Nothing
########################################################################
# Categorical Network Class
setClass("catNetwork",
representation(
objectName = "character",
numnodes = "integer",
nodes = "vector",
meta = "character",
maxpars = "integer", pars="list",
maxcats = "integer", cats="list",
probs = "list",
complx = "integer",
nodecomplx = "ANY",
loglik = "numeric",
nodelik = "ANY",
nodeSampleSizes = "vector"),
validity = function(object) validCatNetwork(object),
package = "sdnet"
)
setGeneric("cnAddNode",
function(object, node, cats, pars, prob)
standardGeneric("cnAddNode")
)
setGeneric("cnNumNodes", function(object)
standardGeneric("cnNumNodes")
)
# returns list of nodes
setGeneric("cnNodes", function(object, which)
standardGeneric("cnNodes")
)
## returns list of edges
setGeneric("cnEdges", function(object, which)
standardGeneric("cnEdges")
)
setGeneric("cnMatEdges", function(object)
standardGeneric("cnMatEdges")
)
## returns pars sets as a list
setGeneric("cnParents", function(object, which)
standardGeneric("cnParents")
)
## returns pars sets as a matrix
setGeneric("cnMatParents",
function(object, nodeorder)
standardGeneric("cnMatParents")
)
setGeneric("cnProb", function(object, which=NULL)
standardGeneric("cnProb")
)
setGeneric("cnPlotProb", function(object, which=NULL)
standardGeneric("cnPlotProb")
)
setGeneric("cnDot", function(object, file=NULL, format="ps", nodestyle=NULL, edgestyle=NULL)
standardGeneric("cnDot")
)
setGeneric("cnSamples", function(object, numsamples=1, pert=NULL, output="frame", as.index=FALSE, naRate=0)
standardGeneric("cnSamples")
)
setGeneric("cnSetProb", function(object, data, pert=NULL, nodeCats=NULL, softmode=FALSE)
standardGeneric("cnSetProb")
)
setGeneric("cnLoglik", function(object, data, pert=NULL, bysample=FALSE, softmode=FALSE)
standardGeneric("cnLoglik")
)
setGeneric("cnNodeLoglik", function(object, node, data, pert=NULL, softmode=FALSE, klmode=FALSE)
standardGeneric("cnNodeLoglik")
)
setGeneric("cnNodeLoglikError", function(object, node, data, pert=NULL)
standardGeneric("cnNodeLoglikError")
)
setGeneric("cnPredict", function(object, data)
standardGeneric("cnPredict")
)
setGeneric("cnEvaluate", function(object, data, pert=NULL, maxParentSet = 0, maxcomplx=0, echo=FALSE)
standardGeneric("cnEvaluate")
)
setGeneric("cnComplexity", function(object, node=NULL, include.unif=TRUE)
standardGeneric("cnComplexity")
)
setGeneric("cnKLComplexity", function(object, node=NULL)
standardGeneric("cnKLComplexity")
)
## returns a graph object
setGeneric("as.graph", function(object)
standardGeneric("as.graph")
)
setGeneric("cnJointProb",
function(object,nodes)
standardGeneric("cnJointProb")
)
setGeneric("cnCondProb",
function(object,x,y)
standardGeneric("cnCondProb")
)
setGeneric("cnJointKLdist",
function(object1, object2, ...)
standardGeneric("cnJointKLdist")
)
setGeneric("cnNodeMarginalProb",
function(object, node)
standardGeneric("cnNodeMarginalProb")
)
setGeneric("cnMarginalKLdist",
function(object1, object2,...)
standardGeneric("cnMarginalKLdist")
)
setGeneric("cnMarginalKLdistList",
function(object1, object2list,...)
standardGeneric("cnMarginalKLdistList")
)
setGeneric("cnCondKLdist",
function(object1, object2, ...)
standardGeneric("cnCondKLdist")
)
setGeneric("cnCompare",
function(object1, object2, extended = FALSE)
standardGeneric("cnCompare")
)
setGeneric("cnSubNetwork",
function(object, nodeIndices, indirectEdges = FALSE)
standardGeneric("cnSubNetwork")
)
setGeneric("cnReorderNodes",
function(object, nodeIndices)
standardGeneric("cnReorderNodes")
)
setGeneric("cnOrder",
function(object)
standardGeneric("cnOrder")
)
setGeneric("cnCluster",
function(object)
standardGeneric("cnCluster")
)
setGeneric("cnClusterSep",
function(object, data, pert=NULL)
standardGeneric("cnClusterSep")
)
# draw a graph
setGeneric("cnPlot",
function(object, file=NULL)
standardGeneric("cnPlot")
)
setGeneric("cnFindAIC", function(object, numsamples)
standardGeneric("cnFindAIC")
)
setGeneric("cnFindBIC", function(object, numsamples)
standardGeneric("cnFindBIC")
)
setGeneric("cnFindKL", function(object, numsamples)
standardGeneric("cnFindKL")
)
setGeneric("addNetworkNode",
function(object, newnode, newparents, loglik, problist, nodecats, ...)
standardGeneric("addNetworkNode")
)
setGeneric("replaceNetworkNode",
function(object, newnode, newparents, loglik, problist, ...)
standardGeneric("replaceNetworkNode")
)
setGeneric("updateNetworkNode",
function(newnet, listnet, ...)
standardGeneric("updateNetworkNode")
)
setGeneric("cnPearsonTest",
function(object, data)
standardGeneric("cnPearsonTest")
)
setGeneric("cnMarParents",
function(object, flags = NULL)
standardGeneric("cnMarParents")
)
#########################################################################
## Categorical Network Diagnostic Class
setClass("catNetworkDistance",
representation(
hamm = "numeric",
hammexp = "ANY",
tp = "numeric",
fp = "numeric",
fn = "numeric",
pr = "numeric",
sp = "numeric",
sn = "numeric",
fscore = "numeric",
skel.tp = "numeric",
skel.fp = "numeric",
skel.fn = "numeric",
order.fp = "ANY",
order.fn = "ANY",
markov.fp = "ANY",
markov.fn = "ANY",
KLdist = "ANY"),
package = "sdnet"
)
setClass("catNetworkEvaluate",
representation(
numnodes = "integer",
numsamples = "integer",
nets = "list",
complx = "vector",
loglik = "vector",
hamm = "vector",
hammexp = "vector",
tp = "vector",
fp = "vector",
fn = "vector",
pr = "vector",
sp = "vector",
sn = "vector",
fscore = "vector",
skel.tp = "vector",
skel.fp = "vector",
skel.fn = "vector",
order.fp = "vector",
order.fn = "vector",
markov.fp = "vector",
markov.fn = "vector",
KLdist = "vector",
time = "numeric"
),
package = "sdnet"
)
setGeneric("cnFind",
function(object, complx=0, alpha=0,factor=1)
standardGeneric("cnFind")
)
setGeneric("cnParHist",
function(object)
standardGeneric("cnParHist")
)
setGeneric("cnProcTime",
function(object)
standardGeneric("cnProcTime")
)
#########################################################################
## for large sets of dags
setClass("dagEvaluate",
representation(
version = "character",
numnodes = "integer",
nodes = "vector",
numsamples = "integer",
maxcats="integer",
cats="list",
maxpars="integer",
parSlots="list",
parLogliks="list",
parComplx="list",
parSampleSize="list",
numDags="integer",
numPars="list",
loglik="vector",
complx="vector",
time = "numeric"),
package = "sdnet"
)
setGeneric("cnCatnetFromDagEvaluate",
function(object, index=1)
standardGeneric("cnCatnetFromDagEvaluate")
)
setGeneric("cnFindBnkl",
function(object, factor=NULL)
standardGeneric("cnFindBnkl")
)
#########################################################################
## Complete Partially Directed Acyclic Graphs
setClass("CPDAG",
representation(
numnodes = "integer",
nodes = "vector",
edges = "list"
),
package = "sdnet"
)
setGeneric("dag2cpdag",
function(object)
standardGeneric("dag2cpdag")
)
#########################################################################
## Some constants
EPSDIFF <- exp(-16)
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