enumerate.models {nem}R Documentation

Exhaustive enumeration of models

Description

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.

Usage

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

Arguments

x either the number of nodes or a vector of node names.
name optionally the nodenames, if they are not provided in x
verbose if TRUE outputs number of (unique) models. Default: TRUE

Details

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).

Value

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

Author(s)

Florian Markowetz <URL: http://genomics.princeton.edu/~florian>

See Also

score, nem

Examples

enumerate.models(2)
enumerate.models(c("Anna","Bert"))

[Package nem version 2.2.1 Index]