bayesplot | bayesplot R package for plotting Bayesian models | Data Visualization library

Assume I have a multilevel structure of data. With a global distribution, from which I draw a highlevel distribution from which i draw a lowlevel distribution from which I draw my response variable. How would I implement such a thing in a stan model.

Below is a minimal example which I hope illustrates the problem. In the stan code there is

• one commented "model" section which is working, but ignores the mutlilevel aspect and treats every lower level equal, irrespective of the highlevel origin and provides therefor not shrinkage by the highlevel order (see pic).
• A "model"section with a forloop, which I though would do what I want, but takes forever to finish, and with a lot of warnings (Rhat, treedepth, Bayesion Fraction, low ESS)

I am quite inexperienced with modeling and all tutorials on ML-Modeling do not have the Loop-Approach I though would make sense here, so I suspect I am completely heading in the wrong direction with that. So any help will be highly appreciated.

R-Code to generate and run the model

I used mcmc_trace function from the bayesplot package to plot traceplot with mcmc list, which is a ggplot item so it can be further edited by ggplot function.

Follows is the plot that produced by the function. I needed to change the title k1...k[20] to subject 1... subject 20. Are there any approaches I can achieve this with ggplot function?

Follows is a simple reproducible model.

I am making the convergence graph of the chains generated using the traceplot function. However, see what unusual lines are appearing on the chart. How would you go about removing them?

data: https://drive.google.com/file/d/1iOuGbjNI_caLWBIz4s7hZX5GlfhLrwr9/view?usp=sharing

Below are the codes.

There is a package supported by Stan called bayesplot that can produce nice density area plots with the area under the density curves partitioned based on credibility intervals on the posterior parameter samples drawn through MCMC, this results in a plot that looks like the following:

I am looking to make a similar style of plot given 1D lists of sampled values using ggplot, that I can pass any generic list of values to without it having to be a Stan fit etc. Does anyone know how to do this? The density part is clear via geom_density, but I am struggling with the fill partitioning.

I'm having trouble adjusting a linear regression model on the stan. When observing the error message, the identification in the block part of the transformed parameters is noted.

See below the structure of the code in stan.