SBC conventions

Hi,

I get the following when I run sbc:

gamma <- stan_model("gammadiffsaddle.stan")
output <- sbc(gamma,
              data = list(N = 100, mu1 = log(500), mu2 = log(200), mu3 = log(1/5), sigma1 =.5, sigma2=.5, sigma3=.5), M = 10,control=list(adapt_delta = .9) )

#1: In sbc(gamma, data = list(N = 100, mu1 = log(500), mu2 = log(200),  :
#  parameter names could not be calculated due to non-compliance with conventions; see help(sbc)

I can’t figure out what are the conventions that I’m missing, maybe someone can take a look at my model?

  real gammadiffs_lpdf(real y, real alpha1, real alpha2, real beta) {
//here is the long function I want to check
}
data {
  int N;
  real mu1;
  real mu2;
  real mu3;
  real sigma1;
  real sigma2;
  real sigma3;
}
transformed data { 
  real alpha1_ = lognormal_rng(mu1,sigma1);
  real alpha2_ = lognormal_rng(mu2,sigma2);
  real beta_ = lognormal_rng(mu3,sigma3);
  real y[N];
  for(i in 1:N){
    real y1 = gamma_rng(alpha1_, beta_);
    real y2 = gamma_rng(alpha2_, beta_);
    y[i] = y1 - y2;
  }
}
parameters {
  real<lower = 0> alpha2;
  real<lower = 0> alpha1;
  real<lower = 0> beta;
}
model {
  target +=  lognormal_lpdf(alpha1 | mu1,sigma1);
  target +=  lognormal_lpdf(alpha2 | mu2,sigma2);
  target +=  lognormal_lpdf(beta | mu3,sigma3);
  for(i in 1:N)
    target += gammadiffs_lpdf(y[i]| alpha1, alpha2, beta);
}
generated quantities { 
  real y_[N] = y;
  vector[3] pars_ = to_vector({alpha1_, alpha2_, beta_});
  int ranks_[3] = {alpha1 > alpha1_, alpha2 > alpha2_, beta > beta_};
  vector[N] log_lik;
  for(n in 1:N)
    log_lik[n] = gammadiffs_lpdf(y[n]| alpha1, alpha2, beta);
}
  • Operating System: Ubuntu

  • RStan Version: rstan_2.21.1

  • Output of writeLines(readLines(file.path(Sys.getenv("HOME"), ".R/Makevars"))):
    CXX14FLAGS=-O3 -march=native -mtune=native -fPIC CXX14=g++

  • Output of devtools::session_info("rstan")

─ Session info ───────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 3.6.3 (2020-02-29)
 os       Ubuntu 18.04.4 LTS          
 system   x86_64, linux-gnu           
 ui       X11                         
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       Europe/Amsterdam            
 date     2020-07-13                  

─ Packages ───────────────────────────────────────────────────────────────────
 package      * version   date       lib source                         
 assertthat     0.2.1     2019-03-21 [3] CRAN (R 3.5.3)                 
 backports      1.1.8     2020-06-17 [3] CRAN (R 3.6.3)                 
 BH             1.72.0-3  2020-01-08 [3] CRAN (R 3.6.2)                 
 callr          3.4.3     2020-03-28 [1] CRAN (R 3.6.3)                 
 checkmate      2.0.0     2020-02-06 [3] CRAN (R 3.6.2)                 
 cli            2.0.2     2020-02-28 [3] CRAN (R 3.6.3)                 
 colorspace     1.4-1     2019-03-18 [3] CRAN (R 3.5.3)                 
 crayon         1.3.4     2017-09-16 [3] CRAN (R 3.5.0)                 
 curl           4.3       2019-12-02 [1] CRAN (R 3.6.2)                 
 desc           1.2.0     2018-05-01 [3] CRAN (R 3.5.0)                 
 digest         0.6.25    2020-02-23 [1] CRAN (R 3.6.3)                 
 ellipsis       0.3.1     2020-05-15 [3] CRAN (R 3.6.3)                 
 evaluate       0.14      2019-05-28 [1] CRAN (R 3.6.2)                 
 fansi          0.4.1     2020-01-08 [3] CRAN (R 3.6.2)                 
 farver         2.0.3     2020-01-16 [1] CRAN (R 3.6.3)                 
 ggplot2      * 3.3.2     2020-06-19 [1] CRAN (R 3.6.3)                 
 glue           1.4.1     2020-05-13 [1] CRAN (R 3.6.3)                 
 gridExtra      2.3       2017-09-09 [3] CRAN (R 3.5.0)                 
 gtable         0.3.0     2019-03-25 [3] CRAN (R 3.5.3)                 
 inline         0.3.15    2018-05-18 [3] CRAN (R 3.5.0)                 
 isoband        0.2.2     2020-06-20 [3] CRAN (R 3.6.3)                 
 jsonlite       1.7.0     2020-06-25 [1] CRAN (R 3.6.3)                 
 labeling       0.3       2014-08-23 [3] CRAN (R 3.5.0)                 
 lattice        0.20-41   2020-04-02 [4] CRAN (R 3.6.3)                 
 lifecycle      0.2.0     2020-03-06 [3] CRAN (R 3.6.3)                 
 loo            2.2.0     2019-12-19 [3] CRAN (R 3.6.2)                 
 magrittr       1.5       2014-11-22 [3] CRAN (R 3.5.0)                 
 MASS           7.3-51.5  2019-12-20 [1] CRAN (R 3.6.2)                 
 Matrix         1.2-18    2019-11-27 [4] CRAN (R 3.6.1)                 
 matrixStats    0.56.0    2020-03-13 [1] CRAN (R 3.6.3)                 
 mgcv           1.8-31    2019-11-09 [4] CRAN (R 3.6.1)                 
 munsell        0.5.0     2018-06-12 [3] CRAN (R 3.5.0)                 
 nlme           3.1-147   2020-04-13 [4] CRAN (R 3.6.3)                 
 pillar         1.4.4     2020-05-05 [3] CRAN (R 3.6.3)                 
 pkgbuild       1.0.8     2020-05-07 [1] CRAN (R 3.6.3)                 
 pkgconfig      2.0.3     2019-09-22 [3] CRAN (R 3.6.1)                 
 pkgload        1.1.0     2020-05-29 [1] CRAN (R 3.6.3)                 
 praise         1.0.0     2015-08-11 [1] CRAN (R 3.6.2)                 
 prettyunits    1.1.1     2020-01-24 [3] CRAN (R 3.6.2)                 
 processx       3.4.3     2020-07-05 [1] CRAN (R 3.6.3)                 
 ps             1.3.3     2020-05-08 [1] CRAN (R 3.6.3)                 
 R6             2.4.1     2019-11-12 [3] CRAN (R 3.6.1)                 
 RColorBrewer   1.1-2     2014-12-07 [3] CRAN (R 3.5.0)                 
 Rcpp           1.0.4.6   2020-04-09 [1] CRAN (R 3.6.3)                 
 RcppEigen      0.3.3.7.0 2019-11-16 [3] CRAN (R 3.6.1)                 
 RcppParallel   5.0.2     2020-06-24 [1] CRAN (R 3.6.3)                 
 rlang          0.4.7     2020-07-09 [1] CRAN (R 3.6.3)                 
 rprojroot      1.3-2     2018-01-03 [1] CRAN (R 3.6.3)                 
 rstan        * 2.21.1    2020-07-02 [1] Github (stan-dev/rstan@d69bb88)
 rstudioapi     0.11      2020-02-07 [1] CRAN (R 3.6.3)                 
 scales         1.1.1     2020-05-11 [3] CRAN (R 3.6.3)                 
 StanHeaders  * 2.21.0-5  2020-06-09 [1] CRAN (R 3.6.3)                 
 testthat       2.3.2     2020-03-02 [1] CRAN (R 3.6.3)                 
 tibble         3.0.1     2020-04-20 [1] CRAN (R 3.6.3)                 
 utf8           1.1.4     2018-05-24 [3] CRAN (R 3.5.0)                 
 V8             3.2.0     2020-06-19 [1] CRAN (R 3.6.3)                 
 vctrs          0.3.1     2020-06-05 [1] CRAN (R 3.6.3)                 
 viridisLite    0.3.0     2018-02-01 [3] CRAN (R 3.5.0)                 
 withr          2.2.0     2020-04-20 [1] CRAN (R 3.6.3)                 

[1] /home/bruno/R/x86_64-pc-linux-gnu-library/3.6
[2] /usr/local/lib/R/site-library
[3] /usr/lib/R/site-library
[4] /usr/lib/R/library

Thanks!
Bruno

1 Like

It might just be an ordering thing. Try

parameters {
  real<lower = 0> alpha1;
  real<lower = 0> alpha2;
  real<lower = 0> beta;
}

no, I still get the same warning.

And when I try to plot I get the following:

Error in data.frame(u = c(u), parameter) : 
  arguments imply differing number of rows: 30, 0

sorry, but any ideas of what’s going on?
Is this maybe a bug? Or are there more examples of sbc used with an lpdf similar to mine?
(The example of the vignette seems very specific)

1 Like