calcPnetLLike: Calculates the log likelihood for a set of data under a Pnet...

In ralmond/Peanut: Parameterized Bayesian Networks, Abstract Classes

Calculates the log likelihood for a set of data under a Pnet model

Description

The function calcPnetLLike calculates the log likelihood for a set of data contained in cases using the current values of the conditional probability table in a Pnet. If it is called after a call to BuildAllTables(net) this will be the current value of the parameters.

Usage

calcPnetLLike(net, cases)

Arguments

net	A Pnet object representing a parameterized network.
cases	An object representing a set of cases. Note the type of object is implementation dependent. It could be either a data frame providing cases or a filename for a case file.

Details

This function provides the convergence test for the GEMfit algorithm. The Pnet represents a model (with parameters set to the value used in the current iteration of the EM algorithm) and cases a set of data. This function gives the log likelihood of the data.

This is a generic function shell. It is assumed that either (a) the native Bayes net implementation provides a way of calculating the log likelihood of a set of cases, or (b) it provides a way of calculating the likelihood of a single case, and the log likelihood of the case set can be calculated though iteration. In either case, the value of cases is implementation dependent. In PNetica-package the cases argument should be a filename of a Netica case file (see write.CaseFile).

Value

A numeric scalar giving the log likelihood of the data in the case file.

Note

The function calcPnetLLike is an abstract generic functions, and it needs specific implementations. See the PNetica-package for an example.

Author(s)

Russell Almond

References

Almond, R. G. (2015) An IRT-based Parameterization for Conditional Probability Tables. Paper presented at the 2015 Bayesian Application Workshop at the Uncertainty in Artificial Intelligence Conference.

See Also

Pnet, GEMfit, calcExpTables, maxAllTableParams

Examples

## Not run: 

library(PNetica) ## Need a specific implementation
sess <- NeticaSession()
startSession(sess)

irt10.base <- ReadNetworks(system.file("testnets","IRT10.2PL.base.dne",
                                package="PNetica"),
                           session=sess)
irt10.base <- as.Pnet(irt10.base)  ## Flag as Pnet, fields already set.
irt10.theta <- PnetFindNode(irt10.base,"theta")
irt10.items <- PnetPnodes(irt10.base)
## Flag items as Pnodes
for (i in 1:length(irt10.items)) {
  irt10.items[[i]] <- as.Pnode(irt10.items[[i]])
  ## Add node to list of observed nodes
  PnodeLabels(irt10.items[[1]]) <-
     union(PnodeLabels(irt10.items[[1]]),"onodes")
}
PnetCompile(irt10.base) ## Netica requirement

casepath <- system.file("testdat","IRT10.2PL.200.items.cas",
                                package="PNetica")

llike <- calcPnetLLike(irt10.base,casepath)

DeleteNetwork(irt10.base)
stopSession(sess)

## End(Not run)

ralmond/Peanut documentation built on Sept. 19, 2023, 8:27 a.m.