enumerate.models {nem} | R Documentation |
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.
enumerate.models(x,name=NULL,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 |
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 <URL: http://genomics.princeton.edu/~florian>
enumerate.models(2) enumerate.models(c("Anna","Bert"))