Functions

cmdstan_model()

cmdstan_model(    ?string $stanFile = null,    ?string $exeFile = null,    bool $quiet = true,    ?string $dir = null,    bool $pedantic = false,    ?array $includePaths = null,    ?string $userHeader = null,    ?array $cppOptions = null,    ?array $stancOptions = null,    ?bool $forceRecompile = null,): CmdStanModel

Returns a CmdStanModel. Give stanFile, whose executable is built beside it or in dir, or exeFile alone to use an existing executable without building. The arguments are those of new CmdStanModel(), which describes them.

$model = CmdStan\cmdstan_model('bernoulli.stan');

compile_stan_file()

compile_stan_file(    string $stanFile,    bool $quiet = true,    ?string $dir = null,    bool $pedantic = false,    ?array $includePaths = null,    ?string $userHeader = null,    ?array $cppOptions = null,    ?array $stancOptions = null,    ?bool $forceRecompile = null,): string

Returns the executable path. Takes cmdstan_model()’s build arguments and reuses an up-to-date executable in the same way.

check_syntax_stan_file()

check_syntax_stan_file(    string $stanFile,    ?array $includePaths = null,    bool $pedantic = false,    array $stancOptions = [],    bool $quiet = false,): bool

Returns true. Throws a RuntimeException with stanc’s message for invalid Stan. pedantic: true adds stanc’s pedantic warnings, and quiet: true suppresses stanc’s output.

format_stan_file()

format_stan_file(    string $stanFile,    ?array $includePaths = null,    bool $overwriteFile = false,    array|bool $canonicalize = false,    bool $backup = true,    ?int $maxLineLength = null,    bool $quiet = false,): string

Returns the formatted program. canonicalize is true for every canonicalization or a list such as ['deprecations', 'braces']. overwriteFile: true rewrites the file and keeps a .bak-YYYYMMDDHHMMSS copy unless backup: false.

variables_stan_file()

variables_stan_file(    string $stanFile,    ?array $includePaths = null,): array

Returns the data, parameters, transformed_parameters, and generated_quantities declarations from stanc --info, each keyed by variable name with its type and number of dimensions.

print_stan_file()

print_stan_file(string $stanFile, ?bool $lineNumbers = null): void

Prints with line numbers when lineNumbers is true. The default comes from the cmdstanr_print_line_numbers option.

write_stan_file()

write_stan_file(    array|string $code,    ?string $file = null,    ?string $dir = null,    ?string $basename = null,    bool $forceOverwrite = false,    string $hashSalt = '',): string

Returns the path. code is a string or a list of lines. Without file, the file is dir/basename, where dir defaults to the cmdstanr_write_stan_file_dir option or the system temporary directory and basename to model_<hash>.stan. An identical existing file is left untouched, so its executable stays current, unless forceOverwrite: true.

stan_build_info()

stan_build_info(string $exeFile): array

Returns the executable’s build record and the features it reports about itself (stan_threads, stan_mpi, stan_opencl, stan_no_range_checks, and stan_version). The same as CmdStanModel::stanBuildInfo().

install_cmdstan()

install_cmdstan(    ?string $version = null,    ?string $dir = null,    ?int $cores = null,    ?float $timeout = null,    bool $overwrite = false,    ?string $releaseUrl = null,    ?string $releaseFile = null,    array $cppOptions = [],    bool $checkToolchain = true,    ?bool $copyMakeLocal = null,): string

Returns the installation directory, ~/.cmdstan/cmdstan-<version> unless dir is given. Without a version, installs the latest release. Versions before 2.37 are rejected. cores sets the parallel make jobs (default: the mc.cores option, else 1), and timeout is in seconds. releaseFile is a local .tar.gz and releaseUrl an HTTPS .tar.gz URL. cppOptions are written to make/local before the build. An existing installation is replaced only with overwrite: true, and it is restored if the new build fails. Installation gives examples.

set_cmdstan_path()

set_cmdstan_path(string $path): void

The path must contain CmdStan’s makefile and bin/stanc. Throws for a missing installation or a version before 2.37. The selection lasts for the PHP process.

cmdstan_path()

cmdstan_path(): string

Without a selection, uses the CMDSTAN environment variable, then the highest supported version under ~/.cmdstan/cmdstan-*. Throws a RuntimeException when none is found.

cmdstan_version()

cmdstan_version(): string

Returns a version string such as 2.40.0.

check_cmdstan_toolchain()

check_cmdstan_toolchain(): array

Returns the path and version of make, CmdStan’s C++ compiler, and stanc when CmdStan is installed. Throws a RuntimeException when make or the compiler is missing. A successful check does not prove that a compilation will succeed.

cmdstan_make_local()

cmdstan_make_local(    ?string $dir = null,    array $cppOptions = [],    bool $append = true,): array

Returns the current make/local lines. Named cppOptions entries are written as NAME=value, with booleans as true and false, and list entries as raw lines. Appends unless append: false. dir defaults to the selected CmdStan.

rebuild_cmdstan()

rebuild_cmdstan(?int $cores = null, ?float $timeout = null): void

Runs make clean-all and make build. cores sets the parallel make jobs, and timeout is in seconds.

write_stan_json()

write_stan_json(    object|array $data,    string $file,    bool $alwaysDecimal = false,    ?array $variables = null,): string

Returns the file path. data is an array, a StanData, or a table. With variables (stanc’s declarations, such as $model->variables()['data']), int variables are written as integers and tuples as Stan’s {"1": ..., "2": ...} objects. alwaysDecimal: true writes every value of a non-int variable as a floating-point number.

Data arrays are named PHP arrays at the top level, with lists for Stan arrays, vectors, and matrices:

• Matrices are lists of rows, with no column-major conversion. Booleans become 0 and 1, complex numbers are [re, im] pairs, and a tuple is a list of its elements. Empty top-level data becomes {}.
• Missing values, strings, objects, nonfinite numbers, sparse indices, invalid variable names, and ragged arrays are rejected, and the error names the variable.
• The fitting methods write data with the model’s declarations. Every declared data variable is required, int variables are written as integers (a non-integer is truncated with a warning), and a single value for a one-dimensional array becomes a one-element array.

read_cmdstan_csv()

read_cmdstan_csv(array|string $files): CmdStanFit

Returns the fit class for the files’ method, such as CmdStanMCMC. Accepts .csv, .csv.gz, and .csv.bz2 files.

as_cmdstan_fit()

as_cmdstan_fit(    array|string $files,    array|string|null $variables = null,    bool $checkDiagnostics = true,    ?string $format = null,): CmdStanFit

With variables, only those variables are read and listed in metadata()['variables'] and draws(). checkDiagnostics: false also skips the sampler diagnostics. format sets the fit’s default draws format.

read_cmdstan_csv_list()

read_cmdstan_csv_list(    array|string $files,    array|string|null $variables = null,    array|string|null $samplerDiagnostics = null,    ?string $format = null,): array

Returns metadata plus, by method: time, inv_metric, step_size, warmup_draws, post_warmup_draws, warmup_sampler_diagnostics, and post_warmup_sampler_diagnostics (sample); draws (variational, laplace, pathfinder); point_estimates (optimize); generated_quantities; or gradients and lp (diagnose). An empty variables or samplerDiagnostics selects none.

draws_to_csv()

draws_to_csv(array $chains, string $dir): array

chains is [chain][iteration][variable => value]. Returns the file paths. Column names follow CmdStan’s naming.

mcmc_trace()

mcmc_trace(CmdStanFit|array $draws, string $variable): Figure

Each figure function returns a Figure, named after its bayesplot or loo counterpart. Echo it for ASCII text, or call vegaLite(), html(), svg(), or png(). draws is a fit or a draws_array, and a variable names one column, such as theta or beta[2]. Figures shows each one.

mcmc_hist()

mcmc_hist(    CmdStanFit|array $draws,    string $variable,    int $bins = 30,): Figure

Bins have equal width over the observed range.

mcmc_dens()

mcmc_dens(CmdStanFit|array $draws, string $variable): Figure

Gaussian kernel with R’s bw.nrd0 bandwidth, as R’s density().

mcmc_dens_overlay()

mcmc_dens_overlay(CmdStanFit|array $draws, string $variable): Figure

One curve per chain, with the same kernel and bandwidth rule as mcmc_dens().

mcmc_intervals()

mcmc_intervals(    CmdStanFit|array $draws,    array|string|null $variables = null,    float $prob = 0.5,    float $probOuter = 0.9,    string $pointEst = 'median',): Figure

null selects every variable except lp__ and other names ending in __. Base names select all their elements. pointEst is 'median', 'mean', or 'none'.

mcmc_rank_hist()

mcmc_rank_hist(    CmdStanFit|array $draws,    string $variable,    int $bins = 20,): Figure

Ranks are pooled over chains, and each panel shows the count expected under uniform ranks.

mcmc_scatter()

mcmc_scatter(    CmdStanFit|array $draws,    string $xVariable,    string $yVariable,): Figure

For MCMC fits, divergent transitions are flagged.

mcmc_acf()

mcmc_acf(    CmdStanFit|array $draws,    string $variable,    int $lags = 20,): Figure

Lags 0 to lags, as bayesplot’s mcmc_acf_bar().

pareto_k_plot()

pareto_k_plot(array $loo): Figure

Takes a CmdStanMCMC::loo() or Loo::loo() result.

cmdstanr_example()

cmdstanr_example(    string $example = 'logistic',    string $method = 'sample',    mixed ...$options,): CmdStanFit

example is logistic, schools, or schools_ncp, and method is any fitting method. The model is compiled in the cmdstanphp_example_dir option’s directory, else <tmp>/cmdstanphp-examples, and fitted with its bundled data. Other options go to the method. quiet (default true) discards console output.

print_example_program()

print_example_program(string $example = 'logistic'): void

example is logistic, schools, or schools_ncp.

num_threads()

num_threads(): ?int

Returns the STAN_NUM_THREADS environment variable as an integer, or null when unset. Deprecated, as in CmdStanR. Use the fit’s metadata().