This worked for me with your example:
source("dumpdata.R")
storage.mode(x.hc$merge) <- "integer"
plot(x.hc)
(R-1.4.1 compiled from source on WinNT4.)
Andy
> -----Original Message-----
> From: Hugh Chipman [mailto:hachipma at icarus.math.uwaterloo.ca]
> Sent: Wednesday, February 20, 2002 5:32 PM
> To: andy_liaw at merck.com
> Cc: r-help at stat.math.ethz.ch
> Subject: Re: [R] plot.hclust: strange behaviour with
"manufactured"
>
>
> Andy:
>
> That's a great idea. And it's certainly part of the problem. I
> verified this by changing the type of the "merge" element of a
valid
> hclust object to be double. As you suggest, it doesn't plot.
>
> What's interesting is that if I change it back to integer again,
> plot.hclust still gives an error. Moreover, the object.size of the
> "merge" component that was transformed integer to double to
integer is
> different from the object.size of the original integer component. Is
> there something that I am missing about integer types?
>
> The original integer type was produced by the interal (C or Fortran)
> code, so maybe I am corrupting it in some way.
>
> An example below gives the details...
> --------------------------------------------------------------
> --------
> > library(mva)
> > set.seed(103)
> > x <- matrix(rnorm(5 * 2), ncol = 2)
> > x.hc <- hclust(dist(x), method = "average")
> > plot.hclust(x.hc)
> > unlist(lapply(x.hc, storage.mode))
> merge height order labels method
> call
> "integer" "double" "integer"
"NULL" "character"
> "language"
> dist.method
> "character"
>
> > unlist(lapply(x.hc, object.size))
> merge height order labels method
> call
> 152 60 52 0 44
> 324
> dist.method
> 52
>
> > x.hc$merge <- as.double(x.hc$merge)
> > plot.hclust(x.hc)
> Error in plot.hclust(x.hc) : invalid dendrogram
> > unlist(lapply(x.hc,storage.mode))
>
> merge height order labels method
> call
> "double" "double" "integer"
"NULL" "character"
> "language"
> dist.method
> "character"
> > unlist(lapply(x.hc,object.size))
>
> merge height order labels method
> call
> 92 60 52 0 44
> 324
> dist.method
> 52
> > x.hc$merge <- as.integer(x.hc$merge)
> > plot.hclust(x.hc)
>
> Error in plot.hclust(x.hc) : invalid dendrogram
> > unlist(lapply(x.hc,storage.mode))
>
> merge height order labels method
> call
> "integer" "double" "integer"
"NULL" "character"
> "language"
> dist.method
> "character"
> > unlist(lapply(x.hc,object.size))
>
> merge height order labels method
> call
> 60 60 52 0 44
> 324
> dist.method
> 52
>
>
> >
> > The problem seems to be that the original merge component
> is stored as int,
> > but the source()'d version is not. Coercing that to int I
> think works.
> >
> > Cheers,
> > Andy
> >
> > > -----Original Message-----
> > > From: Hugh Chipman [mailto:hachipma at icarus.math.uwaterloo.ca]
> > > Sent: Wednesday, February 20, 2002 1:32 PM
> > > To: r-help at stat.math.ethz.ch
> > > Cc: hachipma at icarus.math.uwaterloo.ca
> > > Subject: [R] plot.hclust: strange behaviour with
> "manufactured" hclust
> > > object
> > >
> > >
> > > I've been trying to get plot.hclust to work with a hclust
object I
> > > created and have not had much success. It seems that
> there is some
> > > "hidden" characteristic of a hclust object that I
can't
> see. This is
> > > most easily seen in the following example, where
> plot.hclust works on
> > > one object, but when this object is "dumped" and then
re-read,
> > > plot.hclust no longer works. Is this a scoping problem?
> > >
> > > Script started on Wed Feb 20 13:17:37 2002
> > > 1>@icarus[101]% R
> > >
> > > R : Copyright 2002, The R Development Core Team
> > > Version 1.4.1 (2002-01-30)
> > >
> > > ......(stuff deleted)
> > >
> > > > set.seed(103)
> > > > library(mva)
> > > > x <- matrix(rnorm(5*2),ncol=2)
> > > > x.hc <- hclust(dist(x),method='average')
> > > > plot.hclust(x.hc)
> > > # the above works
> > >
> > > > dump('x.hc')
> > > > source('dumpdata.R')
> > > > plot.hclust(x.hc)
> > > Error in plot.hclust(x.hc) : invalid dendrogram input
> > >
> > > One hypothesis I had was that it might be something like
> the "call"
> > > object that wasn't correctly being re-created by the dump
> & source,
> > > but that doesn't seem to be it. Below, I remove everything
except
> > > merge, order, and height, and plot.hclust still works on
> the original
> > > object and fails on the dump + source object.
> > >
> > > > x.hc <- hclust(dist(x),method='average')
> > > > x.hc$call <- NULL
> > > > x.hc$dist.method <- NULL
> > > > x.hc$method <- NULL
> > > > x.hc$labels <- NULL
> > > > plot.hclust(x.hc)
> > > > dump('x.hc')
> > > > source('dumpdata.R')
> > > > plot.hclust(x.hc)
> > > Error in plot.hclust(x.hc) : invalid dendrogram input
> > > >
> > > > str(x.hc)
> > > List of 3
> > > $ merge : num [1:4, 1:2] -2 -5 -1 -4 -3 1 2 3
> > > $ height: num [1:4] 0.873 1.257 1.633 2.430
> > > $ order : num [1:5] 4 1 5 2 3
> > > - attr(*, "class")= chr "hclust"
> > >
> > > Any help would be greatly appreciated!
> > >
> > > Hugh Chipman
> > >
> > > --
> > > -- Hugh Chipman -- Associate Professor, Statistics &
> > > Actuarial Science --
> > > -- University of Waterloo, Ontario, Canada
> > > --
> > > --
> > > --
> > > -- Visiting Stanford Statistics Department, January-March
> > > 2002 --
> > > -- (650) 725 6148 Fax (650)
> > > 725-8977 --
> > > -- Department of Statistics, Sequoia Hall, 390 Serra Mall
> > > --
> > > -- Stanford University, Stanford, CA 94305-4065
> > > --
> > > -- http://www.stats.uwaterloo.ca/~hachipma/
> > > hachipman at uwaterloo.ca --
> > > -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.
> > > -.-.-.-.-.-.-.-.-
> > > r-help mailing list -- Read
> > > http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
> > > Send "info", "help", or
"[un]subscribe"
> > > (in the "body", not the subject !) To:
> > > r-help-request at stat.math.ethz.ch
> > > _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._.
> > > _._._._._._._._._
> > >
> >
> >
>
>
> --
> -- Hugh Chipman -- Associate Professor, Statistics &
> Actuarial Science --
> -- University of Waterloo, Ontario, Canada
> --
> --
> --
> -- Visiting Stanford Statistics Department, January-March
> 2002 --
> -- (650) 725 6148 Fax (650)
> 725-8977 --
> -- Department of Statistics, Sequoia Hall, 390 Serra Mall
> --
> -- Stanford University, Stanford, CA 94305-4065
> --
> -- http://www.stats.uwaterloo.ca/~hachipma/
> hachipman at uwaterloo.ca --
>
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