[R] Fast lookup in ragged array

[Peter McMahan]

Thanks, I'll give it a try. does R have a limit on variable name  
length? Also, is it better to over-estimate or under-estimate the  
size parameter?
This won't be too hard to implement, either, as I'm already keeping  
the list in a specific environment so all the subprocesses can find  
the same one.

On Mar 16, 2007, at 1:37 PM, Seth Falcon wrote:

> Peter McMahan <peter.mcmahan at gmail.com> writes:
>
>> Well, I hadn't ever seen RBGL before, so that's great. I've been
>> using igraph and sna mainly, but there are a few points lacking
>> between these two. RBGL solves a lot of problems for me!
>>
>> But I'm not sure it will solve this specific problem. Are you
>> suggesting I use RBGL to do a depth-first search of all the
>> subgraphs? For this particular depth-first search I'm not searching
>> every subgraph, but just those that are constructed from a minimal
>> cutset of the parent subgraph. At each level of the search, I have to
>> compute graph cohesion (vertex connectivity), which can take
>> considerable time. A lot of computation time is saved by only
>> searching subgraphs obtained through cutsets. So a complete search of
>> all the subgraphs won't work, but the redundancy I come across is I
>> think unavoidable.
>
> Perhaps you will need a combination of graph/RBGL and some custom
> memoization code to keep track of which subgraphs have already been
> searched.
>
> Some suggestions on that front:
>
> Don't use a list, use an environment.
>
>      searchedBranched = new.env(hash=TRUE, parent=emptyenv(), size=X)
>
> where X is an estimate of the number of branches you will search.
> Using an environment implies you will need unique character names for
> each subgraph.  Do you have that?  If not, you could concatenate node
> names.  For a 200 node graph, that should be ok.
>
> Hope that helps some.
>
> + seth
>
> -- 
> Seth Falcon | Computational Biology | Fred Hutchinson Cancer  
> Research Center
> http://bioconductor.org