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Archive of posts filed under the Bayesian Statistics category.

Introducing shinyStan

As a project for Andrew’s Statistical Communication and Graphics graduate course at Columbia, a few of us (Michael Andreae, Yuanjun Gao, Dongying Song, and I) had the goal of giving RStan’s print and plot functions a makeover. We ended up getting a bit carried away and instead we designed a graphical user interface for interactively exploring virtually […]

Bayes and doomsday

Ben O’Neill writes: I am a fellow Bayesian statistician at the University of New South Wales (Australia).  I have enjoyed reading your various books and articles, and enjoyed reading your recent article on The Perceived Absurdity of Bayesian Inference.  However, I disagree with your assertion that the “doomsday argument” is non-Bayesian; I think if you read […]

Statistical Significance – Significant Problem?

John Carlin, who’s collaborated on some of my recent work on Type S and Type M errors, prepared this presentation for a clinical audience. It might be of interest to some of you. The ideas and some of the examples should be familiar to regular readers of this blog, but it could be useful to […]

Bayesian survival analysis with horseshoe priors—in Stan!

Tomi Peltola, Aki Havulinna, Veikko Salomaa, and Aki Vehtari write: This paper describes an application of Bayesian linear survival regression . . . We compare the Gaussian, Laplace and horseshoe shrinkage priors, and find that the last has the best predictive performance and shrinks strong predictors less than the others. . . . And here’s […]

Stan Down Under

I (Bob, not Andrew) am in Australia until April 30. I’ll be giving some Stan-related and some data annotation talks, several of which have yet to be concretely scheduled. I’ll keep this page updated with what I’ll be up to. All of the talks other than summer school will be open to the public (the […]

Why I keep talking about “generalizing from sample to population”

Someone publishes some claim, some statistical comparison with “p less than .05″ attached to it. My response is: OK, you see this pattern in the sample. Do you think it holds in the population? Why do I ask this? Why don’t I ask the more standard question: Do you really think this result is statistically […]

Total survey error

Erez Shalom writes: It’s election time in Israel and every week several surveys come out trying to predict the ‘mandates’ that each party will get (out of a total of 120). These surveys are historically flakey, and no one takes the ‘sampling error’ they come with seriously, but no one has a good idea of […]

This has nothing to do with the Super Bowl

Joshua Vogelstein writes: The Open Connectome Project at Johns Hopkins University invites outstanding candidates to apply for a postdoctoral or assistant research scientist position in the area of statistical machine learning for big brain imaging data. Our workflow is tightly vertically integrated, ranging from raw data to theory to answering neuroscience questions and back again. […]

About a zillion people pointed me to yesterday’s xkcd cartoon

I have the same problem with Bayes factors, for example this: and this: (which I copied from Wikipedia, except that, unlike you-know-who, I didn’t change the n’s to d’s and remove the superscripting). Either way, I don’t buy the numbers, and I certainly don’t buy the words that go with them. I do admit, though, […]

“It is perhaps merely an accident of history that skeptics and subjectivists alike strain on the gnat of the prior distribution while swallowing the camel that is the likelihood”

I recently bumped into this 2013 paper by Christian Robert and myself, “‘Not Only Defended But Also Applied': The Perceived Absurdity of Bayesian Inference,” which begins: Younger readers of this journal may not be fully aware of the passionate battles over Bayesian inference among statisticians in the last half of the twentieth century. During this […]

“The Statistical Crisis in Science”: My talk this Thurs at the Harvard psychology department

Noon Thursday, January 29, 2015, in William James Hall 765 room 1: The Statistical Crisis in Science Andrew Gelman, Dept of Statistics and Dept of Political Science, Columbia University Top journals in psychology routinely publish ridiculous, scientifically implausible claims, justified based on “p < 0.05.” And this in turn calls into question all sorts of […]

“What then should we teach about hypothesis testing?”

Someone who wishes to remain anonymous writes in: Last week, I was looking forward to a blog post titled “Why continue to teach and use hypothesis testing?” I presume that this scheduled post merely became preempted by more timely posts. But I am still interested in reading the exchange that will follow. My feeling is […]

Cross-validation, LOO and WAIC for time series

This post is by Aki. Jonah asked in Stan users mailing list Suppose we have J groups and T time periods, so y[t,j] is the observed value of y at time t for group j. (We also have predictors x[t,j].) I’m wondering if WAIC is appropriate in this scenario assuming that our interest in predictive accuracy is for […]

Stan comes through . . . again!

Erikson Kaszubowski writes in: I missed your call for Stan research stories, but the recent post about stranded dolphins mentioned it again. When I read about the Crowdstorming project in your blog, I thought it would be a good project to apply my recent studies in Bayesian modeling. The project coordinators shared a big dataset […]

Planning my class for this semester: Thinking aloud about how to move toward active learning?

I’m teaching two classes this semester: – Design and Analysis of Sample Surveys (in the political science department, but the course has lots of statistics content); – Statistical Communication and Graphics (in the statistics department, but last time I taught it, many of the students were from other fields). I’ve taught both classes before. I […]

“Why continue to teach and use hypothesis testing?”

Greg Werbin points us to an online discussion of the following question: Why continue to teach and use hypothesis testing (with all its difficult concepts and which are among the most statistical sins) for problems where there is an interval estimator (confidence, bootstrap, credibility or whatever)? What is the best explanation (if any) to be […]

The Use of Sampling Weights in Bayesian Hierarchical Models for Small Area Estimation

All this discussion of plagiarism is leaving a bad taste in my mouth (or, I guess I should say, a bad feeling in my fingers, given that I’m expressing all this on the keyboard) so I wanted to close off the workweek with something more interesting. I happened to come across the above-titled paper by […]

Expectation propagation as a way of life

Aki Vehtari, Pasi Jylänki, Christian Robert, Nicolas Chopin, John Cunningham, and I write: We revisit expectation propagation (EP) as a prototype for scalable algorithms that partition big datasets into many parts and analyze each part in parallel to perform inference of shared parameters. The algorithm should be particularly efficient for hierarchical models, for which the […]

Bayesian Cognitive Modeling Models Ported to Stan

Hats off for Martin Šmíra, who has finished porting the models from Michael Lee and Eric-Jan Wagenmakers’ book Bayesian Cognitive Modeling  to Stan. Here they are: Bayesian Cognitive Modeling: Stan Example Models Martin managed to port 54 of the 57 models in the book and verified that the Stan code got the same answers as […]

A question about varying-intercept, varying-slope multilevel models for cross-national analysis

Sean de Hoon writes: In many cross-national comparative studies, mixed effects models are being used in which a number of slopes are fixed and the slopes of one or two variables of interested are allowed to vary across countries. The aim is often then to explain the varying slopes by referring to some country-level characteristic. […]