Utilities to manipulate fitted Bayesian networks
Assign, extract or compute various quantities of interest from an object of
class bn.fit, bn.fit.dnode, bn.fit.gnode,
bn.fit.cgnode or bn.fit.onode.
## methods available for "bn.fit" ## S3 method for class 'bn.fit' fitted(object, ...) ## S3 method for class 'bn.fit' coef(object, ...) ## S3 method for class 'bn.fit' residuals(object, ...) ## S3 method for class 'bn.fit' sigma(object, ...) ## S3 method for class 'bn.fit' logLik(object, data, nodes, by.sample = FALSE, ...) ## S3 method for class 'bn.fit' AIC(object, data, ..., k = 1) ## S3 method for class 'bn.fit' BIC(object, data, ...) ## methods available for "bn.fit.dnode" ## S3 method for class 'bn.fit.dnode' coef(object, for.parents, ...) ## methods available for "bn.fit.onode" ## S3 method for class 'bn.fit.onode' coef(object, for.parents, ...) ## methods available for "bn.fit.gnode" ## S3 method for class 'bn.fit.gnode' fitted(object, ...) ## S3 method for class 'bn.fit.gnode' coef(object, ...) ## S3 method for class 'bn.fit.gnode' residuals(object, ...) ## S3 method for class 'bn.fit.gnode' sigma(object, ...) ## methods available for "bn.fit.cgnode" ## S3 method for class 'bn.fit.cgnode' fitted(object, ...) ## S3 method for class 'bn.fit.cgnode' coef(object, for.parents, ...) ## S3 method for class 'bn.fit.cgnode' residuals(object, ...) ## S3 method for class 'bn.fit.cgnode' sigma(object, for.parents, ...)
object |
an object of class |
nodes |
a vector of character strings, the label of a nodes whose log-likelihood components are to be computed. |
data |
a data frame containing the variables in the model. |
... |
additional arguments, currently ignored. |
k |
a numeric value, the penalty coefficient to be used; the default
|
by.sample |
a boolean value. If |
for.parents |
a named list in which each element contains |
coef() (and its alias coefficients()) extracts model coefficients
(which are conditional probabilities for discrete nodes and linear regression
coefficients for Gaussian and conditional Gaussian nodes).
residuals() (and its alias resid()) extracts model residuals and
fitted() (and its alias fitted.values()) extracts fitted values
from Gaussian and conditional Gaussian nodes. If the bn.fit object
does not include the residuals or the fitted values for the node of interest
both functions return NULL.
sigma() extracts the standard deviations of the residuals from Gaussian
and conditional Gaussian networks and nodes.
logLik() returns the log-likelihood for the observations in data.
The for.parents argument in the methods for coef() and
sigma() can be used to have both functions return the parameters
associated with a specific configuration of the discrete parents of a node.
If for.parents is not specified, all relevant parameters are returned.
logLik() returns a numeric vector or a single numeric value, depending
on the value of by.sample. AIC and BIC always return a
single numeric value.
All the other functions return a list with an element for each node in the
network (if object has class bn.fit) or a numeric vector or
matrix (if object has class bn.fit.dnode, bn.fit.gnode,
bn.fit.cgnode or bn.fit.onode).
Marco Scutari
data(gaussian.test) res = hc(gaussian.test) fitted = bn.fit(res, gaussian.test) coefficients(fitted) coefficients(fitted$C) str(residuals(fitted)) data(learning.test) res2 = hc(learning.test) fitted2 = bn.fit(res2, learning.test) coefficients(fitted2$E) coefficients(fitted2$E, for.parents = list(F = "a", B = "b"))
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