# General

**URL:** https://discourse.mc-stan.org/c/general/24.md

[Latest](https://discourse.mc-stan.org/latest.md) · [Categories](https://discourse.mc-stan.org/categories.md) · [Tags](https://discourse.mc-stan.org/tags.md)

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## [About the General category](https://discourse.mc-stan.org/t/about-the-general-category/61)

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**Author:** [@syclik](https://discourse.mc-stan.org/u/syclik)\
**Replies:** 0

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This category is for general discussion that doesn't fit within any of the existing categories.

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## [SBC derived quantities with vector of parameters](https://discourse.mc-stan.org/t/sbc-derived-quantities-with-vector-of-parameters/41618)

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**Author:** [@jkbest2](https://discourse.mc-stan.org/u/jkbest2)\
**Replies:** 3\
**Last updated:** [September 28, 2026, 5:20pm UTC](https://discourse.mc-stan.org/t/sbc-derived-quantities-with-vector-of-parameters/41618 "2026-09-28T17:20:54Z")

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I’d like to include a derived quantity in my SBC run that uses a parameter vector as input. The simple version of the function takes the vector log\_lambda as its argument: tot\_abund \<- function(log\_lambda) { sum(rpois…

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## [Call for Papers: Advanced Geographic Data Science and Modelling for Vector-Borne Diseases and NTDs](https://discourse.mc-stan.org/t/call-for-papers-advanced-geographic-data-science-and-modelling-for-vector-borne-diseases-and-ntds/41586)

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**Author:** [@UCLPG-MSC-SGDS](https://discourse.mc-stan.org/u/UCLPG-MSC-SGDS)\
**Replies:** 7\
**Last updated:** [September 23, 2026, 6:13pm UTC](https://discourse.mc-stan.org/t/call-for-papers-advanced-geographic-data-science-and-modelling-for-vector-borne-diseases-and-ntds/41586 "2026-09-23T18:13:32Z")

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Dear all, I hope this message finds you well. I just want to take this opportunity to share news on this platform about our Special Issue with those working with Bayesian models applied to vector-borne diseases (or neg…

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## [Setting up Emacs for Stan in 2026](https://discourse.mc-stan.org/t/setting-up-emacs-for-stan-in-2026/40970)

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**Author:** [@WardBrian](https://discourse.mc-stan.org/u/WardBrian)\
**Replies:** 10\
**Last updated:** [September 15, 2026, 4:57pm UTC](https://discourse.mc-stan.org/t/setting-up-emacs-for-stan-in-2026/40970 "2026-09-15T16:57:09Z")

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It is easier than ever to set up Emacs for Stan development. Here’s a screen shot of the kind of thing you can expect: The entire init.el needed to get this behavior is below (excluding the theme, which is zenburn). …

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## [CmdStan & Stan 2.40 Release Candidates](https://discourse.mc-stan.org/t/cmdstan-stan-2-40-release-candidates/41585)

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**Author:** [@WardBrian](https://discourse.mc-stan.org/u/WardBrian)\
**Replies:** 11\
**Last updated:** [September 12, 2026, 10:21pm UTC](https://discourse.mc-stan.org/t/cmdstan-stan-2-40-release-candidates/41585 "2026-09-12T22:21:32Z")

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I am happy to announce that the latest release candidates of CmdStan and Stan are now available on Github! You can find the release candidate for CmdStan here. Instructions for installing are given at the bottom of this…

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## [Mixis and E\_loo](https://discourse.mc-stan.org/t/mixis-and-e-loo/40602)

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**Author:** [@gregd](https://discourse.mc-stan.org/u/gregd)\
**Replies:** 25\
**Last updated:** [September 9, 2026, 11:41am UTC](https://discourse.mc-stan.org/t/mixis-and-e-loo/40602 "2026-09-09T11:41:58Z")

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hello E\_loo uses the weights generated by loo to estimate the leave-one-out mean (and quantiles). However, “A small Pareto k estimate is necessary, but not sufficient, for E\_loo() to give reliable estimates.” Mixis is m…

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## [Posteriordb v. 1.1.0 released](https://discourse.mc-stan.org/t/posteriordb-v-1-1-0-released/41565)

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**Author:** [@mans\_magnusson](https://discourse.mc-stan.org/u/mans_magnusson)\
**Replies:** 0\
**Last updated:** [September 5, 2026, 6:24am UTC](https://discourse.mc-stan.org/t/posteriordb-v-1-1-0-released/41565 "2026-09-05T06:24:21Z")

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We are happy to announce the release of posteriordb 1.1. posteriordb is a database of Bayesian posterior inference problems, containing models, datasets, posterior definitions, and reference posterior draws. It is inten…

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## [\`stanflow\` v0.2.0 is out](https://discourse.mc-stan.org/t/stanflow-v0-2-0-is-out/41560)

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**Author:** [@jonah](https://discourse.mc-stan.org/u/jonah)\
**Replies:** 1\
**Last updated:** [August 31, 2026, 10:32pm UTC](https://discourse.mc-stan.org/t/stanflow-v0-2-0-is-out/41560 "2026-08-31T22:32:18Z")

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It’s been a while, but stanflow v0.2.0 has just been released by @Visruth. stanflow is a metapackage a la tidyverse to provide a convenient way to install and manage R Stan packages. (See Soft release of a "tidyverse" …

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## [Interpolating in a look-up table](https://discourse.mc-stan.org/t/interpolating-in-a-look-up-table/41533)

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**Author:** [@bmelinden](https://discourse.mc-stan.org/u/bmelinden)\
**Replies:** 3\
**Last updated:** [August 30, 2026, 5:36pm UTC](https://discourse.mc-stan.org/t/interpolating-in-a-look-up-table/41533 "2026-08-30T17:36:32Z")

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In a recent project I was missing a look-up functionality in stan, meaning I wanted to define some problem-specific function (of one variable) and use it in my model specification. An example would be if my model include…

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## [Stanli: Stan language interpreter, embedded in Python, or it can run in the browser and is often faster than CmdStan!](https://discourse.mc-stan.org/t/stanli-stan-language-interpreter-embedded-in-python-or-it-can-run-in-the-browser-and-is-often-faster-than-cmdstan/41504)

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**Author:** [@seantalts](https://discourse.mc-stan.org/u/seantalts)\
**Replies:** 19\
**Last updated:** [August 26, 2026, 11:15am UTC](https://discourse.mc-stan.org/t/stanli-stan-language-interpreter-embedded-in-python-or-it-can-run-in-the-browser-and-is-often-faster-than-cmdstan/41504 "2026-08-26T11:15:08Z")

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Check it out: stanli: Stan Language Interpreter, browser edition It’s using stanc3, the Stan Math library (though it’s using the autodiff in weird ways for perf reasons), and the Stan algorithms verbatim with no upstrea…

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## [LOO Continuously Ranked Probability Score](https://discourse.mc-stan.org/t/loo-continuously-ranked-probability-score/35239)

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**Author:** [@cwolfe](https://discourse.mc-stan.org/u/cwolfe)\
**Replies:** 4\
**Last updated:** [August 11, 2026, 2:33pm UTC](https://discourse.mc-stan.org/t/loo-continuously-ranked-probability-score/35239 "2026-08-11T14:33:55Z")

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I am comparing 2 models using the LOO implementation of continuously ranked probability scores. I just want to ensure I am interpreting the results correctly. It seems in most circumstances in applied research the CRPS i…

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## [Phylogenetic signal lambda calculation for zero-inflated negative binomial distribution](https://discourse.mc-stan.org/t/phylogenetic-signal-lambda-calculation-for-zero-inflated-negative-binomial-distribution/41493)

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**Author:** [@dpaun](https://discourse.mc-stan.org/u/dpaun)\
**Replies:** 3\
**Last updated:** [August 10, 2026, 7:51pm UTC](https://discourse.mc-stan.org/t/phylogenetic-signal-lambda-calculation-for-zero-inflated-negative-binomial-distribution/41493 "2026-08-10T19:51:56Z")

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Hi everyone. I am currently doing some brms for phylogenetic signal estimation and I am using the zero-inflated binomial distribution. As Bürkner explains in “Estimating Phylogenetic Multilevel Models with brms” it can b…

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## [How to assess model fit for a Bayesian conditional logistic regression model?](https://discourse.mc-stan.org/t/how-to-assess-model-fit-for-a-bayesian-conditional-logistic-regression-model/41498)

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**Author:** [@spn](https://discourse.mc-stan.org/u/spn)\
**Replies:** 1\
**Last updated:** [August 10, 2026, 9:25am UTC](https://discourse.mc-stan.org/t/how-to-assess-model-fit-for-a-bayesian-conditional-logistic-regression-model/41498 "2026-08-10T09:25:19Z")

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I am analyzing case-control data with conditional logistic regression. I am using the stan\_clogit() function from rstanarm. Since the stratum intercepts are conditioned out and not estimated, I understand that we do not …

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## [Marathon Uppsala weekend before Stancon 2026](https://discourse.mc-stan.org/t/marathon-uppsala-weekend-before-stancon-2026/40760)

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**Author:** [@spinkney](https://discourse.mc-stan.org/u/spinkney)\
**Replies:** 1\
**Last updated:** [August 8, 2026, 7:19am UTC](https://discourse.mc-stan.org/t/marathon-uppsala-weekend-before-stancon-2026/40760 "2026-08-08T07:19:36Z")

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Hi all, I’m planning to do either the 5 or 10k option of the 6 Lakes race Aug 15 in Uppsala, Sweden prior to Stancon. My wife is doing the marathon. You get to jump in the lake afterward! Reply here or PM me if you’re in…

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## [JAGS vs Stan performance - how to compare 'workflow efficiency'?](https://discourse.mc-stan.org/t/jags-vs-stan-performance-how-to-compare-workflow-efficiency/41473)

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**Author:** [@buf](https://discourse.mc-stan.org/u/buf)\
**Replies:** 7\
**Last updated:** [August 6, 2026, 12:45pm UTC](https://discourse.mc-stan.org/t/jags-vs-stan-performance-how-to-compare-workflow-efficiency/41473 "2026-08-06T12:45:33Z")

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Hi everyone, I have a bunch of models in JAGS and have translated them to Stan. The Stan versions, however, are not identical to the JAGS versions (I had to introduce some smoothing for Stan to work). The posteriors of …

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## [New User's Guide Intro, SEM, and user-defined constrained parameters chapters](https://discourse.mc-stan.org/t/new-users-guide-intro-sem-and-user-defined-constrained-parameters-chapters/41430)

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**Author:** [@Bob\_Carpenter](https://discourse.mc-stan.org/u/Bob_Carpenter)\
**Replies:** 11\
**Last updated:** [August 4, 2026, 9:34pm UTC](https://discourse.mc-stan.org/t/new-users-guide-intro-sem-and-user-defined-constrained-parameters-chapters/41430 "2026-08-04T21:34:25Z")

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After feedback from @WardBrian and @mitzimorris, I just merged two new chapters for the User’s Guide right up front in a new introductory part. The Stan Ecosystem How Stan Works I’m not sure what the schedule is for r…

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## [Bayesplot mcmc\_pairs divergences error](https://discourse.mc-stan.org/t/bayesplot-mcmc-pairs-divergences-error/41457)

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**Author:** [@gregd](https://discourse.mc-stan.org/u/gregd)\
**Replies:** 5\
**Last updated:** [July 24, 2026, 5:56pm UTC](https://discourse.mc-stan.org/t/bayesplot-mcmc-pairs-divergences-error/41457 "2026-07-24T17:56:30Z")

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Hope this is my error and simple! Using bayesplot version 1.15.0.9000 with a reproducible example, some but not all divergences are shown in the mcmc\_pairs plot. library(rstan) rstan\_options(auto\_write = TRUE) library(b…

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## [Vibe coded 3D Anaglyph animation of HMC](https://discourse.mc-stan.org/t/vibe-coded-3d-anaglyph-animation-of-hmc/41431)

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**Author:** [@Bob\_Carpenter](https://discourse.mc-stan.org/u/Bob_Carpenter)\
**Replies:** 0\
**Last updated:** [July 8, 2026, 7:18pm UTC](https://discourse.mc-stan.org/t/vibe-coded-3d-anaglyph-animation-of-hmc/41431 "2026-07-08T19:18:48Z")

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This is just a reprint of the blog post I put on @andrewgelman’s blog. Claude builds 3D Hamiltonian Monte Carlo animation in one shot with anaglyphs The blog let me embed it, but Discourse will not. So you will have …

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## [Diststan — distributed Stan fits across a network of computers](https://discourse.mc-stan.org/t/diststan-distributed-stan-fits-across-a-network-of-computers/41392)

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**Author:** [@ssp3nc3r](https://discourse.mc-stan.org/u/ssp3nc3r)\
**Replies:** 2\
**Last updated:** [June 27, 2026, 2:10pm UTC](https://discourse.mc-stan.org/t/diststan-distributed-stan-fits-across-a-network-of-computers/41392 "2026-06-27T14:10:54Z")

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Run chains for one fit across a few machines on your network — by hand? To cut the manual friction of distributing, monitoring, and collecting the draw files, I wrote myself a package and thought I’d share in case anyon…

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## [Hessian matrix of log-likelhood function that uses structure-of-array var\_value\<VectorXd\>](https://discourse.mc-stan.org/t/hessian-matrix-of-log-likelhood-function-that-uses-structure-of-array-var-value-vectorxd/41395)

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**Author:** [@qminor](https://discourse.mc-stan.org/u/qminor)\
**Replies:** 4\
**Last updated:** [June 25, 2026, 7:23pm UTC](https://discourse.mc-stan.org/t/hessian-matrix-of-log-likelhood-function-that-uses-structure-of-array-var-value-vectorxd/41395 "2026-06-25T19:23:00Z")

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I have a log-likelihood function that uses not only stan::math::var’s, but also involves stan::math::var\_value \<\<Eigen::VectorXd\> \> (and var\_value \< MatrixXd \> as well) since it involves pixel operations with thousands o…

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## [Informative Priors and Fitting Issues in Meta-Analysis Regression with Missing Covariates](https://discourse.mc-stan.org/t/informative-priors-and-fitting-issues-in-meta-analysis-regression-with-missing-covariates/41388)

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**Author:** [@Stream\_On](https://discourse.mc-stan.org/u/Stream_On)\
**Replies:** 1\
**Last updated:** [June 25, 2026, 4:43pm UTC](https://discourse.mc-stan.org/t/informative-priors-and-fitting-issues-in-meta-analysis-regression-with-missing-covariates/41388 "2026-06-25T16:43:13Z")

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Hi Stan Community, I am currently experiencing convergence and fitting issues with a hierarchical Bayesian meta-analysis model implemented in Stan. Context & Data Layer The goal of the model is to estimate effect size…

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## [Introducing the Stan JetBrains plugin](https://discourse.mc-stan.org/t/introducing-the-stan-jetbrains-plugin/41323)

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**Author:** [@jachymb](https://discourse.mc-stan.org/u/jachymb)\
**Replies:** 2\
**Last updated:** [June 25, 2026, 11:19am UTC](https://discourse.mc-stan.org/t/introducing-the-stan-jetbrains-plugin/41323 "2026-06-25T11:19:46Z")

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I created a JetBrains plugin for the Stan language support. If you use PyCharm, DataSpell, IntelliJ or any other compatible IDE, you can check it out. So far it’s intended only to help with editing stan language files, i…

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## [LOO-pit for folded predictions: gamma regression vs gaussian regression](https://discourse.mc-stan.org/t/loo-pit-for-folded-predictions-gamma-regression-vs-gaussian-regression/41377)

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**Author:** [@llewmills](https://discourse.mc-stan.org/u/llewmills)\
**Replies:** 1\
**Last updated:** [June 24, 2026, 12:16pm UTC](https://discourse.mc-stan.org/t/loo-pit-for-folded-predictions-gamma-regression-vs-gaussian-regression/41377 "2026-06-24T12:16:07Z")

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I am following the workflow described in this notebook by Aki Vehtari. I’m going through the section comparing loo-pit for folded predictions plots. I am comparing the fit of a gamma regression to a gaussian regression f…

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## [Tidybayes, posterior prediction, and cmdstanr](https://discourse.mc-stan.org/t/tidybayes-posterior-prediction-and-cmdstanr/35062)

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**Author:** [@cwolfe](https://discourse.mc-stan.org/u/cwolfe)\
**Replies:** 5\
**Last updated:** [June 24, 2026, 10:36am UTC](https://discourse.mc-stan.org/t/tidybayes-posterior-prediction-and-cmdstanr/35062 "2026-06-24T10:36:09Z")

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Apologies if this is inappropriate here, but I figured I would give it a shot. I am trying to plot posterior prediction curves (or even the expectation of the prediction) much like the code here from @mjskay vignette on…

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## ['Disjunction' of type traits (for combined varmat/matvar custom C++ template)?](https://discourse.mc-stan.org/t/disjunction-of-type-traits-for-combined-varmat-matvar-custom-c-template/41359)

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**Author:** [@bifouba](https://discourse.mc-stan.org/u/bifouba)\
**Replies:** 11\
**Last updated:** [June 18, 2026, 11:47am UTC](https://discourse.mc-stan.org/t/disjunction-of-type-traits-for-combined-varmat-matvar-custom-c-template/41359 "2026-06-18T11:47:14Z")

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This builds on a previous conversation about custom C++ implementations of multivariate functions: Vector-valued functions with manual gradients in external C++ I have successfully got the attached small example working…

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## [Vector-valued functions with manual gradients in external C++](https://discourse.mc-stan.org/t/vector-valued-functions-with-manual-gradients-in-external-c/32297)

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**Author:** [@alphillips](https://discourse.mc-stan.org/u/alphillips)\
**Replies:** 20\
**Last updated:** [June 15, 2026, 7:36am UTC](https://discourse.mc-stan.org/t/vector-valued-functions-with-manual-gradients-in-external-c/32297 "2026-06-15T07:36:11Z")

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Hi, I’m trying to develop an ODE model which will eventually use values from an external C++ library to inform the derivatives (and gradients of this function). Hence, I’ve started by writing a very simple ODE model wit…

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## [Naive Savage Dickey ratio on correlations with LKJ prior on correlation matrix suitable?](https://discourse.mc-stan.org/t/naive-savage-dickey-ratio-on-correlations-with-lkj-prior-on-correlation-matrix-suitable/41121)

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**Author:** [@spn](https://discourse.mc-stan.org/u/spn)\
**Replies:** 5\
**Last updated:** [June 9, 2026, 2:48pm UTC](https://discourse.mc-stan.org/t/naive-savage-dickey-ratio-on-correlations-with-lkj-prior-on-correlation-matrix-suitable/41121 "2026-06-09T14:48:21Z")

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I am trying to find correlations between multiple variables. To do so, I model them jointly from a multivariate normal (based on this). I placed LKJ(1) on the correlation matrix (to be unbiased) vars \<- colnames(dfcorra…

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## [Interaction is significant, but neither simple effects nor Bayes analysis](https://discourse.mc-stan.org/t/interaction-is-significant-but-neither-simple-effects-nor-bayes-analysis/41357)

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**Author:** [@J111](https://discourse.mc-stan.org/u/J111)\
**Replies:** 3\
**Last updated:** [June 9, 2026, 2:45pm UTC](https://discourse.mc-stan.org/t/interaction-is-significant-but-neither-simple-effects-nor-bayes-analysis/41357 "2026-06-09T14:45:41Z")

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I am currently running a 2 x 2 x 2 repeated measures ANCOVA in JASP. I have 2 within factors (animacy, word pairing) and one between factor (group). I have found a significant interaction of animacy \* group. However, wh…

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## [Differences between jacobian += and target+=?](https://discourse.mc-stan.org/t/differences-between-jacobian-and-target/39685)

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**Author:** [@bnicenboim](https://discourse.mc-stan.org/u/bnicenboim)\
**Replies:** 12\
**Last updated:** [June 5, 2026, 7:15pm UTC](https://discourse.mc-stan.org/t/differences-between-jacobian-and-target/39685 "2026-06-05T19:15:57Z")

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Hi! Thanks for another release :) I’m a bit confused by jacobian +=, and I don’t find much about it. When should I use it? How is it different from target +=?

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## [CmdStan & Stan 2.39 Release Candidates](https://discourse.mc-stan.org/t/cmdstan-stan-2-39-release-candidates/41122)

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**Author:** [@WardBrian](https://discourse.mc-stan.org/u/WardBrian)\
**Replies:** 2\
**Last updated:** [May 18, 2026, 8:05pm UTC](https://discourse.mc-stan.org/t/cmdstan-stan-2-39-release-candidates/41122 "2026-05-18T20:05:16Z")

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I am happy to announce that the latest release candidates of CmdStan and Stan are now available on Github! This release cycle brings the embedded laplace approximation, new functions, and many fixes. You can find the r…

[Next page](https://discourse.mc-stan.org/c/general/24.md?page=1)