[R] Implementing trees in R

[Gabor Grothendieck]

On 3/16/07, Gabor Grothendieck <ggrothendieck at gmail.com> wrote:
> 1. Here is your example redone using proto:
>
> library(proto)
>
> parent <- proto()
> child <- proto(a = 1)
> parent$child1 <- child
> child$parent.env <- parent

This last line should have been:

parent.env(child) <- parent


>
> # also just for illustration lets change a
>
> parent$child1$a # 1
> child$a <- 2
> parent$child1$a # 2
>
> 2. To redefine $<- use S3 or S4 but it can be done
> in conjunction with proto like this:
>
> # constructor
> node <- function(. = parent.frame(), ...)
>   structure(proto(...), class = c("node", "proto"))
>
> "$<-.node" <- function(this, s, value) {
>    if (s == ".super")
>        parent.env(this) <- value
>    if (is.function(value))
>        environment(value) <- this
>    if (inherits(value, "node"))
>        parent.env(value) <- this
>    this[[as.character(substitute(s))]] <- value
>    this
> }
>
>
> p <- node(a = 1)
> p$child <- node(b = 2)
> p$child$parent.env()
> p # same
>
>
>
> On 3/16/07, Yuk Lap Yip (Kevin) <yuklap.yip at yale.edu> wrote:
> > Hi Gabor,
> >
> >    Thanks for the suggestions. I tried to look for the proto vignette
> > document but could not find it, could you tell me how to reach it?
> >
> >    Besides, is it possible to define my own node object type with a
> > default behavior for the "<-" operator of its member variables being
> > referencing rather than copying? Any good reference material/ similar
> > code examples?
> >
> >    Thanks.
> >
> > Gabor Grothendieck wrote:
> > > Lists are not good for this.  There is an example in section 3.3 of
> > > the proto vignette of using proto objects for this.  That section
> > > also references an S4 example although its pretty messy with S4.
> > >
> > > You might want to look at the graph, RBGL and graphviz packages
> > > in Bioconductor and the dynamicgraph, mathgraph and sna packages
> > > on CRAN.
> > >
> > > On 3/16/07, Yuk Lap Yip (Kevin) <yuklap.yip at yale.edu> wrote:
> > >> Hi all,
> > >>
> > >>    I am rather new to R. Recently I have been trying to implement some
> > >> tree algorithms in R. I used lists to model tree nodes. I thought
> > >> something like this would work:
> > >>
> > >>    parent <- list();
> > >>    child <- list();
> > >>    parent$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
> > >>
> > >> ______________________________________________
> > >> R-help at stat.math.ethz.ch mailing list
> > >> https://stat.ethz.ch/mailman/listinfo/r-help
> > >> PLEASE do read the posting guide
> > >> http://www.R-project.org/posting-guide.html
> > >> and provide commented, minimal, self-contained, reproducible code.
> > >>
> >
> > --
> >
> >
> >        God bless.
> >
> >        Kevin
> >
> >
>