# \#shinystan

**URL:** https://discourse.mc-stan.org/tag/shinystan/32.md

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## [CmdStan, CmdStanR, CmdStanPy workflow resulting in errors with \`as.shinystan\` function](https://discourse.mc-stan.org/t/cmdstan-cmdstanr-cmdstanpy-workflow-resulting-in-errors-with-as-shinystan-function/40672)

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**Author:** [@danni\_storm](https://discourse.mc-stan.org/u/danni_storm)\
**Replies:** 6\
**Last updated:** [December 11, 2025, 2:43pm UTC](https://discourse.mc-stan.org/t/cmdstan-cmdstanr-cmdstanpy-workflow-resulting-in-errors-with-as-shinystan-function/40672 "2025-12-11T14:43:05Z")

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My model successfully runs and produces CSV files. However, when trying to use R and ShinyStan, I am unable to get ShinyStan to accept my model files using CmdStanR. I have been digging into the documentation and it look…

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## [Install issues with shinystan with R](https://discourse.mc-stan.org/t/install-issues-with-shinystan-with-r/1506)

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**Author:** [@felixmueller](https://discourse.mc-stan.org/u/felixmueller)\
**Replies:** 4\
**Last updated:** [December 17, 2024, 10:15am UTC](https://discourse.mc-stan.org/t/install-issues-with-shinystan-with-r/1506 "2024-12-17T10:15:27Z")

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Hi there! I was trying to install shinystan which gave me the error message ERROR: configuration failed for package ‘RCurl’ \* removing ‘/usr/local/lib/R/site-library/RCurl’ ERROR: dependency ‘RCurl’ is not available fo…

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## [Shinystan launch error: Unused Argument](https://discourse.mc-stan.org/t/shinystan-launch-error-unused-argument/33721)

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**Author:** [@ormvi](https://discourse.mc-stan.org/u/ormvi)\
**Replies:** 3\
**Last updated:** [June 11, 2024, 3:39pm UTC](https://discourse.mc-stan.org/t/shinystan-launch-error-unused-argument/33721 "2024-06-11T15:39:11Z")

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Hello, I am new to shinystan so apologies if I don’t provide enough info/format wrong or something, I can fix as required. I am having a problem when launching shinystan for my model & after some forum searching I foun…

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## [Shiny stan for sensitivity analysis](https://discourse.mc-stan.org/t/shiny-stan-for-sensitivity-analysis/32412)

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**Author:** [@natparry212](https://discourse.mc-stan.org/u/natparry212)\
**Replies:** 1\
**Last updated:** [August 10, 2023, 4:57pm UTC](https://discourse.mc-stan.org/t/shiny-stan-for-sensitivity-analysis/32412 "2023-08-10T16:57:23Z")

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Hi! I have a model and I want to do a sensitivity analysis. I have seen in articles that it is possible to do it using shinystan but I am not able to figure out how to add two models into the shiny stan app. Any help wou…

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## [MCMC Monitor -- Online monitoring of Stan runs](https://discourse.mc-stan.org/t/mcmc-monitor-online-monitoring-of-stan-runs/31568)

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**Author:** [@JSoules](https://discourse.mc-stan.org/u/JSoules)\
**Replies:** 3\
**Last updated:** [June 1, 2023, 5:44pm UTC](https://discourse.mc-stan.org/t/mcmc-monitor-online-monitoring-of-stan-runs/31568 "2023-06-01T17:44:01Z")

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Hello, Stan community! I’d like to make you aware of a new tool we’re developing here at Flatiron: MCMC Monitor. It allows monitoring of Stan runs, both in progress and after completion. Consider it a ShinyStan that als…

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## [Best way to identify pathologies from divergent transitions (general step by step workflow)](https://discourse.mc-stan.org/t/best-way-to-identify-pathologies-from-divergent-transitions-general-step-by-step-workflow/4358)

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**Author:** [@stemangiola](https://discourse.mc-stan.org/u/stemangiola)\
**Replies:** 14\
**Last updated:** [September 11, 2022, 9:00pm UTC](https://discourse.mc-stan.org/t/best-way-to-identify-pathologies-from-divergent-transitions-general-step-by-step-workflow/4358 "2022-09-11T21:00:08Z")

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Hello, following the post Redirecting to Google Groups I am interested in learning how to do what @betanalpha suggested At that most general level diverges occur when the posterior on the unconstrained scaled featur…

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## [ShinyStan showing number boxes instead of Numbers on axis](https://discourse.mc-stan.org/t/shinystan-showing-number-boxes-instead-of-numbers-on-axis/27800)

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**Author:** [@Madhav\_Kanda](https://discourse.mc-stan.org/u/Madhav_Kanda)\
**Replies:** 0\
**Last updated:** [June 11, 2022, 6:06pm UTC](https://discourse.mc-stan.org/t/shinystan-showing-number-boxes-instead-of-numbers-on-axis/27800 "2022-06-11T18:06:16Z")

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The graphs that I am getting using ShinyStan are having such square boxed numbers instead of numbers on the axis. How should I fix this?

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## [Shinystan with separate generated quantities](https://discourse.mc-stan.org/t/shinystan-with-separate-generated-quantities/25754)

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**Author:** [@adamConnerSax](https://discourse.mc-stan.org/u/adamConnerSax)\
**Replies:** 4\
**Last updated:** [March 9, 2022, 2:04pm UTC](https://discourse.mc-stan.org/t/shinystan-with-separate-generated-quantities/25754 "2022-03-09T14:04:26Z")

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I’m trying to build a work flow to accommodate running a model once and then post-stratifying (or doing something in the generated quantities block) in a separate cmdstan run, using standalone generate quantities. I’ve …

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## [Shinystan "not an available theme" workaround](https://discourse.mc-stan.org/t/shinystan-not-an-available-theme-workaround/26648)

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**Author:** [@jonah](https://discourse.mc-stan.org/u/jonah)\
**Replies:** 0\
**Last updated:** [March 3, 2022, 7:57pm UTC](https://discourse.mc-stan.org/t/shinystan-not-an-available-theme-workaround/26648 "2022-03-03T19:57:20Z")

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Some users are reporting a strange error from shinystan: Error in shinythemes::shinytheme: flatly is not an available theme. Valid themes are: . 82: stop 81: shinythemes::shinytheme I’m not yet sure why this is hap…

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## [Library(cmdstanr) in shinyapps.io path not set](https://discourse.mc-stan.org/t/library-cmdstanr-in-shinyapps-io-path-not-set/25510)

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**Author:** [@gusvanherf](https://discourse.mc-stan.org/u/gusvanherf)\
**Replies:** 3\
**Last updated:** [December 1, 2021, 11:03am UTC](https://discourse.mc-stan.org/t/library-cmdstanr-in-shinyapps-io-path-not-set/25510 "2021-12-01T11:03:41Z")

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Hi all While publishing my shiny app to shinyapp. io, i get an error on library(cmdstanr) saying that the path is not set correctly. From this article: Chapter 2 Getting Started | shinyapps.io user guide , i can see th…

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## [Shinystan: An error has occurred! in example of as.shinystan](https://discourse.mc-stan.org/t/shinystan-an-error-has-occurred-in-example-of-as-shinystan/24303)

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**Author:** [@twitterbitter](https://discourse.mc-stan.org/u/twitterbitter)\
**Replies:** 1\
**Last updated:** [September 13, 2021, 4:15pm UTC](https://discourse.mc-stan.org/t/shinystan-an-error-has-occurred-in-example-of-as-shinystan/24303 "2021-09-13T16:15:08Z")

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I am trying to run as.shinystan with the example provided in the function documentation. chain1 \<- cbind(beta1 = rnorm(100), beta2 = rnorm(100), sigma = rexp(100)) chain2 \<- cbind(beta1 = rnorm(100), beta2 = rnorm(100),…

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## [Easiest file format (or loading files with custom R code) to use custom MCMC chain with shinystan](https://discourse.mc-stan.org/t/easiest-file-format-or-loading-files-with-custom-r-code-to-use-custom-mcmc-chain-with-shinystan/24139)

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**Author:** [@jlperla](https://discourse.mc-stan.org/u/jlperla)\
**Replies:** 3\
**Last updated:** [September 11, 2021, 9:00am UTC](https://discourse.mc-stan.org/t/easiest-file-format-or-loading-files-with-custom-r-code-to-use-custom-mcmc-chain-with-shinystan/24139 "2021-09-11T09:00:26Z")

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I am interested in using shinystan and related visualization tools for MCMC chains generated from custom code (i.e., not from a standard MCMC DSL). Given that shinystan seems to support multiple backends, I suspect this…

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## [Mcse/sd Diagnostic in Shinystan](https://discourse.mc-stan.org/t/mcse-sd-diagnostic-in-shinystan/24098)

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**Author:** [@Thomas](https://discourse.mc-stan.org/u/Thomas)\
**Replies:** 1\
**Last updated:** [September 7, 2021, 8:28am UTC](https://discourse.mc-stan.org/t/mcse-sd-diagnostic-in-shinystan/24098 "2021-09-07T08:28:49Z")

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On the Diagnose tab in Shinystan there is a histogram of the Monte Carlo standard error divided by the posterior standard deviation, i.e., “mcse/sd”. Is this simply the ratio of “mcse\_mean” and “sd” in the summary stati…

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## [Shinystan and \>1000 parameters](https://discourse.mc-stan.org/t/shinystan-and-1000-parameters/22291)

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**Author:** [@tomli](https://discourse.mc-stan.org/u/tomli)\
**Replies:** 2\
**Last updated:** [May 11, 2021, 5:36pm UTC](https://discourse.mc-stan.org/t/shinystan-and-1000-parameters/22291 "2021-05-11T17:36:45Z")

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I only get to access to the first 1000 parameters when I launch shinystan. Googling, I found I’m not alone: how to raise limit above 1000 parameters? · Issue #187 · stan-dev/shinystan · GitHub Is there a workaround for …

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## [Shinystan for cmdstan output](https://discourse.mc-stan.org/t/shinystan-for-cmdstan-output/20043)

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**Author:** [@ducoveen](https://discourse.mc-stan.org/u/ducoveen)\
**Replies:** 6\
**Last updated:** [January 6, 2021, 2:55pm UTC](https://discourse.mc-stan.org/t/shinystan-for-cmdstan-output/20043 "2021-01-06T14:55:16Z")

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Hello everyone, I’ve spend a little bit of time on creating a version of shinystan that will take as upload .csv file(s) output from cmdstan. This way it should be more accessible, not only for R users. Please take a lo…

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## [Will launch\_shinystan work soon for cmdstanr?](https://discourse.mc-stan.org/t/will-launch-shinystan-work-soon-for-cmdstanr/17269)

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**Author:** [@aaa](https://discourse.mc-stan.org/u/aaa)\
**Replies:** 2\
**Last updated:** [August 6, 2020, 4:02am UTC](https://discourse.mc-stan.org/t/will-launch-shinystan-work-soon-for-cmdstanr/17269 "2020-08-06T04:02:16Z")

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It seems that cmdstanr runs create a new type of object incompatible with launch\_shinystan. Is there a workaround?

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## [Visualizing rstan fit with R Shiny](https://discourse.mc-stan.org/t/visualizing-rstan-fit-with-r-shiny/16291)

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**Author:** [@stan\_beginer](https://discourse.mc-stan.org/u/stan_beginer)\
**Replies:** 5\
**Last updated:** [July 1, 2020, 1:34pm UTC](https://discourse.mc-stan.org/t/visualizing-rstan-fit-with-r-shiny/16291 "2020-07-01T13:34:46Z")

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I am wondering whether there is any convenient way to visualize the posterior distribution and related quantities using Rshiny after I get my rstan fitted result saved as Rdata? Thx!

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## [ShinyStan 3.0 Alpha test](https://discourse.mc-stan.org/t/shinystan-3-0-alpha-test/12664)

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**Author:** [@ducoveen](https://discourse.mc-stan.org/u/ducoveen)\
**Replies:** 16\
**Last updated:** [April 6, 2020, 8:09am UTC](https://discourse.mc-stan.org/t/shinystan-3-0-alpha-test/12664 "2020-04-06T08:09:48Z")

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Hello Everyone, @jonah and I have been working on an update for shinystan and we would be very happy if you could try it out and provide feedback. We replaced the entire back end for the shiny application and used modul…

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## [Shinystan with stan\_jm model](https://discourse.mc-stan.org/t/shinystan-with-stan-jm-model/12461)

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**Author:** [@Lawrence\_Hunsicker](https://discourse.mc-stan.org/u/Lawrence_Hunsicker)\
**Replies:** 12\
**Last updated:** [January 6, 2020, 8:57pm UTC](https://discourse.mc-stan.org/t/shinystan-with-stan-jm-model/12461 "2020-01-06T20:57:20Z")

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Please also provide the following information in addition to your question: Operating System: Windows 10 64 bit up-to-date rstanarm Version: 2.19.2 I have run a stan\_jm model that runs forever and ends with multiple…

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## [Launching ShinyStan without blocking R session](https://discourse.mc-stan.org/t/launching-shinystan-without-blocking-r-session/3286)

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**Author:** [@martinmodrak](https://discourse.mc-stan.org/u/martinmodrak)\
**Replies:** 3\
**Last updated:** [July 29, 2019, 12:06pm UTC](https://discourse.mc-stan.org/t/launching-shinystan-without-blocking-r-session/3286 "2019-07-29T12:06:12Z")

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This is a neat trick I found on Tyler Morgan-Wall’s Twitter and originally attributed to Joe Cheng. You can run ShinyStan (or anything else Shiny) without blocking the session (which was always a pain point for me). My h…

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## [Posterior predictive checks in ShinyStan](https://discourse.mc-stan.org/t/posterior-predictive-checks-in-shinystan/9311)

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**Author:** [@Pia](https://discourse.mc-stan.org/u/Pia)\
**Replies:** 12\
**Last updated:** [June 20, 2019, 1:55pm UTC](https://discourse.mc-stan.org/t/posterior-predictive-checks-in-shinystan/9311 "2019-06-20T13:55:58Z")

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Hi, This is probably a very simple problem but I just can’t figure it out. I’ve estimated a multivariate multiple membership model using brms and launched ShinyStan and now want to do the graphical PPchecks. I have diff…

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## [Divergent Transitions with R\_hat \< 1.1](https://discourse.mc-stan.org/t/divergent-transitions-with-r-hat-1-1/9052)

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**Author:** [@BG\_2019](https://discourse.mc-stan.org/u/BG_2019)\
**Replies:** 14\
**Last updated:** [June 13, 2019, 4:15am UTC](https://discourse.mc-stan.org/t/divergent-transitions-with-r-hat-1-1/9052 "2019-06-13T04:15:20Z")

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Hi, I am trying to fit a model in stan, which is producing around 0.6% - 1% divergent transitions, but my coefficients are all significant with Bayes R\_hat \< 1.1. I even verified the coefficient plot using shinystan whi…

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## [Resources of desirable MCMC representativeness](https://discourse.mc-stan.org/t/resources-of-desirable-mcmc-representativeness/8518)

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**Author:** [@You\_Ishi](https://discourse.mc-stan.org/u/You_Ishi)\
**Replies:** 2\
**Last updated:** [April 18, 2019, 1:04pm UTC](https://discourse.mc-stan.org/t/resources-of-desirable-mcmc-representativeness/8518 "2019-04-18T13:04:22Z")

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Hi everyone! Now I’m using shinystan and checking MCMC representativeness by Rhat, MCSE/se and neff/N. Do you happen to know about the evidence of the number of these indexes? I guess Rhat less than 1.1 is written in …

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## [Shinystan fails to install - following the website's instructions - on Debian 8 - latest R 3.5.2](https://discourse.mc-stan.org/t/shinystan-fails-to-install-following-the-websites-instructions-on-debian-8-latest-r-3-5-2/7265)

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**Author:** [@Jozsef\_Hegedus](https://discourse.mc-stan.org/u/Jozsef_Hegedus)\
**Replies:** 15\
**Last updated:** [January 14, 2019, 6:47pm UTC](https://discourse.mc-stan.org/t/shinystan-fails-to-install-following-the-websites-instructions-on-debian-8-latest-r-3-5-2/7265 "2019-01-14T18:47:06Z")

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Hi, What might be the error if : I got the error message shown below when I write into R : install.packages("rstan", repos = "https://cloud.r-project.org/", dependencies = TRUE) If your question relates to installa…

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## [Launch\_shinystan](https://discourse.mc-stan.org/t/launch-shinystan/6836)

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**Author:** [@nlpacestan](https://discourse.mc-stan.org/u/nlpacestan)\
**Replies:** 4\
**Last updated:** [December 19, 2018, 5:57am UTC](https://discourse.mc-stan.org/t/launch-shinystan/6836 "2018-12-19T05:57:09Z")

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Please also provide the following information in addition to your question: Operating System: Windows 2016 Server rstanarm Version: 2.18.2 I have estimated a stan\_lm object. There are 1.1 M observations and 41 predic…

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## [Shinystan bug, launches by itself](https://discourse.mc-stan.org/t/shinystan-bug-launches-by-itself/5511)

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**Author:** [@nschiett](https://discourse.mc-stan.org/u/nschiett)\
**Replies:** 2\
**Last updated:** [September 6, 2018, 2:13pm UTC](https://discourse.mc-stan.org/t/shinystan-bug-launches-by-itself/5511 "2018-09-06T14:13:52Z")

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Hi! I am encountering a very odd issue in rstudio. Shinystan is launching repeatedly showing an older version of a model, without me running the launch shinystan function. I even removed the command from all tabs. Whenev…

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## [Export stanfit object from Matlab to R](https://discourse.mc-stan.org/t/export-stanfit-object-from-matlab-to-r/2777)

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**Author:** [@elsafouragnan](https://discourse.mc-stan.org/u/elsafouragnan)\
**Replies:** 2\
**Last updated:** [December 15, 2017, 6:52pm UTC](https://discourse.mc-stan.org/t/export-stanfit-object-from-matlab-to-r/2777 "2017-12-15T18:52:30Z")

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Hi, I wonder if some of you have try exporting your results to R from Matlab (stanfit object) and then use ShinyStan? Thank you! Elsa

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## [1001 dalmiterations, shinystan](https://discourse.mc-stan.org/t/1001-dalmiterations-shinystan/2500)

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**Author:** [@sakrejda](https://discourse.mc-stan.org/u/sakrejda)\
**Replies:** 4\
**Last updated:** [November 27, 2017, 8:59pm UTC](https://discourse.mc-stan.org/t/1001-dalmiterations-shinystan/2500 "2017-11-27T20:59:39Z")

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I ran a new model for 1001 iterations just to have something to plot and when I launch “shinystan” it … crashes. Ok, maybe 1 sampling iterations is a corner case so I edit my CmdStan output .csv file to pretend it has 9…

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## [Deselecting parameters in ShinyStan](https://discourse.mc-stan.org/t/deselecting-parameters-in-shinystan/1936)

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**Author:** [@Guido\_Biele](https://discourse.mc-stan.org/u/Guido_Biele)\
**Replies:** 1\
**Last updated:** [September 20, 2017, 1:26am UTC](https://discourse.mc-stan.org/t/deselecting-parameters-in-shinystan/1936 "2017-09-20T01:26:59Z")

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After selecting parameters in ShinyStan, for eksample to show posterior intervals in the Estimation tab, parameters have to deselected one by one if one wants to select a different group of parameters. Is there a way to…

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## [rOpenSci review?](https://discourse.mc-stan.org/t/ropensci-review/1746)

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**Author:** [@Bob\_Carpenter](https://discourse.mc-stan.org/u/Bob_Carpenter)\
**Replies:** 3\
**Last updated:** [September 4, 2017, 12:22am UTC](https://discourse.mc-stan.org/t/ropensci-review/1746 "2017-09-04T00:22:35Z")

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rOpenSci is another NumFOCUS project that is offering to do “peer review” of R software for data science. Here’s an overview of the process from the NumFOCUS blog I figure any feedback is good. We can always ignore…

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