rstan

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Rstan should reset environment variables it sets

1

See https://github.com/nlmixr2/nlmixr2/issues/253. Rstan sets some environement variables: `PKG_CPPFLAGS`, `PKG_LIBS` and `USE_CXX17`. These variables interfere with other R packages using `R CMD SHLIB`, such as `nlmixr2`, and make them unable to...

jhjourdan

`rstan` fails to read `cmdstanr` output .csv files

16

#### Summary: `rstan::read_stan_csv()` no longer works for for .csv files produced by `cmdstanr` #### Description: It seems that `rstan` expects the `save_warmup` field to be an integer value, but `cmdstanr`...

santikka

"Global state has changed" warning

1

Transferred from paul-buerkner/brms#1670 --- We rely on `brms` / `rstan` in the [`report`](https://easystats.github.io/report) package, and we have a workflow checking for warnings in tests. The workflow is failing due to...

rempsyc

Conflict with conflicted library, remove uses of `apropos()`?

5

Hello, It appears that Rstan's use of the `apropos()` function is causing conflicts with the `conflicted` library, so I was advised to open an issue here to see if all...

emstruong

`rstan` missing `BH` from imports / suggests

6

#### Summary: It appears that `rstan` requires the `BH` to be available at run time when it compiles the Stan models otherwise an error is thrown e.g. ``` > stan_model

gowerc

Output of `optimizing` does not return the number of used iterations or reason why the optimization was terminated

2

It would be great if the output of `optimizing` contained the number of iterations the optimizer ran. This could be then to check whether the optimization terminated because of hitting...

helske

#### Summary Complete documentation of verification of rstan using the RStan example. #### Description: For new stan users like myself, the below could use clarification: 1. In the section Verifying...

evelynstrombom

#### Summary: It seems that there is an error in the documentation regarding the `save_iterations` argument as generated quantities are computed at each iteration of the optimizer by default, but...

helske

BFMI is inconsistent with the paper

1

#### Summary: The BFMI implementation is inconsistent with the [original paper](https://arxiv.org/pdf/1604.00695v1.pdf). #### Description: The numerator in `get_bfmi` is divided by the length of `x` https://github.com/stan-dev/rstan/blob/f79dae16e3bc187601520a165916b4d39d83af8d/rstan/rstan/R/check_hmc_diagnostics.R#L231 This is consistent with the...

sethaxen

Compatibility with changes in Stan RNG type

1

For the 2.32 -> 2.36+ transition, we need to account for the changes in Stan's rng otherwise CRAN `rstan` won't build against the next `StanHeaders`: ``` Module.cpp:106:21: error: no viable...

andrjohns