Cmdstanr and Rmarkdown: inconsistent error message

Modeling
1

Here is a simple user-defined function:

functions{

  real minpdf( real z, real[,] v){
    real result;
    for (j in 1:4) {
      if (z <= v[j + 1, 1]){ 
        result = v[j, 2] + 
        (v[j + 1,2]-v[j, 2]) * (z-v[j, 1]) / (v[j + 1, 1]-v[j, 1]); 
        break;
      }  
    } 
    return(result);
  }
}

Using Rstudio I click on Save with Click on save activated. All goes well:

rstan:::rstudio_stanc("stantest2.stan")
stantest2.stan is syntactically correct.

But if I put the same code into an Rmarkdown document such as this:

 ---
title: "stantest"
author: "Jeremy Colman"
date: "`r Sys.Date()`"
output: pdf_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)

library(cmdstanr) 
register_knitr_engine(override = FALSE)

functions{

  real minpdf( real z, real[,] v){
    real result;
    for (j in 1:4) {
      if (z <= v[j + 1, 1]){ 
        result = v[j, 2] + 
        (v[j + 1,2]-v[j, 2]) * (z-v[j, 1]) / (v[j + 1, 1]-v[j, 1]); 
        break;
      }  
    } 
    return(result);
  }
}

and then click on Knit it all goes wrong:

Syntax error in '/var/folders/fx/8zjr0h4d789bdxlr_ptj66jw0000gs/T/RtmpQjp6RG/model-1eaed49f4f4.stan', line 3, column 27 to column 28, parsing error:
   -------------------------------------------------
     1:  functions{
     2:  
     3:    real minpdf( real z, real[,] v){
                                    ^
     4:      real result;
     5:      for (j in 1:4) {
   -------------------------------------------------

An identifier is expected as a function argument name.

make: *** [/var/folders/fx/8zjr0h4d789bdxlr_ptj66jw0000gs/T/RtmpQjp6RG/model-1eaed49f4f4.hpp] Error 1


Quitting from lines 19-34 [unnamed-chunk-2] (stantest.Rmd)
Execution halted

Is there an error in my code or not? If there is, why does it not show up in the first test? And if there is an error what is it?
Grateful for any help.

1 Like
2

The issue is array syntax was changed several versions ago, but RStan only recently was able to update, so depending on your local version you may not see the warnings that were supposed to be shown during the deprecation period.

A 2-d array of reals in a function signature would now be written array[,] real v

More information is available in the docs

2 Likes
3

Many thanks for such a clear explanation.