Check syntax of a Stan program

The $check_syntax() method of a CmdStanModel object checks the Stan program for syntax errors and returns TRUE (invisibly) if parsing succeeds. If invalid syntax in found an error is thrown.

check_syntax(
  pedantic = FALSE,
  include_paths = NULL,
  stanc_options = list(),
  quiet = FALSE
)

Arguments

pedantic

(logical) Should pedantic mode be turned on? The default is FALSE. Pedantic mode attempts to warn you about potential issues in your Stan program beyond syntax errors. For details see the Pedantic mode chapter in the Stan Reference Manual.

include_paths

(character vector) Paths to directories where Stan should look for files specified in #include directives in the Stan program.

stanc_options

(list) Any other Stan-to-C++ transpiler options to be used when compiling the model. See the documentation for the $compile() method for details.

quiet

(logical) Should informational messages be suppressed? The default is FALSE, which will print a message if the Stan program is valid or the compiler error message if there are syntax errors. If TRUE, only the error message will be printed.

Value

The $check_syntax() method returns TRUE (invisibly) if the model is valid.

See also

The CmdStanR website (mc-stan.org/cmdstanr) for online documentation and tutorials.

The Stan and CmdStan documentation:

• Stan documentation: mc-stan.org/users/documentation

• CmdStan User’s Guide: mc-stan.org/docs/cmdstan-guide

Other CmdStanModel methods: model-method-compile, model-method-diagnose, model-method-expose_functions, model-method-format, model-method-generate-quantities, model-method-optimize, model-method-sample_mpi, model-method-sample, model-method-variables, model-method-variational

Examples

# \dontrun{
file <- write_stan_file("
data {
  int N;
  int y[N];
}
parameters {
  // should have <lower=0> but omitting to demonstrate pedantic mode
  real lambda;
}
model {
  y ~ poisson(lambda);
}
")
mod <- cmdstan_model(file, compile = FALSE)

# the program is syntactically correct, however...
mod$check_syntax()
#> Warning in '/var/folders/s0/zfzm55px2nd2v__zlw5xfj2h0000gn/T/RtmpFBtN6X/model_74b584fd23ea8c78eceda86d1d425fe8.stan', line 4, column 2: Declaration
#>     of arrays by placing brackets after a variable name is deprecated and
#>     will be removed in Stan 2.33.0. Instead use the array keyword before the
#>     type. This can be changed automatically using the auto-format flag to
#>     stanc
#> Stan program is syntactically correct

# pedantic mode will warn that lambda should be constrained to be positive
# and that lambda has no prior distribution
mod$check_syntax(pedantic = TRUE)
#> Warning in '/var/folders/s0/zfzm55px2nd2v__zlw5xfj2h0000gn/T/RtmpFBtN6X/model_74b584fd23ea8c78eceda86d1d425fe8.stan', line 4, column 2: Declaration
#>     of arrays by placing brackets after a variable name is deprecated and
#>     will be removed in Stan 2.33.0. Instead use the array keyword before the
#>     type. This can be changed automatically using the auto-format flag to
#>     stanc
#> Warning in '/var/folders/s0/zfzm55px2nd2v__zlw5xfj2h0000gn/T/RtmpFBtN6X/model_74b584fd23ea8c78eceda86d1d425fe8.stan', line 11, column 14: A
#>     poisson distribution is given parameter lambda as a rate parameter
#>     (argument 1), but lambda was not constrained to be strictly positive.
#> Warning: The parameter lambda has no priors. This means either no prior is
#>     provided, or the prior(s) depend on data variables. In the later case,
#>     this may be a false positive.
#> Stan program is syntactically correct
# }