# API¶

 stan([file, model_name, model_code, fit, …]) Fit a model using Stan. stanc([file, charset, model_code, …]) Translate Stan model specification into C++ code. StanModel([file, charset, model_name, …]) Model described in Stan’s modeling language compiled from C++ code.

pystan.stan(file=None, model_name='anon_model', model_code=None, fit=None, data=None, pars=None, chains=4, iter=2000, warmup=None, thin=1, init='random', seed=None, algorithm=None, control=None, sample_file=None, diagnostic_file=None, verbose=False, boost_lib=None, eigen_lib=None, include_paths=None, n_jobs=-1, **kwargs)[source]

Fit a model using Stan.

The pystan.stan function was deprecated in version 2.17 and will be removed in version 3.0. Compiling and using a Stan Program (e.g., for drawing samples) should be done in separate steps.

Parameters: Returns: file (string {'filename', file-like object}) – Model code must found via one of the following parameters: file or model_code. If file is a filename, the string passed as an argument is expected to be a filename containing the Stan model specification. If file is a file object, the object passed must have a ‘read’ method (file-like object) that is called to fetch the Stan model specification. charset (string, optional) – If bytes or files are provided, this charset is used to decode. ‘utf-8’ by default. model_code (string) – A string containing the Stan model specification. Alternatively, the model may be provided with the parameter file. model_name (string, optional) – A string naming the model. If none is provided ‘anon_model’ is the default. However, if file is a filename, then the filename will be used to provide a name. ‘anon_model’ by default. fit (StanFit instance) – An instance of StanFit derived from a previous fit, None by default. If fit is not None, the compiled model associated with a previous fit is reused and recompilation is avoided. data (dict) – A Python dictionary providing the data for the model. Variables for Stan are stored in the dictionary as expected. Variable names are the keys and the values are their associated values. Stan only accepts certain kinds of values; see Notes. pars (list of string, optional) – A list of strings indicating parameters of interest. By default all parameters specified in the model will be stored. chains (int, optional) – Positive integer specifying number of chains. 4 by default. iter (int, 2000 by default) – Positive integer specifying how many iterations for each chain including warmup. warmup (int, iter//2 by default) – Positive integer specifying number of warmup (aka burin) iterations. As warmup also specifies the number of iterations used for stepsize adaption, warmup samples should not be used for inference. thin (int, optional) – Positive integer specifying the period for saving samples. Default is 1. init ({0, '0', 'random', function returning dict, list of dict}, optional) – Specifies how initial parameter values are chosen: - 0 or ‘0’ initializes all to be zero on the unconstrained support. - ‘random’ generates random initial values. An optional parameter init_r controls the range of randomly generated initial values for parameters in terms of their unconstrained support; list of size equal to the number of chains (chains), where the list contains a dict with initial parameter values; function returning a dict with initial parameter values. The function may take an optional argument chain_id. seed (int or np.random.RandomState, optional) – The seed, a positive integer for random number generation. Only one seed is needed when multiple chains are used, as the other chain’s seeds are generated from the first chain’s to prevent dependency among random number streams. By default, seed is random.randint(0, MAX_UINT). algorithm ({"NUTS", "HMC", "Fixed_param"}, optional) – One of the algorithms that are implemented in Stan such as the No-U-Turn sampler (NUTS, Hoffman and Gelman 2011) and static HMC. sample_file (string, optional) – File name specifying where samples for all parameters and other saved quantities will be written. If not provided, no samples will be written. If the folder given is not writable, a temporary directory will be used. When there are multiple chains, an underscore and chain number are appended to the file name. By default do not write samples to file. diagnostic_file (string, optional) – File name specifying where diagnostic information should be written. By default no diagnostic information is recorded. boost_lib (string, optional) – The path to a version of the Boost C++ library to use instead of the one supplied with PyStan. eigen_lib (string, optional) – The path to a version of the Eigen C++ library to use instead of the one in the supplied with PyStan. include_paths (list of strings, optional) – Paths for #include files defined in Stan code. verbose (boolean, optional) – Indicates whether intermediate output should be piped to the console. This output may be useful for debugging. False by default. control (dict, optional) – A dictionary of parameters to control the sampler’s behavior. Default values are used if control is not specified. The following are adaptation parameters for sampling algorithms. These are parameters used in Stan with similar names: adapt_engaged : bool adapt_gamma : float, positive, default 0.05 adapt_delta : float, between 0 and 1, default 0.8 adapt_kappa : float, between default 0.75 adapt_t0 : float, positive, default 10 adapt_init_buffer : int, positive, defaults to 75 adapt_term_buffer : int, positive, defaults to 50 adapt_window : int, positive, defaults to 25 In addition, the algorithm HMC (called ‘static HMC’ in Stan) and NUTS share the following parameters: stepsize: float, positive stepsize_jitter: float, between 0 and 1 metric : str, {“unit_e”, “diag_e”, “dense_e”} In addition, depending on which algorithm is used, different parameters can be set as in Stan for sampling. For the algorithm HMC we can set int_time: float, positive For algorithm NUTS, we can set max_treedepth : int, positive n_jobs (int, optional) – Sample in parallel. If -1 all CPUs are used. If 1, no parallel computing code is used at all, which is useful for debugging. fit StanFit instance chain_id (int, optional) – chain_id can be a vector to specify the chain_id for all chains or an integer. For the former case, they should be unique. For the latter, the sequence of integers starting from the given chain_id are used for all chains. init_r (float, optional) – init_r is only valid if init == “random”. In this case, the intial values are simulated from [-init_r, init_r] rather than using the default interval (see the manual of (Cmd)Stan). test_grad (bool, optional) – If test_grad is True, Stan will not do any sampling. Instead, the gradient calculation is tested and printed out and the fitted StanFit4Model object is in test gradient mode. By default, it is False. append_samples (bool, optional) refresh (int, optional) – Argument refresh can be used to control how to indicate the progress during sampling (i.e. show the progress every code{refresh} iterations). By default, refresh is max(iter/10, 1). obfuscate_model_name (boolean, optional) – obfuscate_model_name is only valid if fit is None. True by default. If False the model name in the generated C++ code will not be made unique by the insertion of randomly generated characters. Generally it is recommended that this parameter be left as True.

Examples

>>> from pystan import stan
>>> import numpy as np
>>> model_code = '''
... parameters {
...   real y[2];
... }
... model {
...   y[1] ~ normal(0, 1);
...   y[2] ~ double_exponential(0, 2);
... }'''
>>> fit1 = stan(model_code=model_code, iter=10)
>>> print(fit1)
>>> excode = '''
... transformed data {
...     real y[20];
...     y[1] = 0.5796;  y[2]  = 0.2276;   y[3] = -0.2959;
...     y[4] = -0.3742; y[5]  = 0.3885;   y[6] = -2.1585;
...     y[7] = 0.7111;  y[8]  = 1.4424;   y[9] = 2.5430;
...     y[10] = 0.3746; y[11] = 0.4773;   y[12] = 0.1803;
...     y[13] = 0.5215; y[14] = -1.6044;  y[15] = -0.6703;
...     y[16] = 0.9459; y[17] = -0.382;   y[18] = 0.7619;
...     y[19] = 0.1006; y[20] = -1.7461;
... }
... parameters {
...     real mu;
...     real<lower=0, upper=10> sigma;
...     vector[2] z[3];
...     real<lower=0> alpha;
... }
... model {
...     y ~ normal(mu, sigma);
...     for (i in 1:3)
...     z[i] ~ normal(0, 1);
...     alpha ~ exponential(2);
... }'''
>>>
>>> def initfun1():
...     return dict(mu=1, sigma=4, z=np.random.normal(size=(3, 2)), alpha=1)
>>> exfit0 = stan(model_code=excode, init=initfun1)
>>> def initfun2(chain_id=1):
...     return dict(mu=1, sigma=4, z=np.random.normal(size=(3, 2)), alpha=1 + chain_id)
>>> exfit1 = stan(model_code=excode, init=initfun2)

pystan.stanc(file=None, charset='utf-8', model_code=None, model_name='anon_model', include_paths=None, verbose=False, obfuscate_model_name=True)[source]

Translate Stan model specification into C++ code.

Parameters: file ({string, file}, optional) – If filename, the string passed as an argument is expected to be a filename containing the Stan model specification. If file, the object passed must have a ‘read’ method (file-like object) that is called to fetch the Stan model specification. charset (string, 'utf-8' by default) – If bytes or files are provided, this charset is used to decode. model_code (string, optional) – A string containing the Stan model specification. Alternatively, the model may be provided with the parameter file. model_name (string, 'anon_model' by default) – A string naming the model. If none is provided ‘anon_model’ is the default. However, if file is a filename, then the filename will be used to provide a name. include_paths (list of strings, optional) – Paths for #include files defined in Stan code. verbose (boolean, False by default) – Indicates whether intermediate output should be piped to the console. This output may be useful for debugging. obfuscate_model_name (boolean, True by default) – If False the model name in the generated C++ code will not be made unique by the insertion of randomly generated characters. Generally it is recommended that this parameter be left as True. stanc_ret – A dictionary with the following keys: model_name, model_code, cpp_code, and status. Status indicates the success of the translation from Stan code into C++ code (success = 0, error = -1). dict

Notes

C++ reserved words and Stan reserved words may not be used for variable names; see the Stan User’s Guide for a complete list.

The #include method follows a C/C++ syntax #include foo/my_gp_funs.stan. The method needs to be at the start of the row, no whitespace is allowed. After the included file no whitespace or comments are allowed. pystan.experimental(PyStan 2.18) has a fix_include-function to clean the #include statements from the model_code. Example: from pystan.experimental import fix_include model_code = fix_include(model_code)

StanModel()
Class representing a compiled Stan model
stan()
Fit a model using Stan

References

The Stan Development Team (2013) Stan Modeling Language User’s Guide and Reference Manual. <http://mc-stan.org/>.

Examples

>>> stanmodelcode = '''
... data {
...   int<lower=0> N;
...   real y[N];
... }
...
... parameters {
...   real mu;
... }
...
... model {
...   mu ~ normal(0, 10);
...   y ~ normal(mu, 1);
... }
... '''
>>> r = stanc(model_code=stanmodelcode, model_name = "normal1")
>>> sorted(r.keys())
['cppcode', 'model_code', 'model_cppname', 'model_name', 'status']
>>> r['model_name']
'normal1'

class pystan.StanModel(file=None, charset='utf-8', model_name='anon_model', model_code=None, stanc_ret=None, include_paths=None, boost_lib=None, eigen_lib=None, verbose=False, obfuscate_model_name=True, extra_compile_args=None)[source]

Model described in Stan’s modeling language compiled from C++ code.

Instances of StanModel are typically created indirectly by the functions stan and stanc.

Parameters: file (string {'filename', 'file'}) – If filename, the string passed as an argument is expected to be a filename containing the Stan model specification. If file, the object passed must have a ‘read’ method (file-like object) that is called to fetch the Stan model specification. charset (string, 'utf-8' by default) – If bytes or files are provided, this charset is used to decode. model_name (string, 'anon_model' by default) – A string naming the model. If none is provided ‘anon_model’ is the default. However, if file is a filename, then the filename will be used to provide a name. model_code (string) – A string containing the Stan model specification. Alternatively, the model may be provided with the parameter file. stanc_ret (dict) – A dict returned from a previous call to stanc which can be used to specify the model instead of using the parameter file or model_code. include_paths (list of strings) – Paths for #include files defined in Stan program code. boost_lib (string) – The path to a version of the Boost C++ library to use instead of the one supplied with PyStan. eigen_lib (string) – The path to a version of the Eigen C++ library to use instead of the one in the supplied with PyStan. verbose (boolean, False by default) – Indicates whether intermediate output should be piped to the console. This output may be useful for debugging. kwargs (keyword arguments) – Additional arguments passed to stanc.
model_name
Type: string
model_code

Stan code for the model.

Type: string
model_cpp

C++ code for the model.

Type: string
module

Python module created by compiling the C++ code for the model.

Type: builtins.module
show()[source]

Print the Stan model specification.

sampling()[source]

Draw samples from the model.

optimizing()[source]

Obtain a point estimate by maximizing the log-posterior.

get_cppcode()[source]

Return the C++ code for the module.

get_cxxflags()[source]

Return the ‘CXXFLAGS’ used for compiling the model.

get_include_paths()[source]

Return include_paths used for compiled model.

stanc
Compile a Stan model specification
stan
Fit a model using Stan

Notes

More details of Stan, including the full user’s guide and reference manual can be found at <URL: http://mc-stan.org/>.

There are three ways to specify the model’s code for stan_model.

1. parameter model_code, containing a string to whose value is the Stan model specification,
2. parameter file, indicating a file (or a connection) from which to read the Stan model specification, or
3. parameter stanc_ret, indicating the re-use of a model
generated in a previous call to stanc.

References

The Stan Development Team (2013) Stan Modeling Language User’s Guide and Reference Manual. <URL: http://mc-stan.org/>.

Examples

>>> model_code = 'parameters {real y;} model {y ~ normal(0,1);}'
>>> model_code; m = StanModel(model_code=model_code)
... # doctest: +ELLIPSIS
'parameters ...
>>> m.model_name
'anon_model'

optimizing(data=None, seed=None, init='random', sample_file=None, algorithm=None, verbose=False, as_vector=True, **kwargs)[source]

Obtain a point estimate by maximizing the joint posterior.

Parameters: Returns: data (dict) – A Python dictionary providing the data for the model. Variables for Stan are stored in the dictionary as expected. Variable names are the keys and the values are their associated values. Stan only accepts certain kinds of values; see Notes. seed (int or np.random.RandomState, optional) – The seed, a positive integer for random number generation. Only one seed is needed when multiple chains are used, as the other chain’s seeds are generated from the first chain’s to prevent dependency among random number streams. By default, seed is random.randint(0, MAX_UINT). init ({0, '0', 'random', function returning dict, list of dict}, optional) – Specifies how initial parameter values are chosen: - 0 or ‘0’ initializes all to be zero on the unconstrained support. - ‘random’ generates random initial values. An optional parameter init_r controls the range of randomly generated initial values for parameters in terms of their unconstrained support; list of size equal to the number of chains (chains), where the list contains a dict with initial parameter values; function returning a dict with initial parameter values. The function may take an optional argument chain_id. sample_file (string, optional) – File name specifying where samples for all parameters and other saved quantities will be written. If not provided, no samples will be written. If the folder given is not writable, a temporary directory will be used. When there are multiple chains, an underscore and chain number are appended to the file name. By default do not write samples to file. algorithm ({"LBFGS", "BFGS", "Newton"}, optional) – Name of optimization algorithm to be used. Default is LBFGS. verbose (boolean, optional) – Indicates whether intermediate output should be piped to the console. This output may be useful for debugging. False by default. as_vector (boolean, optional) – Indicates an OrderedDict will be returned rather than a nested dictionary with keys ‘par’ and ‘value’. optim – Depending on as_vector, returns either an OrderedDict having parameters as keys and point estimates as values or an OrderedDict with components ‘par’ and ‘value’. optim['par'] is a dictionary of point estimates, indexed by the parameter name. optim['value'] stores the value of the log-posterior (up to an additive constant, the lp__ in Stan) corresponding to the point identified by optim[‘par’]. OrderedDict iter (int, optional) – The maximum number of iterations. save_iterations (bool, optional) refresh (int, optional) init_alpha (float, optional) – For BFGS and LBFGS, default is 0.001 tol_obj (float, optional) – For BFGS and LBFGS, default is 1e-12. tol_grad (float, optional) – For BFGS and LBFGS, default is 1e-8. tol_param (float, optional) – For BFGS and LBFGS, default is 1e-8. tol_rel_grad (float, optional) – For BFGS and LBFGS, default is 1e7. history_size (int, optional) – For LBFGS, default is 5. Refer to the manuals for both CmdStan and Stan for more details.

Examples

>>> from pystan import StanModel
>>> m = StanModel(model_code='parameters {real y;} model {y ~ normal(0,1);}')
>>> f = m.optimizing()

sampling(data=None, pars=None, chains=4, iter=2000, warmup=None, thin=1, seed=None, init='random', sample_file=None, diagnostic_file=None, verbose=False, algorithm=None, control=None, n_jobs=-1, **kwargs)[source]

Draw samples from the model.

Parameters: Returns: data (dict) – A Python dictionary providing the data for the model. Variables for Stan are stored in the dictionary as expected. Variable names are the keys and the values are their associated values. Stan only accepts certain kinds of values; see Notes. pars (list of string, optional) – A list of strings indicating parameters of interest. By default all parameters specified in the model will be stored. chains (int, optional) – Positive integer specifying number of chains. 4 by default. iter (int, 2000 by default) – Positive integer specifying how many iterations for each chain including warmup. warmup (int, iter//2 by default) – Positive integer specifying number of warmup (aka burn-in) iterations. As warmup also specifies the number of iterations used for step-size adaption, warmup samples should not be used for inference. warmup=0 forced if algorithm=”Fixed_param”. thin (int, 1 by default) – Positive integer specifying the period for saving samples. seed (int or np.random.RandomState, optional) – The seed, a positive integer for random number generation. Only one seed is needed when multiple chains are used, as the other chain’s seeds are generated from the first chain’s to prevent dependency among random number streams. By default, seed is random.randint(0, MAX_UINT). algorithm ({"NUTS", "HMC", "Fixed_param"}, optional) – One of algorithms that are implemented in Stan such as the No-U-Turn sampler (NUTS, Hoffman and Gelman 2011), static HMC, or Fixed_param. Default is NUTS. init ({0, '0', 'random', function returning dict, list of dict}, optional) – Specifies how initial parameter values are chosen: 0 or ‘0’ initializes all to be zero on the unconstrained support; ‘random’ generates random initial values; list of size equal to the number of chains (chains), where the list contains a dict with initial parameter values; function returning a dict with initial parameter values. The function may take an optional argument chain_id. sample_file (string, optional) – File name specifying where samples for all parameters and other saved quantities will be written. If not provided, no samples will be written. If the folder given is not writable, a temporary directory will be used. When there are multiple chains, an underscore and chain number are appended to the file name. By default do not write samples to file. verbose (boolean, False by default) – Indicates whether intermediate output should be piped to the console. This output may be useful for debugging. control (dict, optional) – A dictionary of parameters to control the sampler’s behavior. Default values are used if control is not specified. The following are adaptation parameters for sampling algorithms. These are parameters used in Stan with similar names: adapt_engaged : bool, default True adapt_gamma : float, positive, default 0.05 adapt_delta : float, between 0 and 1, default 0.8 adapt_kappa : float, between default 0.75 adapt_t0 : float, positive, default 10 In addition, the algorithm HMC (called ‘static HMC’ in Stan) and NUTS share the following parameters: stepsize: float, positive stepsize_jitter: float, between 0 and 1 metric : str, {“unit_e”, “diag_e”, “dense_e”} In addition, depending on which algorithm is used, different parameters can be set as in Stan for sampling. For the algorithm HMC we can set int_time: float, positive For algorithm NUTS, we can set max_treedepth : int, positive n_jobs (int, optional) – Sample in parallel. If -1 all CPUs are used. If 1, no parallel computing code is used at all, which is useful for debugging. fit – Instance containing the fitted results. StanFit4Model chain_id (int or iterable of int, optional) – chain_id can be a vector to specify the chain_id for all chains or an integer. For the former case, they should be unique. For the latter, the sequence of integers starting from the given chain_id are used for all chains. init_r (float, optional) – init_r is only valid if init == “random”. In this case, the intial values are simulated from [-init_r, init_r] rather than using the default interval (see the manual of Stan). test_grad (bool, optional) – If test_grad is True, Stan will not do any sampling. Instead, the gradient calculation is tested and printed out and the fitted StanFit4Model object is in test gradient mode. By default, it is False. append_samples (bool, optional) refresh (int, optional) – Argument refresh can be used to control how to indicate the progress during sampling (i.e. show the progress every code{refresh} iterations). By default, refresh is max(iter/10, 1). check_hmc_diagnostics (bool, optional) – After sampling run pystan.diagnostics.check_hmc_diagnostics function. Default is True. Checks for n_eff and rhat skipped if the flat parameter count is higher than 1000, unless user explicitly defines check_hmc_diagnostics=True.

Examples

>>> from pystan import StanModel
>>> m = StanModel(model_code='parameters {real y;} model {y ~ normal(0,1);}')
>>> m.sampling(iter=100)

vb(data=None, pars=None, iter=10000, seed=None, init='random', sample_file=None, diagnostic_file=None, verbose=False, algorithm=None, **kwargs)[source]

Call Stan’s variational Bayes methods.

Parameters: data (dict) – A Python dictionary providing the data for the model. Variables for Stan are stored in the dictionary as expected. Variable names are the keys and the values are their associated values. Stan only accepts certain kinds of values; see Notes. pars (list of string, optional) – A list of strings indicating parameters of interest. By default all parameters specified in the model will be stored. seed (int or np.random.RandomState, optional) – The seed, a positive integer for random number generation. Only one seed is needed when multiple chains are used, as the other chain’s seeds are generated from the first chain’s to prevent dependency among random number streams. By default, seed is random.randint(0, MAX_UINT). sample_file (string, optional) – File name specifying where samples for all parameters and other saved quantities will be written. If not provided, samples will be written to a temporary file and read back in. If the folder given is not writable, a temporary directory will be used. When there are multiple chains, an underscore and chain number are appended to the file name. By default do not write samples to file. diagnostic_file (string, optional) – File name specifying where diagnostics for the variational fit will be written. iter (-) – Positive integer specifying how many iterations for each chain including warmup. algorithm ({'meanfield', 'fullrank'}) – algorithm}{One of “meanfield” and “fullrank” indicating which variational inference algorithm is used. meanfield: mean-field approximation; fullrank: full-rank covariance. The default is ‘meanfield’. verbose (boolean, False by default) – Indicates whether intermediate output should be piped to the console. This output may be useful for debugging. optional parameters, refer to the manuals for both CmdStan (Other) – Stan. (and) – iter – grad_samples the number of samples for Monte Carlo enumerate of (-) – gradients, defaults to 1. elbo_samples the number of samples for Monte Carlo estimate of ELBO (-) – (objective function), defaults to 100. (ELBO stands for “the evidence lower bound”.) eta positive stepsize weighting parameters for variational (-) – inference but is ignored if adaptation is engaged, which is the case by default. adapt_engaged flag indicating whether to automatically adapt the (-) – stepsize and defaults to True. tol_rel_objconvergence tolerance on the relative norm of the (-) – objective, defaults to 0.01. eval_elbo, evaluate ELBO every Nth iteration, defaults to 100 (-) – output_samples number of posterior samples to draw and save, (-) – defaults to 1000. adapt_iter number of iterations to adapt the stepsize if (-) – adapt_engaged is True and ignored otherwise. results – Dictionary containing information related to results. dict

Examples

>>> from pystan import StanModel
>>> m = StanModel(model_code='parameters {real y;} model {y ~ normal(0,1);}')
>>> results = m.vb()
>>> # results saved on disk in format inspired by CSV
>>> print(results['args']['sample_file'])


## StanFit4model¶

Each StanFit instance is model-specific, so the name of the class will be something like: StanFit4anon_model. The StanFit4model instances expose a number of methods.

class pystan.StanFit4model
plot(pars=None)

Visualize samples from posterior distributions

Parameters

pars : sequence of str
names of parameters

This is currently an alias for the traceplot method.

extract(pars=None, permuted=True, inc_warmup=False, dtypes=None)

Extract samples in different forms for different parameters.

Parameters

pars : sequence of str
names of parameters (including other quantities)
permuted : bool
If True, returned samples are permuted. All chains are merged and warmup samples are discarded.
inc_warmup : bool
If True, warmup samples are kept; otherwise they are discarded. If permuted is True, inc_warmup is ignored.
dtypes : dict
datatype of parameter(s). If nothing is passed, np.float will be used for all parameters.

Returns

samples : dict or array If permuted is True, return dictionary with samples for each parameter (or other quantity) named in pars.

If permuted is False and pars is None, an array is returned. The first dimension of the array is for the iterations; the second for the number of chains; the third for the parameters. Vectors and arrays are expanded to one parameter (a scalar) per cell, with names indicating the third dimension. Parameters are listed in the same order as model_pars and flatnames.

If permuted is False and pars is not None, return dictionary with samples for each parameter (or other quantity) named in pars. The first dimension of the sample array is for the iterations; the second for the number of chains; the rest for the parameters. Parameters are listed in the same order as pars.

stansummary(pars=None, probs=(0.025, 0.25, 0.5, 0.75, 0.975), digits_summary=2)

Summary statistic table. Parameters ———- pars : str or sequence of str, optional

Parameter names. By default use all parameters
probs : sequence of float, optional
Quantiles. By default, (0.025, 0.25, 0.5, 0.75, 0.975)
digits_summary : int, optional
Number of significant digits. By default, 2
summary : string
Table includes mean, se_mean, sd, probs_0, …, probs_n, n_eff and Rhat.
>>> model_code = 'parameters {real y;} model {y ~ normal(0,1);}'
>>> m = StanModel(model_code=model_code, model_name="example_model")
>>> fit = m.sampling()
>>> print(fit.stansummary())
Inference for Stan model: example_model.
4 chains, each with iter=2000; warmup=1000; thin=1;
post-warmup draws per chain=1000, total post-warmup draws=4000.
mean se_mean     sd   2.5%    25%    50%    75%  97.5%  n_eff   Rhat
y      0.01    0.03    1.0  -2.01  -0.68   0.02   0.72   1.97   1330    1.0
lp__   -0.5    0.02   0.68  -2.44  -0.66  -0.24  -0.05-5.5e-4   1555    1.0
Samples were drawn using NUTS at Thu Aug 17 00:52:25 2017.
For each parameter, n_eff is a crude measure of effective sample size,
and Rhat is the potential scale reduction factor on split chains (at
convergence, Rhat=1).

summary(pars=None, probs=None)

Summarize samples (compute mean, SD, quantiles) in all chains. REF: stanfit-class.R summary method Parameters ———- fit : StanFit4Model object pars : str or sequence of str, optional

Parameter names. By default use all parameters
probs : sequence of float, optional
Quantiles. By default, (0.025, 0.25, 0.5, 0.75, 0.975)
summaries : OrderedDict of array
Array indexed by ‘summary’ has dimensions (num_params, num_statistics). Parameters are unraveled in row-major order. Statistics include: mean, se_mean, sd, probs_0, …, probs_n, n_eff, and Rhat. Array indexed by ‘c_summary’ breaks down the statistics by chain and has dimensions (num_params, num_statistics_c_summary, num_chains). Statistics for c_summary are the same as for summary with the exception that se_mean, n_eff, and Rhat are absent. Row names and column names are also included in the OrderedDict.
log_prob(upar, adjust_transform=True, gradient=False)

Expose the log_prob of the model to stan_fit so user can call this function.

Parameters

upar :
The real parameters on the unconstrained space.
Whether we add the term due to the transform from constrained space to unconstrained space implicitly done in Stan.

Note

In Stan, the parameters need be defined with their supports. For example, for a variance parameter, we must define it on the positive real line. But inside Stan’s sampler, all parameters defined on the constrained space are transformed to unconstrained space, so the log density function need be adjusted (i.e., adding the log of the absolute value of the Jacobian determinant). With the transformation, Stan’s samplers work on the unconstrained space and once a new iteration is drawn, Stan transforms the parameters back to their supports. All the transformation are done inside Stan without interference from the users. However, when using the log density function for a model exposed to Python, we need to be careful. For example, if we are interested in finding the mode of parameters on the constrained space, we then do not need the adjustment. For this reason, there is an argument named adjust_transform for functions log_prob and grad_log_prob.

grad_log_prob(upars, adjust_transform=True)

Expose the grad_log_prob of the model to stan_fit so user can call this function.

Parameters

upar : array
The real parameters on the unconstrained space.
Whether we add the term due to the transform from constrained space to unconstrained space implicitly done in Stan.
get_adaptation_info()

Obtain adaptation information for sampler, which now only NUTS2 has.

The results are returned as a list, each element of which is a character string for a chain.

get_logposterior(inc_warmup=True)

Get the log-posterior (up to an additive constant) for all chains.

Each element of the returned array is the log-posterior for a chain. Optional parameter inc_warmup indicates whether to include the warmup period.

get_sampler_params(inc_warmup=True)

Obtain the parameters used for the sampler such as stepsize and treedepth. The results are returned as a list, each element of which is an OrderedDict a chain. The dictionary has number of elements corresponding to the number of parameters used in the sampler. Optional parameter inc_warmup indicates whether to include the warmup period.

get_posterior_mean()

Get the posterior mean for all parameters

Returns

means : array of shape (num_parameters, num_chains)
Order of parameters is given by self.model_pars or self.flatnames if parameters of interest include non-scalar parameters. An additional column for mean lp__ is also included.
constrain_pars(np.ndarray[double, ndim=1, mode="c"] upar not None)

Transform parameters from unconstrained space to defined support

unconstrain_pars(par)

Transform parameters from defined support to unconstrained space

get_seed()
get_inits()
get_stancode()
to_dataframe(pars=None, permuted=True, dtypes=None, inc_warmup=False, diagnostics=True)

Extract samples as a pandas datafriame for different parameters.

pars : {str, sequence of str}
parameter (or quantile) name(s). If permuted is False, pars is ignored.
permuted : bool, default False
If True, returned samples are permuted. All chains are merged and warmup samples are discarded.
dtypes : dict
datatype of parameter(s). If nothing is passed, np.float will be used for all parameters.
inc_warmup : bool
If True, warmup samples are kept; otherwise they are discarded. If permuted is True, inc_warmup is ignored.
diagnostics : bool
If True, include MCMC diagnostics in dataframe. If permuted is True, diagnostics is ignored.

df : pandas dataframe

Unlike default in extract (permuted=True) .to_dataframe method returns non-permuted samples (permuted=False) with diagnostics params included.