Help on class understanding in pymc code
Peter Otten
__peter__ at web.de
Sun Dec 13 20:09:51 EST 2015
Robert wrote:
> Hi,
>
> I follow code example at link:
>
> https://users.obs.carnegiescience.edu/cburns/ipynbs/PyMC.html
>
>
> There is the following code line:
>
> sampler = pymc.MCMC([alpha,betax,betay,eps,model,tau,z_obs,x_true,y_true])
>
>
> I want to know the detail of pymc.MCMC, then I get help content of it
> with:
>
> /////////////
> help(pymc.MCMC)
> Help on class MCMC in module pymc.MCMC:
>
> class MCMC(pymc.Model.Sampler)
> | This class fits probability models using Markov Chain Monte Carlo.
> | Each stochastic variable is assigned a StepMethod object, which makes
> | it take a single MCMC step conditional on the rest of the model. These
> | step methods are called in turn.
> |
> | >>> A = MCMC(input, db, verbose=0)
> |
> \\\\\\\\\\\\\\\\\\
>
>
> help('pymc.Model.Sampler')
> no Python documentation found for 'pymc.Model.Sampler'
>
>
> help('pymc.Model')
> Help on class Model in pymc:
>
> pymc.Model = class Model(pymc.Container.ObjectContainer)
> | The base class for all objects that fit probability models. Model is
> | initialized with:
> |
> | >>> A = Model(input, verbose=0)
> |
> | :Parameters:
> | - input : module, list, tuple, dictionary, set, object or nothing.
> | Model definition, in terms of Stochastics, Deterministics,
> | Potentials and Containers. If nothing, all nodes are collected
> | from the base namespace.
> |
> | Attributes:
> | - deterministics
> | - stochastics (with observed=False)
> | - data (stochastic variables with observed=True)
> | - variables
> | - potentials
> | - containers
> | - nodes
> | - all_objects
> | - status: Not useful for the Model base class, but may be used by
> | subclasses.
> |
> | The following attributes only exist after the appropriate method is
> | called:
> | - moral_neighbors: The edges of the moralized graph. A dictionary,
> | keyed by stochastic variable,
> | whose values are sets of stochastic variables. Edges exist between
> | the key variable and all variables in the value. Created by method
> | _moralize.
> | - extended_children: The extended children of self's stochastic
> | variables. See the docstring of
> | extend_children. This is a dictionary keyed by stochastic
> | variable.
> | - generations: A list of sets of stochastic variables. The members
> | of each element only have parents in
> | previous elements. Created by method find_generations.
> |
> | Methods:
> | - sample_model_likelihood(iter): Generate and return iter samples
> | of p(data and potentials|model).
> | Can be used to generate Bayes' factors.
> |
> | :SeeAlso: Sampler, MAP, NormalApproximation, weight, Container, graph.
> |
> | Method resolution order:
> | Model
> | pymc.Container.ObjectContainer
> | pymc.six.NewBase
> | pymc.Node.ContainerBase
> | __builtin__.object
> |
> | Methods defined here:
> |
> | __init__(self, input=None, name=None, verbose=-1)
> | Initialize a Model instance.
> |
> | :Parameters:
> | - input : module, list, tuple, dictionary, set, object or
> | nothing.
> | Model definition, in terms of Stochastics, Deterministics,
> | Potentials and Containers. If nothing, all nodes are
> | collected from the base namespace.
> |
> | draw_from_prior(self)
> | Sets all variables to random values drawn from joint 'prior',
> | meaning contributions of data and potentials to the joint
> | distribution are not considered.
> |
> | get_node(self, node_name)
> | Retrieve node with passed name
> |
> | seed(self)
> | Seed new initial values for the stochastics.
> |
> | ----------------------------------------------------------------------
> | Data descriptors defined here:
> |
> | generations
> |
> | ----------------------------------------------------------------------
> | Data and other attributes defined here:
> |
> | __slotnames__ = []
> |
> | register = False
> |
> | ----------------------------------------------------------------------
> | Methods inherited from pymc.Container.ObjectContainer:
> |
> | replace(self, item, new_container, key)
> |
> | ----------------------------------------------------------------------
> | Data descriptors inherited from pymc.Container.ObjectContainer:
> |
> | value
> | A copy of self, with all variables replaced by their values.
> |
> | ----------------------------------------------------------------------
> | Methods inherited from pymc.Node.ContainerBase:
> |
> | assimilate(self, new_container)
> |
> | ----------------------------------------------------------------------
> | Data descriptors inherited from pymc.Node.ContainerBase:
> |
> | __dict__
> | dictionary for instance variables (if defined)
> |
> | __weakref__
> | list of weak references to the object (if defined)
> |
> | logp
> | The summed log-probability of all stochastic variables (data
> | or otherwise) and factor potentials in self.
> |
> | ----------------------------------------------------------------------
> | Data and other attributes inherited from pymc.Node.ContainerBase:
> |
> | change_methods = []
> |
> | containing_classes = []
> ---------
>
>
> Now, I have puzzles on the class constructor input parameter:
> [alpha,betax,betay,eps,model,tau,z_obs,x_true,y_true]
>
> 1. 'class MCMC(pymc.Model.Sampler)' says its inheritance is from
> 'pymc.Model.Sampler'
>
> 2. When I try to get help on 'pymc.Model.Sampler', it says:
> 'no Python documentation found for 'pymc.Model.Sampler'
>
> 3. When I continue to catch help on 'pymc.Model.Sampler', I don't see
> content mentions 'Sampler'. This complete help message is shown above.
>
> So, what is 'pymc.Model.Sampler'?
Unfortunately there is a module pymc.Model and a class pymc.Model.Model, and
in pymc.__init__.py there is code that overwrites the module with the class.
Therefore when you write
pymc.Model
you get
pymc.Model.Model
as you can see when you type
>>> import pymc
>>> pymc.Model
<class 'pymc.Model.Model'>
To get around this bad naming use
>>> from pymc.Model import Sampler
>>> help(Sampler)
More information about the Python-list
mailing list