rstan | RStan , the R interface to Stan | Data Visualization library

A basic feature of R6 is that methods belong to objects. They are not bound in the package namespace, per se, so it is not surprising that you are not able to access them with :: or :::. Here is an example taken directly from ?R6::R6Class:

It seems that devtools::test evaluates the test code in a setting where S4 dispatch does not work in the usual way, at least for packages that you load explicitly in the test file (in this case rstan). As a result, summary dispatches to summary.default instead of the S4 method implemented in rstan for class "stanfit".

The behaviour that you're seeing might relate to this issue on the testthat repo, which seems unresolved.

Here is a minimal example that tries to illuminate what is happening, showing one possible (admittedly inconvenient) work-around.

The apply function can be your friend here:

Run example

I used the print() statement in the transformed parameters block to see which value is Nan (as it's stated in the error). So this is what I did:

found the mistake: I needed to map the lowlevel values to the highlevel ones, with a look up table. Below is now a working version, which also just takes a second to finish.

I got a solution:

Apperently there are to many (unnecessary) intermediate variables, which then crashes the program. You can get rid of theta by substituting "binomial()" with "binomial_logit()". And the for-loop can be also substituted with a more elegant alternativ.

By setting col="black" you have removed the information ggplot needs to keep the traces for each chain separate. Adding aes(group=chain) as below appears to work (although I would consider whether you really want to make the chains indistinguishable from each other: part of the point of showing a trace plot is to verify that the different chains have similar behaviour ...)

It looks like I finally managed to fix this, and I'm posting my solution here for anyone who encounters the same problem.

I ran env in terminal to see my current user environment. I copy-pasted the full output to the top of my crontab file. (Simply adding the PATH variable was not sufficient. I suppose it was SHELL or perhaps both PATH and SHELL that did the trick, but I haven't explored this further.)

To edit my user's crontab, I ran crontab -e, then pressed i to edit the file, pasted everything from env at the top of the file, stopped editing by pressing ctrl + c, and quit by typing :wq and hitting enter.

Face similar problem... Looks like a folder had previously made so the new R Tools cannot be installed and run the program properly