theory and directions for future research, making an analogy with generalized linear models and random effect models, and illustrating the theory with various examples of applications. In particular, we consider Poisson, Gibbs, and Cox process models, diagnostic tools and model checking, Markov chain Monte Carlo algorithms, computational methods for likelihoodbased inference, and quick nonlikelihood approaches to inference.
Bayesian statespace modeling of agestructured data: fitting a model is just the beginning
 Canadian Journal of Fisheries and Aquatic Sciences
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A Case Study on the Choice, Interpretation and Checking of Multilevel Models for Longitudinal Binary Outcomes
"... Recent advances in statistical software have led to the rapid diffusion of new methods for modeling longitudinal data. Multilevel (also known as hierarchical or random effects) models for binary outcomes have been generally based on a logisticnormal specification, by analogy with earlier work for n ..."
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Cited by 23 (3 self)
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Recent advances in statistical software have led to the rapid diffusion of new methods for modeling longitudinal data. Multilevel (also known as hierarchical or random effects) models for binary outcomes have been generally based on a logisticnormal specification, by analogy with earlier work for normally distributed data. The appropriate application and interpretation of these models remains somewhat unclear, especially when compared with the computationally more straightforward marginal modeling (GEE) approaches. In this paper we pose two interrelated questions. First, what limits should be placed on the interpretation of the coefficients and inferences derived from random effect models involving binary outcomes? Second, what are the minimum diagnostic checks that are required to evaluate whether such random effect models provide appropriate fits to the data? We address these questions by means of an extended case study using data on adolescent smoking from a large cohort study. Bay...