Error in the_dims[[2]] : subscript out of bounds

Modeling
1

I often use the Rethinking package as an interface to RStan. Here is the model I’m working on now, in rethinking:

sleep1 ← ulam(
alist(

# Dark phase
nNREMS_Dark ~ dgampois(mu_nNREMS_Dark, scale_nNREMS_Dark),
dNREMS_Dark ~ dgamma2(mu_dNREMS_Dark, scale_dNREMS_Dark),
nREMS_Dark ~ dgampois(mu_nREMS_Dark, scale_nREMS_Dark),
dREMS_Dark ~ dgamma2(mu_dREMS_Dark, scale_dREMS_Dark),
SWA_Dark ~ dgamma2(mu_SWA_Dark, scale_SWA_Dark),

    ## Multivariate prior for means of dark-phase measures
    c(log(mu_nNREMS_Dark), 
      log(mu_dNREMS_Dark), 
      log(mu_nREMS_Dark),
      log(mu_dREMS_Dark),
      log(mu_SWA_Dark)) ~ multi_normal(c(nu_nNREMS_Dark,
                                         nu_dNREMS_Dark,
                                         nu_nREMS_Dark,
                                         nu_dREMS_Dark,
                                         nu_SWA_Dark), 
                                       Rho_Sleep_Dark, 
                                       Sigma_Sleep_Dark),
        Rho_Sleep_Dark ~ lkj_corr(1),
        Sigma_Sleep_Dark ~ dexp(1),
    
        ### Linear models 
            # (Independent Animal intercepts may confound CCL; 
            # in which case, need to replace a_LPSxCCL priors with a_Sleep priors)
        nu_nNREMS_Dark <- a_nNREMS_Dark[Animal] + a_LPSxCCL_nNREMS_Dark[LPSxCCL],
        nu_dNREMS_Dark <- a_dNREMS_Dark[Animal] + a_LPSxCCL_dNREMS_Dark[LPSxCCL],
        nu_nREMS_Dark <- a_nREMS_Dark[Animal] + a_LPSxCCL_nREMS_Dark[LPSxCCL],
        nu_dREMS_Dark <- a_dREMS_Dark[Animal] + a_LPSxCCL_dREMS_Dark[LPSxCCL],
        nu_SWA_Dark <- a_SWA_Dark[Animal] + a_LPSxCCL_SWA_Dark[LPSxCCL],
        
            #### Priors for linear models
            a_nNREMS_Dark[Animal] ~ dnorm(log(48), 0.5), # based on idea that 1/3 spent in NREMS
            a_dNREMS_Dark[Animal] ~ dnorm(log(300), 0.5), # w/avg dNREMS ~ 5 min
            a_nREMS_Dark[Animal] ~ dnorm(log(48), 0.5), # based on idea that 1/10 spent in REMS
            a_dREMS_Dark[Animal] ~ dnorm(log(90), 0.5), # w/avg dREMS ~ 1.5 min
            a_SWA_Dark[Animal] ~ dnorm(log(100000), 0.5),
            
            c(a_LPSxCCL_nNREMS_Dark[LPSxCCL],
              a_LPSxCCL_dNREMS_Dark[LPSxCCL],
              a_LPSxCCL_nREMS_Dark[LPSxCCL],
              a_LPSxCCL_dREMS_Dark[LPSxCCL],
              a_LPSxCCL_dREMS_Dark[LPSxCCL]) ~ dnorm(0.0, 0.5),
        
    ## Priors for scale parameters
    c(scale_nNREMS_Dark,
      scale_dNREMS_Dark,
      scale_nREMS_Dark,
      scale_dREMS_Dark,
      scale_SWA_Dark) ~ dexp(1)

), data=sleep.dlist, chains=4, cores=4, iter=1000
)

In this model, and otherwise commonly, I get the following error

Error in the_dims[[2]] : subscript out of bounds

This is frustrating because I have no indication where the error occurs. My question is, is this a warning from Stan or from R? Is there a remedy or way to diagnose efficiently?

Many thanks

2

This will be something to do with the rethinking package, your best bet will be to open an issue on the package github here: GitHub - rmcelreath/rethinking: Statistical Rethinking course and book package