def traceplot(fit, pars, dtypes, **kwargs):
"""
Use pymc's traceplot to display parameters.
Additional arguments are passed to pymc.plots.traceplot.
"""
# FIXME: eventually put this in the StanFit object
# FIXME: write a to_pymc(_trace) function
# Deprecation warning added in PyStan 2.18
logger.warning("Deprecation warning."\
" PyStan plotting deprecated, use ArviZ library (Python 3.5+)."\
" `pip install arviz`; `arviz.plot_trace(fit)`)")
try:
from pystan.external.pymc import plots
except ImportError:
logger.critical("matplotlib required for plotting.")
raise
if pars is None:
pars = list(fit.model_pars) + ["lp__"]
values = fit.extract(dtypes=dtypes, pars=pars, permuted=False)
values = {
key: arr.reshape(-1, int(np.multiply.reduce(arr.shape[2:])), order="F")
for key, arr in values.items()
}
return plots.traceplot(values, pars, **kwargs)
def traceplot(fit, pars):
"""Use pymc's traceplot to display parameters"""
# FIXME: eventually put this in the StanFit object
# FIXME: write a to_pymc(_trace) function
try:
from pystan.external.pymc import plots
except ImportError:
logger.critical("matplotlib required for plotting.")
raise
return plots.traceplot(fit.extract(), pars)
def traceplot(fit, vars=None):
"""Use pymc's traceplot to display parameters"""
# FIXME: eventually put this in the StanFit object
# FIXME: write a to_pymc(_trace) function
samples = fit.extract()
if vars is None:
vars = [v for v in samples.keys() if v != 'lp__']
try:
from pystan.external.pymc import plots
except ImportError:
logger.critical("matplotlib required for plotting.")
raise
return plots.traceplot(fit.extract(), vars)
def traceplot(fit, pars, dtypes, **kwargs):
"""
Use pymc's traceplot to display parameters.
Additional arguments are passed to pymc.plots.traceplot.
"""
# FIXME: eventually put this in the StanFit object
# FIXME: write a to_pymc(_trace) function
try:
from pystan.external.pymc import plots
except ImportError:
logger.critical("matplotlib required for plotting.")
raise
return plots.traceplot(fit.extract(dtypes=dtypes), pars, **kwargs)
def traceplot(fit, pars, dtypes, **kwargs):
"""
Use pymc's traceplot to display parameters.
Additional arguments are passed to pymc.plots.traceplot.
"""
# FIXME: eventually put this in the StanFit object
# FIXME: write a to_pymc(_trace) function
# Deprecation warning added in PyStan 2.18
logger.warning("Deprecation warning."\
" In future, use ArviZ library (`pip install arviz`)")
try:
from pystan.external.pymc import plots
except ImportError:
logger.critical("matplotlib required for plotting.")
raise
if pars is None:
pars = list(fit.model_pars) + ["lp__"]
values = fit.extract(dtypes=dtypes, pars=pars, permuted=False)
values = {key : arr.reshape(-1, int(np.multiply.reduce(arr.shape[2:])), order="F") for key, arr in values.items()}
return plots.traceplot(values, pars, **kwargs)
