Run stanc's auto-formatter on the model code.

The $format() method of a CmdStanModel object runs stanc's auto-formatter on the model code. Either saves the formatted model directly back to the file or prints it for inspection.

format(
  overwrite_file = FALSE,
  canonicalize = FALSE,
  backup = TRUE,
  max_line_length = NULL,
  quiet = FALSE
)

Arguments

overwrite_file

(logical) Should the formatted code be written back to the input model file. The default is FALSE.

canonicalize

(list or logical) Defines whether or not the compiler should 'canonicalize' the Stan model, removing things like deprecated syntax. Default is FALSE. If TRUE, all canonicalizations are run. You can also supply a list of strings which represent options. In that case the options are passed to stanc (new in Stan 2.29). See the User's guide section for available canonicalization options.

backup

(logical) If TRUE, create stanfile.bak backups before writing to the file. Disable this option if you're sure you have other copies of the file or are using a version control system like Git. Defaults to TRUE. The value is ignored if overwrite_file = FALSE.

max_line_length

(integer) The maximum length of a line when formatting. The default is NULL, which defers to the default line length of stanc.

quiet

(logical) Should informational messages be suppressed? The default is FALSE.

Value

The $format() 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-check_syntax, model-method-compile, model-method-diagnose, model-method-expose_functions, model-method-generate-quantities, model-method-laplace, model-method-optimize, model-method-pathfinder, model-method-sample, model-method-sample_mpi, model-method-variables, model-method-variational

Examples

# \dontrun{

# Example of fixing old syntax
# real x[2] --> array[2] real x;
file <- write_stan_file("
parameters {
  real x[2];
}
model {
  x ~ std_normal();
}
")

# set compile=FALSE then call format to fix old syntax
mod <- cmdstan_model(file, compile = FALSE)
mod$format(canonicalize = list("deprecations"))
#> Syntax error in '/var/folders/s0/zfzm55px2nd2v__zlw5xfj2h0000gn/T/RtmpiACQ3q/model_1fc88c86300d78667dd3e476a636c279.stan', line 3, column 9 to column 10, parsing error:
#>    -------------------------------------------------
#>      1:  
#>      2:  parameters {
#>      3:    real x[2];
#>                   ^
#>      4:  }
#>      5:  model {
#>    -------------------------------------------------
#> 
#> ";" expected after variable declaration.
#> It looks like you are trying to use the old array syntax.
#> Please use the new syntax:
#> array[2] real x;
#> Error: Syntax error found! See the message above for more information.

# overwrite the original file instead of just printing it
mod$format(canonicalize = list("deprecations"), overwrite_file = TRUE)
#> Syntax error in '/var/folders/s0/zfzm55px2nd2v__zlw5xfj2h0000gn/T/RtmpiACQ3q/model_1fc88c86300d78667dd3e476a636c279.stan', line 3, column 9 to column 10, parsing error:
#>    -------------------------------------------------
#>      1:  
#>      2:  parameters {
#>      3:    real x[2];
#>                   ^
#>      4:  }
#>      5:  model {
#>    -------------------------------------------------
#> 
#> ";" expected after variable declaration.
#> It looks like you are trying to use the old array syntax.
#> Please use the new syntax:
#> array[2] real x;
#> Error: Syntax error found! See the message above for more information.
mod$compile()
#> Syntax error in '/var/folders/s0/zfzm55px2nd2v__zlw5xfj2h0000gn/T/RtmpiACQ3q/model-59c028cea1fd.stan', line 3, column 9 to column 10, parsing error:
#>    -------------------------------------------------
#>      1:  
#>      2:  parameters {
#>      3:    real x[2];
#>                   ^
#>      4:  }
#>      5:  model {
#>    -------------------------------------------------
#> 
#> ";" expected after variable declaration.
#> It looks like you are trying to use the old array syntax.
#> Please use the new syntax:
#> array[2] real x;
#> make: *** [/var/folders/s0/zfzm55px2nd2v__zlw5xfj2h0000gn/T/RtmpiACQ3q/model-59c028cea1fd.hpp] Error 1
#> Error: An error occured during compilation! See the message above for more information.


# Example of removing unnecessary whitespace
file <- write_stan_file("
data {
  int N;
  array[N] int y;
}
parameters {
  real                     lambda;
}
model {
  target +=
 poisson_lpmf(y | lambda);
}
")
mod <- cmdstan_model(file, compile = FALSE)
mod$format(canonicalize = TRUE)
#> data {
#>   int N;
#>   array[N] int y;
#> }
#> parameters {
#>   real lambda;
#> }
#> model {
#>   target += poisson_lpmf(y | lambda);
#> }
#> 
#> 
# }