enumerate.models: Exhaustive enumeration of models
In cbg-ethz/pcNEM: Probabilistic combinatorial nested effects model

Description Usage Arguments Details Value Author(s) See Also Examples

The function enumerate.models is used to create the model space for inference by exhaustive enumeration. It computes a list of all transitively closed directed graphs on a given number of nodes.

1	enumerate.models(x,name=NULL,trans.close=TRUE,verbose=TRUE)

`x`	either the number of nodes or a vector of node names.
`name`	optionally the nodenames, if they are not provided in x
`trans.close`	should graphs be transitively closed?
`verbose`	if TRUE outputs number of (unique) models. Default: TRUE

The model space of Nested Effects Models consists of all transitively closed directed graphs. The function enumerate.models creates them in three steps: (1.) build all directed graphs on x (or length(x)) nodes, (2.) transitively close each one of them, and (3.) remove redundant models to yield a unique set. So far, enumeration is limited to up to 5 nodes.

I'm aware that this is inefficient! It would be very desirable to enumerate the models directly (i.e. without creating all directed graphs as an intermediate step).

a list of models. Each entry is a transitively closed adjacency matrix with unit main diagonal.

Florian Markowetz

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