Implementing trees in R
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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