bn.fit: Fit the parameters of a Bayesian network

Description

Fit the parameters of a Bayesian network conditional on its structure.

Usage

bn.fit(x, data, cluster = NULL, method = "mle", …, keep.fitted = TRUE,
  debug = FALSE)
custom.fit(x, dist, ordinal, debug = FALSE)
bn.net(x, debug = FALSE)

Arguments

an object of class bn (for bn.fit() and custom.fit()) or an object of class bn.fit (for bn.net).

data

a data frame containing the variables in the model.

cluster

an optional cluster object from package parallel.

dist

a named list, with element for each node of x. See below.

method

a character string, either mle for Maximum Likelihood parameter estimation or bayes for Bayesian parameter estimation (currently implemented only for discrete data).

...

additional arguments for the parameter estimation procedure, see below.

ordinal

a vector of character strings, the labels of the discrete nodes which should be saved as ordinal random variables (bn.fit.onode) instead of unordered factors (bn.fit.dnode).

keep.fitted

a boolean value. If TRUE, the object returned by bn.fit will contain fitted values and residuals for all Gaussian and conditional Gaussian nodes, and the configurations of the discrete parents for conditional Gaussian nodes.

debug

a boolean value. If TRUE a lot of debugging output is printed; otherwise the function is completely silent.

Value

bn.fit() and custom.fit()returns an object of class bn.fit, bn.net() an object of class bn. See bn class and bn.fit class for details.

Details

bn.fit() fits the parameters of a Bayesian network given its structure and a data set; bn.net returns the structure underlying a fitted Bayesian network.

Additional arguments for the bn.fit() function:

iss: a numeric value, the imaginary sample size used by the bayes method to estimate the conditional probability tables associated with discrete nodes (see score for details).
replace.unidentifiable: a boolean value. If TRUE and method is mle, unidentifiable parameters are replaced by zeroes (in the case of regression coefficients and standard errors in Gaussian and conditional Gaussian nodes) or by uniform conditional probabilities (in discrete nodes).

If FALSE (the default), the conditional probabilities in the local distributions of discrete nodes have a mximum likelihood estimate of NaN for all parents configurations that are not observed in data. Similarly, regression coefficients are set to NA if the linear regressions correspoding to the local distributions of continuous nodes are singular. Such missing values propagate to the results of functions such as predict().

An in-place replacement method is available to change the parameters of each node in a bn.fit object; see the examples for discrete, continuous and hybrid networks below. For a discrete node (class bn.fit.dnode or bn.fit.onode), the new parameters must be in a table object. For a Gaussian node (class bn.fit.gnode), the new parameters can be defined either by an lm, glm or pensim object (the latter is from the penalized package) or in a list with elements named coef, sd and optionally fitted and resid. For a conditional Gaussian node (class bn.fit.cgnode), the new parameters can be defined by a list with elements named coef, sd and optionally fitted, resid and configs. In both cases coef should contain the new regression coefficients, sd the standard deviation of the residuals, fitted the fitted values and resid the residuals. configs should contain the configurations if the discrete parents of the conditional Gaussian node, stored as a factor.

custom.fit() takes a set of user-specified distributions and their parameters and uses them to build a bn.fit object. Its purpose is to specify a Bayesian network (complete with the parameters, not only the structure) using knowledge from experts in the field instead of learning it from a data set. The distributions must be passed to the function in a list, with elements named after the nodes of the network structure x. Each element of the list must be in one of the formats described above for in-place replacement.

Examples

Run this code

# NOT RUN {
data(learning.test)

# learn the network structure.
res = gs(learning.test)
# set the direction of the only undirected arc, A - B.
res = set.arc(res, "A", "B")
# estimate the parameters of the Bayesian network.
fitted = bn.fit(res, learning.test)
# replace the parameters of the node B.
new.cpt = matrix(c(0.1, 0.2, 0.3, 0.2, 0.5, 0.6, 0.7, 0.3, 0.1),
            byrow = TRUE, ncol = 3,
            dimnames = list(B = c("a", "b", "c"), A = c("a", "b", "c")))
fitted$B = as.table(new.cpt)
# the network structure is still the same.
all.equal(res, bn.net(fitted))

# learn the network structure.
res = hc(gaussian.test)
# estimate the parameters of the Bayesian network.
fitted = bn.fit(res, gaussian.test)
# replace the parameters of the node F.
fitted$F = list(coef = c(1, 2, 3, 4, 5), sd = 3)
# set again the original parameters
fitted$F = lm(F ~ A + D + E + G, data = gaussian.test)

# discrete Bayesian network from expert knowledge.
net = model2network("[A][B][C|A:B]")
cptA = matrix(c(0.4, 0.6), ncol = 2, dimnames = list(NULL, c("LOW", "HIGH")))
cptB = matrix(c(0.8, 0.2), ncol = 2, dimnames = list(NULL, c("GOOD", "BAD")))
cptC = c(0.5, 0.5, 0.4, 0.6, 0.3, 0.7, 0.2, 0.8)
dim(cptC) = c(2, 2, 2)
dimnames(cptC) = list("C" = c("TRUE", "FALSE"), "A" =  c("LOW", "HIGH"),
                   "B" = c("GOOD", "BAD"))
cfit = custom.fit(net, dist = list(A = cptA, B = cptB, C = cptC))
# for ordinal nodes it is nearly the same.
cfit = custom.fit(net, dist = list(A = cptA, B = cptB, C = cptC),
         ordinal = c("A", "B"))

# Gaussian Bayesian network from expert knowledge.
distA = list(coef = c("(Intercept)" = 2), sd = 1)
distB = list(coef = c("(Intercept)" = 1), sd = 1.5)
distC = list(coef = c("(Intercept)" = 0.5, "A" = 0.75, "B" = 1.32), sd = 0.4)
cfit = custom.fit(net, dist = list(A = distA, B = distB, C = distC))

# conditional Gaussian Bayesian network from expert knowledge.
cptA = matrix(c(0.4, 0.6), ncol = 2, dimnames = list(NULL, c("LOW", "HIGH")))
distB = list(coef = c("(Intercept)" = 1), sd = 1.5)
distC = list(coef = matrix(c(1.2, 2.3, 3.4, 4.5), ncol = 2,
               dimnames = list(c("(Intercept)", "B"), NULL)),
          sd = c(0.3, 0.6))
cgfit = custom.fit(net, dist = list(A = cptA, B = distB, C = distC))
# }