BFSlevel                Build (generalized) hierarchy by Breath-First
                        Search
BoutrosRNAi2002         RNAi data on Drosophila innate immune response
FULLmLL                 Full marginal likelihood of a phenotypic
                        hierarchy
SCCgraph                Combines Strongly Connected Components into
                        single nodes
enumerate.models        Exhaustive enumeration of models
local.model.prior       Computes a prior to be used for edge-wise model
                        inference
mLL                     Marginal likelihood of a phenotypic hierarchy
moduleNetwork           Infers a phenotypic hierarchy using the module
                        network
nem                     Nested Effects Models - main function
nem.cont.preprocess     Calculate classification probabilities of
                        perturbation data according to control
                        experiments
nem.discretize          Discretize perturbation data according to
                        control experiments
nemModelSelection       model selection for nested effect models
network.AIC             AIC criterion for network graph
pairwise.posterior      Infers a phenotypic hierarchy edge by edge
plot.effects            Plots data according to a phenotypic hierarchy
plot.nem                plot nested effect model
score                   Computes the marginal likelihood of phenotypic
                        hierarchies
subsets                 Subsets
transitive.closure      Computes the transitive closure of a directed
                        graph
transitive.reduction    Computes the transitive reduction of a graph
triples.posterior       Infers a phenotypic hierarchy from triples
