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Archive of posts filed under the Statistical computing category.

“It’s not reproducible if it only runs on your laptop”: Jon Zelner’s tips for a reproducible workflow in R and Stan

Jon Zelner writes: Reproducibility is becoming more and more a part of the conversation when it comes to public health and social science research. . . . But comparatively little has been said about another dimension of the reproducibility crisis, which is the difficulty of re-generating already-complete analyses using the exact same input data. But […]

Yes, despite what you may have heard, you can easily fit hierarchical mixture models in Stan

There was some confusion on the Stan list that I wanted to clear up, having to do with fitting mixture models. Someone quoted this from John Kruschke’s book, Doing Bayesian Data Analysis: The lack of discrete parameters in Stan means that we cannot do model comparison as a hierarchical model with an indexical parameter at […]

Practical Bayesian model evaluation in Stan and rstanarm using leave-one-out cross-validation

Our (Aki, Andrew and Jonah) paper Practical Bayesian model evaluation using leave-one-out cross-validation and WAIC was recently published in Statistics and Computing. In the paper we show why it’s better to use LOO instead of WAIC for model evaluation how to compute LOO quickly and reliably using the full posterior sample how Pareto smoothing importance […]

Mathematica, now with Stan

Vincent Picaud developed a Mathematica interface to Stan: MathematicaStan You can find everything you need to get started by following the link above. If you have questions, comments, or suggestions, please let us know through the Stan user’s group or the GitHub issue tracker. MathematicaStan interfaces to Stan through a CmdStan process. Stan programs are […]

Tenure Track Professor in Machine Learning, Aalto University, Finland

Posted by Aki. I promise that next time I’ll post something else than a job advertisement, but before that here’s another great opportunity to join Aalto Univeristy where I work, too. “We are looking for a professor to either further strengthen our strong research fields, with keywords including statistical machine learning, probabilistic modelling, Bayesian inference, […]

Stan case studies!

In the spirit of reproducible research, we (that is, Bob*) set up this beautiful page of Stan case studies. Check it out. * Bob here. Michael set the site up, I set this page up, and lots of people have contributed case studies and we’re always looking for more to publish.

“Crimes Against Data”: My talk at Ohio State University this Thurs; “Solving Statistics Problems Using Stan”: My talk at the University of Michigan this Fri

Crimes Against Data Statistics has been described as the science of uncertainty. But, paradoxically, statistical methods are often used to create a sense of certainty where none should exist. The social sciences have been rocked in recent years by highly publicized claims, published in top journals, that were reported as “statistically significant” but are implausible […]

Let’s play Twister, let’s play Risk

Alex Terenin, Dan Simpson, and David Draper write: Some months ago we shared with you an arxiv draft of our paper, Asynchronous Distributed Gibbs Sampling.​ Through comments we’ve received, for which we’re highly grateful, we came to understand that (a) our convergence proof was wrong, and (b) we actually have two algorithms, one exact and […]

Stan users group hits 2000 registrations

Of course, there are bound to be duplicate emails, dead emails, and people who picked up Stan, joined the list, and never came back. But still, that’s a lot of people who’ve expressed interest! It’s been an amazing ride that’s only going to get better as we learn more and continue to improve Stan’s speed […]

Several postdoc positions in probabilistic modeling and machine learning in Aalto, Helsinki

This post is by Aki In addition to the postdoc position I advertised recently, now Aalto University and University of Helsinki have 20 more open postdoc and research fellow positions. Many of the positions are in probabilistic models and machine learning. You could work with me (I’m also part of HIIT), but I can also […]

R demos for BDA3

Last year we published some Matlab/Octave and Python demos for BDA3. During the summer my student Markus Paasiniemi ported these demos to R. New R BDA3 demos are now available in github. We hope these are helpful for someone. They are now just R code, although R Markdown would be cool. Btw. we are expecting […]

How paracompact is that?

Dominic on stan-users writes: I was reading through and came across the term with which I was not familiar: “paracompact.” I wrote a short blog post about it: It may be of interest to other folks reading the aforementioned paper. I would have used a partition of unity to justify the corollary myself […]

Fast CAR: Two weird tricks for fast conditional autoregressive models in Stan

Max Joseph writes: Conditional autoregressive (CAR) models are popular as prior distributions for spatial random effects with areal spatial data. Historically, MCMC algorithms for CAR models have benefitted from efficient Gibbs sampling via full conditional distributions for the spatial random effects. But, these conditional specifications do not work in Stan, where the joint density needs […]

Free workshop on Stan for pharmacometrics (Paris, 22 September 2016); preceded by (non-free) three day course on Stan for pharmacometrics

So much for one post a day… Workshop: Stan for Pharmacometrics Day If you are interested in a free day of Stan for pharmacometrics in Paris on 22 September 2016, see the registration page: Stan for Pharmacometrics Day (free workshop) Julie Bertrand (statistical pharmacologist from Paris-Diderot and UCL) has finalized the program: When Who What […]

Postdoc in Finland with Aki

I’m looking for a postdoc to work with me at Aalto University, Finland. The person hired will participate in research on Gaussian processes, functional constraints, big data, approximative Bayesian inference, model selection and assessment, deep learning, and survival analysis models (e.g. cardiovascular diseases and cancer). Methods will be implemented mostly in GPy and Stan. The […]

A little story of the Folk Theorem of Statistical Computing

I know I promised I wouldn’t blog, but this one is so clean and simple. And I already wrote it for the stan-users list anyway so it’s almost no effort to post it here too: A colleague and I were working on a data analysis problem, had a very simple overdispersed Poisson regression with a […]

Some insider stuff on the Stan refactor

From the stan-dev list, Bob wrote [and has since added brms based on comments; the * packages are ones that aren’t developed or maintained by the stan-dev team, so we only know what we hear from their authors]: The bigger picture is this, and you see the stan-dev/stan repo really spans three logical layers: stan […]

Reproducible Research with Stan, R, knitr, Docker, and Git (with free GitLab hosting)

Jon Zelner recently developed a neat Docker packaging of Stan, R, and knitr for fully reproducible research. The first in his series of posts (with links to the next parts) is here: * Reproducibility, part 1 The post on making changes online and auto-updating results using GitLab’s continuous integration service is here: * GitLab continuous […]

“Simple, Scalable and Accurate Posterior Interval Estimation”

Cheng Li, Sanvesh Srivastava, and David Dunson write: We propose a new scalable algorithm for posterior interval estimation. Our algorithm first runs Markov chain Monte Carlo or any alternative posterior sampling algorithm in parallel for each subset posterior, with the subset posteriors proportional to the prior multiplied by the subset likelihood raised to the full […]

Short course on Bayesian data analysis and Stan 18-20 July in NYC!

Jonah Gabry, Vince Dorie, and I are giving a 3-day short course in two weeks. Before class everyone should install R, RStudio and RStan on their computers. (If you already have these, please update to the latest version of R and the latest version of Stan, which is 2.10.) If problems occur please join the […]