It’s Sunday, and I [Bob] am just sitting on the couch peacefully ggplotting to illustrate basic sample spaces using spinners (a trick I’m borrowing from Jim Albert’s book Curve Ball). There’s an underlying continuous outcome (i.e., where the spinner lands) and a quantization into a number of regions to produce a discrete outcome (e.g., “success” […]

**R**

## Stan Weekly Roundup, 14 July 2017

Another week, another bunch of Stan updates. Kevin Van Horn and Elea McDonnell Feit put together a tutorial on Stan [GitHub link] that covers linear regression, multinomial logistic regression, and hierarchical multinomial logistic regression. Andrew has been working on writing up our “workflow”. That includes Chapter 1, Verse 1 of Bayesian Data Analysis of (1) […]

## Stan Weekly Roundup, 7 July 2017

Holiday weekend, schmoliday weekend. Ben Goodrich and Jonah Gabry shipped RStan 2.16.2 (their numbering is a little beyond base Stan, which is at 2.16.0). This reintroduces error reporting that got lost in the 2.15 refactor, so please upgrade if you want to debug your Stan programs! Joe Haupt translated the JAGS examples in the second […]

## Stan Weekly Roundup, 30 June 2017

Here’s some things that have been going on with Stan since the last week’s roundup Stan® and the logo were granted a U.S. Trademark Registration No. 5,222,891 and a U.S. Serial Number: 87,237,369, respectively. Hard to feel special when there were millions of products ahead of you. Trademarked names are case insensitive and they required […]

## Ensemble Methods are Doomed to Fail in High Dimensions

Ensemble methods [cat picture] By ensemble methods, I (Bob, not Andrew) mean approaches that scatter points in parameter space and then make moves by inteprolating or extrapolating among subsets of them. Two prominent examples are: Ter Braak’s differential evolution Goodman and Weare’s walkers There are extensions and computer implementations of these algorithms. For example, […]

## A book on RStan in Japanese: *Bayesian Statistical Modeling Using Stan and R* (Wonderful R, Volume 2)

Wonderful, indeed, to have an RStan book in Japanese: Kentarou Matsuura. 2016. Bayesian Statistical Modeling Using Stan and R. Wonderful R Series, Volume 2. Kyoritsu Shuppan Co., Ltd. Google translate makes the following of the description posted on Amazon Japan (linked from the title above): In recent years, understanding of the phenomenon by fitting a […]

## 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 […]

## Kéry and Schaub’s *Bayesian Population Analysis* Translated to Stan

Hiroki ITÔ has done everyone a service in translating to Stan the example models [update: only chapters 3–9 so far, not the whole book; the rest are in the works] from Marc Kéry and Michael Schaub (2012) Bayesian Population Analysis using WinBUGS: A Hierarchical Perspective. Academic Press. You can find the code in our example-models […]

## Jim Albert’s Baseball Blog

Jim Albert has a baseball blog: Baseball with R I sent a link internally to people I knew were into baseball, to which Andrew replied, “I agree that it’s cool that he doesn’t just talk, he has code.” (No kidding—the latest post as of writing this was on an R package to compute value above […]

## McElreath’s *Statistical Rethinking: A Bayesian Course with Examples in R and Stan *

We’re not even halfway through with January, but the new year’s already rung in a new book with lots of Stan content: Richard McElreath (2016) Statistical Rethinking: A Bayesian Course with Examples in R and Stan. Chapman & Hall/CRC Press. This one got a thumbs up from the Stan team members who’ve read it, and […]

## rstanarm and more!

Ben Goodrich writes: The rstanarm R package, which has been mentioned several times on stan-users, is now available in binary form on CRAN mirrors (unless you are using an old version of R and / or an old version of OSX). It is an R package that comes with a few precompiled Stan models — […]

## R sucks

I’m doing an analysis and one of the objects I’m working on is a multidimensional array called “attitude.” I took a quick look: > dim(attitude) [1] 30 7 Huh? It’s not supposed to be 30 x 7. Whassup? I search through my scripts for a “attitude” but all I find is the three-dimensional array. Where […]

## Stan 2.7 (CRAN, variational inference, and much much more)

Stan 2.7 is now available for all interfaces. As usual, everything you need can be found starting from the Stan home page: http://mc-stan.org/ Highlights RStan is on CRAN!(1) Variational Inference in CmdStan!!(2) Two new Stan developers!!! A whole new logo!!!! Math library with autodiff now available in its own repo!!!!! (1) Just doing install.packages(“rstan”) isn’t […]

## Short course on Bayesian data analysis and Stan 19-21 July in NYC!

Bob Carpenter, Daniel Lee, 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 problems occur please join the stan-users group and post any questions. It’s important that all participants get Stan running and bring their laptops to the course. Class […]

## 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 […]

## What does CNN have in common with Carmen Reinhart, Kenneth Rogoff, and Richard Tol: They all made foolish, embarrassing errors that would never have happened had they been using R Markdown

Rachel Cunliffe shares this delight: Had the CNN team used an integrated statistical analysis and display system such as R Markdown, nobody would’ve needed to type in the numbers by hand, and the above embarrassment never would’ve occurred. And CNN should be embarrassed about this: it’s much worse than a simple typo, as it indicates […]

## Stan goes to the World Cup

I thought it would be fun to fit a simple model in Stan to estimate the abilities of the teams in the World Cup, then I could post everything here on the blog, the whole story of the analysis from beginning to end, showing the results of spending a couple hours on a data analysis. […]

## Comment of the week

This one, from DominikM: Really great, the simple random intercept – random slope mixed model I did yesterday now runs at least an order of magnitude faster after installing RStan 2.3 this morning. You are doing an awesome job, thanks a lot!

## (Py, R, Cmd) Stan 2.3 Released

We’re happy to announce RStan, PyStan and CmdStan 2.3. Instructions on how to install at: http://mc-stan.org/ As always, let us know if you’re having problems or have comments or suggestions. We’re hoping to roll out the next release a bit quicker this time, because we have lots of good new features that are almost ready […]

## Identifying pathways for managing multiple disturbances to limit plant invasions

Andrew Tanentzap, William Lee, Adrian Monks, Kate Ladley, Peter Johnson, Geoffrey Rogers, Joy Comrie, Dean Clarke, and Ella Hayman write: We tested a multivariate hypothesis about the causal mechanisms underlying plant invasions in an ephemeral wetland in South Island, New Zealand to inform management of this biodiverse but globally imperilled habitat. . . . We […]