[R] Implementing trees in R

Yuk Lap Yip (Kevin) yuklap.yip at yale.edu
Fri Mar 16 15:41:34 CET 2007

Hi Gabor,

    Thanks for the suggestions. I tried to look for the proto vignette 
document but could not find it, could you tell me how to reach it?

    Besides, is it possible to define my own node object type with a 
default behavior for the "<-" operator of its member variables being 
referencing rather than copying? Any good reference material/ similar 
code examples?


Gabor Grothendieck wrote:
> Lists are not good for this.  There is an example in section 3.3 of
> the proto vignette of using proto objects for this.  That section
> also references an S4 example although its pretty messy with S4.
> You might want to look at the graph, RBGL and graphviz packages
> in Bioconductor and the dynamicgraph, mathgraph and sna packages
> on CRAN.
> On 3/16/07, Yuk Lap Yip (Kevin) <yuklap.yip at yale.edu> wrote:
>> Hi all,
>>    I am rather new to R. Recently I have been trying to implement some
>> tree algorithms in R. I used lists to model tree nodes. I thought
>> something like this would work:
>>    parent <- list();
>>    child <- list();
>>    parent$child1 <- child;
>>    child$parent <- parent;
>>    When I tried to check whether a node is its parent's first child
>> using "if (node$parent$child1 == node)", it always returned false. Then
>> I realized that it does not really work because "parent$child1 <- child"
>> actually makes a copy of child instead of referencing it. I think one
>> possible fix is to keep a list of node objects, and make references
>> using the positions in the list. For example, I think the following
>> would work:
>>    parent <- list();
>>    child <- list();
>>    nodes <- list(parent, child);
>>    parent$child1 <- 2;
>>    child$parent <- 1;
>>    Then the "first child" test can be rewritten as "if
>> (nodes[[nodes[[nodeId]]$parent]]$child1 == nodeId)". However, I would
>> prefer not to implement trees in this way, as it requires the
>> inconvenient and error-prone manipulations of node IDs.
>>    May I know if there is a way to make object references to lists? Or
>> are there other ways to implement tree data structures in R?
>>    BTW, I checked how hclust was implemented, and noticed that it calls
>> an external Fortran program. I would want a solution not involving any
>> external programs.
>>    Thanks.
>> -- 
>>        God bless.
>>        Kevin
>> ______________________________________________
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	God bless.


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