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Archive of posts filed under the Stan category.

Soil Scientists Seeking Super Model

I (Bob) spent last weekend at Biosphere 2, collaborating with soil carbon biogeochemists on a “super model.” Model combination and expansion The biogeochemists (three sciences in one!) have developed hundreds of competing models and the goal of the workshop was to kick off some projects on putting some of them together intos wholes that are […]

Stan hits bigtime

First Wikipedia, then the Times (featuring Yair Ghitza), now Slashdot (featuring Allen “PyStan” Riddell). Just get us on Gawker and we’ll have achieved total media saturation. Next step, backlash. Has Stan jumped the shark? Etc. (We’d love to have a “jump the shark” MCMC algorithm but I don’t know if or when we’ll get there. […]

“The Firth bias correction, penalization, and weakly informative priors: A case for log-F priors in logistic and related regressions”

Sander Greenland sent me this paper that he wrote with Mohammad Ali Mansournia, which discusses possible penalty functions for penalized maximum likelihood or, equivalently, possible prior distributions for Bayesian posterior mode estimation, in the context of logistic regression. Greenland and Mansournia write: We consider some questions that arise when considering alternative penalties . . . […]

Stan 2.5, now with MATLAB, Julia, and ODEs

As usual, you can find everything on the Stan Home Page. Drop us a line on the stan-users group if you have problems with installs or questions about Stan or coding particular models. New Interfaces We’d like to welcome two new interfaces: MatlabStan by Brian Lau, and  Stan.jl (for Julia) by Rob Goedman. The new […]

“We have used Stan to study dead dolphins”

In response to our call for references to successful research using Stan, Matthieu Authier points us to this: @article{ year={2014}, journal={Biodiversity and Conservation}, volume={23}, number={10}, doi={10.1007/s10531-014-0741-3}, title={How much are stranding records affected by variation in reporting rates? A case study of small delphinids in the Bay of Biscay}, url={}, keywords={Monitoring; Marine mammal; Strandings}, author={Authier, Matthieu […]

Bayesian Cognitive Modeling  Examples Ported to Stan

There’s a new intro to Bayes in town. Michael Lee and Eric-Jan Wagenmaker. 2014. Bayesian Cognitive Modeling: A Practical Course. Cambridge Uni. Press. This book’s a wonderful introduction to applied Bayesian modeling. But don’t take my word for it — you can download and read the first two parts of the book (hundreds of pages […]

My talk with David Schiminovich this Wed noon: “The Birth of the Universe and the Fate of the Earth: One Trillion UV Photons Meet Stan”

This talk will have two parts. (1) Astronomy professor David Schiminovich will discuss the ways in which recent large-scale sky surveys that include billions of data points can address questions such as, What will happen to the Earth and other planets when the Sun becomes a white dwarf? (2) Statistics professor Andrew Gelman will discuss […]

Stanny Stanny Stannitude

On the stan-users list, Richard McElreath reports: With 2.4 out, I ran a quick test of how much speedup I could get by changing my old non-vectorized multi_normal sampling to the new vectorized form. I get a 40% time savings, without even trying hard. This is much better than I expected. Timings with vectorized multi_normal: […]

Stan NYC Meetup – Thurs, July 31

The next Stan NYC meetup is happening on Thursday, July 31, at 7 pm. If you’re interested, registration is required and closes on Wednesday night:   The third session will focus on using the Stan language. If you’re bringing a laptop, please come with RStan, PyStan, or CmdStan already installed.   We’re going to […]

Stan 2.4, New and Improved

We’re happy to announce that all three interfaces (CmdStan, PyStan, and RStan) are up and ready to go for Stan 2.4. As usual, you can find full instructions for installation on the Stan Home Page. Here are the release notes with a list of what’s new and improved: New Features ———— * L-BFGS optimization (now […]