Errors running the vignette example for a beta regression
Nobody has claimed this yet.
- Dominant language
- R
- Stars
- 401
- Forks
- 136
- PR merge metrics
- No merged PRs in 30d
Description
Hello, I am trying to run a beta regression in rstanarm. I was getting errors using my dataset so I tried using the example code. I still get errors, even with that code.
rstanarm version 2.19.3
r version 3.6.3 Mac OS X 10.15.4
Here is my r session info:
R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.4
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
other attached packages:
[1] rstanarm_2.19.3 Rcpp_1.0.3
loaded via a namespace (and not attached):
[1] splines_3.6.3 gtools_3.8.1 StanHeaders_2.21.0-1
[4] threejs_0.3.3 Formula_1.2-3 shiny_1.4.0
[7] assertthat_0.2.1 stats4_3.6.3 pillar_1.4.3
[10] lattice_0.20-38 glue_1.3.1 digest_0.6.24
[13] promises_1.1.0 minqa_1.2.4 sandwich_2.5-1
[16] colorspace_1.4-1 htmltools_0.4.0 httpuv_1.5.2
[19] Matrix_1.2-18 plyr_1.8.5 dygraphs_1.1.1.6
[22] pkgconfig_2.0.3 rstan_2.19.3 purrr_0.3.3
[25] xtable_1.8-4 scales_1.1.0 processx_3.4.2
[28] later_1.0.0 lme4_1.1-21 tibble_2.1.3
[31] bayesplot_1.7.1 ggplot2_3.2.1 DT_0.12
[34] shinyjs_1.1 nnet_7.3-12 lazyeval_0.2.2
[37] cli_2.0.1 survival_3.1-8 magrittr_1.5
[40] crayon_1.3.4 mime_0.9 ps_1.3.2
[43] fansi_0.4.1 nlme_3.1-144 MASS_7.3-51.5
[46] xts_0.12-0 pkgbuild_1.0.6 colourpicker_1.0
[49] rsconnect_0.8.16 tools_3.6.3 loo_2.2.0
[52] prettyunits_1.1.1 lifecycle_0.1.0 matrixStats_0.55.0
[55] stringr_1.4.0 munsell_0.5.0 callr_3.4.2
[58] compiler_3.6.3 rlang_0.4.4 nloptr_1.2.1
[61] grid_3.6.3 ggridges_0.5.2 rstudioapi_0.11
[64] htmlwidgets_1.5.1 crosstalk_1.0.0 igraph_1.2.4.2
[67] miniUI_0.1.1.1 base64enc_0.1-3 boot_1.3-24
[70] codetools_0.2-16 gtable_0.3.0 flexmix_2.3-15
[73] inline_0.3.15 markdown_1.1 reshape2_1.4.3
[76] R6_2.4.1 gridExtra_2.3 rstantools_2.0.0
[79] zoo_1.8-7 dplyr_0.8.4 fastmap_1.0.1
[82] shinystan_2.5.0 shinythemes_1.1.2 betareg_3.1-3
[85] modeltools_0.2-22 stringi_1.4.5 parallel_3.6.3
[88] lmtest_0.9-37 tidyselect_1.0.0
Description:
A full description of the problem (or question).
Reproducible Steps:
If applicable, the steps required to reproduce the issue. If you have a reproducible example, please include it.
Here is the exact code (from empty workspace:
SEED <- 1234
set.seed(SEED)
eta <- c(1, -0.2)
gamma <- c(1.8, 0.4)
N <- 200
x <- rnorm(N, 2, 2)
z <- rnorm(N, 0, 2)
mu <- binomial(link = logit)$linkinv(eta[1] + eta[2]*x)
phi <- binomial(link = log)$linkinv(gamma[1] + gamma[2]*z)
y <- rbeta(N, mu * phi, (1 - mu) * phi)
dat <- data.frame(cbind(y, x, z))
hist(dat$y, col = "darkgrey", border = F, main = "Distribution of Outcome Variable", xlab = "y", breaks = 20, freq = F)
library(rstanarm)
fit1 <- stan_betareg(y ~ x | z, data = dat, link = "logit", link.phi = "log",
cores = 2, seed = 12345)
And here is the error
starting worker pid=17814 on localhost:11523 at 13:47:15.793
starting worker pid=17828 on localhost:11523 at 13:47:16.095
SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000406 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 4.06 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
[1] "Error in sampler$call_sampler(args_list[[i]]) : "
[2] " c++ exception (unknown reason)"
error occurred during calling the sampler; sampling not done
SAMPLING FOR MODEL 'continuous' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.000341 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 3.41 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
[1] "Error in sampler$call_sampler(args_list[[i]]) : "
[2] " c++ exception (unknown reason)"
error occurred during calling the sampler; sampling not done
SAMPLING FOR MODEL 'continuous' NOW (CHAIN 3).
Chain 3: empty_nested() must be true before calling recover_memory()
[1] "Error in sampler$call_sampler(args_list[[i]]) : "
[2] " empty_nested() must be true before calling recover_memory()"
error occurred during calling the sampler; sampling not done
SAMPLING FOR MODEL 'continuous' NOW (CHAIN 4).
Chain 4: empty_nested() must be true before calling recover_memory()
[1] "Error in sampler$call_sampler(args_list[[i]]) : "
[2] " empty_nested() must be true before calling recover_memory()"
error occurred during calling the sampler; sampling not done
here are whatever error messages were returned
[[1]]
Stan model 'continuous' does not contain samples.
[[2]]
Stan model 'continuous' does not contain samples.
[[3]]
Stan model 'continuous' does not contain samples.
[[4]]
Stan model 'continuous' does not contain samples.
Error in check_stanfit(stanfit) :
Invalid stanfit object produced please report bug
In addition: Warning message:
In .local(object, ...) :
some chains had errors; consider specifying chains = 1 to debug
Contributor guide
No contributing guide indexed for this repository
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by running the exact beta-regression example in the issue with the reported R and rstanarm versions, first checking the behavior with the suggested single-chain configuration. Compare the sampler output and determine why the reproducible example fails; done means the documented vignette example runs successfully or the failure is clearly isolated and reported with supporting evidence.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- r
- Domain
- data
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100