From kleiweg@let.rug.nl  Thu Jan 10 19:36:09 2002
From: kleiweg@let.rug.nl (kleiweg@let.rug.nl)
Date: Thu, 10 Jan 2002 20:36:09 +0100 (MET)
Subject: [Rd] Size of type double in object type dist (PR#1255)
Message-ID: <200201101936.UAA14534@pubhealth.ku.dk>


The following problem occurs in R 1.4.0 and 1.3.1 for Windows95,
but not in R 1.2.0 for Windows95.

The problem does not occur in R 1.4.0 for Linux PC, Linux Alpha
and HP-UX.

Sometimes, the type of 'Size' of an object of type 'dist'
changes from integer into double. Running cmdscale on such a
'dist' object gives invalid results.

I don't know what should be considered a bug, the type of 'Size'
changing into 'double', or cmdscale not able to process a 'dist'
object with a 'Size' of type 'double'. Perhaps both.

I have not been able to locate a single cause of this problem.
The following example is when it goes wrong:

    # PA is an object of class 'dist' with 'Size' 67
    > data(PA)
    > attr(PA, "Size")
    [1] 67
    >
    > MDS <- function (dif, dim)
    + {
    +     a <- cmdscale(dif, k = dim, eig = FALSE)
    +     row.names(a) <- names(dif)
    +     a
    + }
    >
    > vec <- MDS(PA, 2)
    > attr(PA, "Size")
    [1] 67
    > plot(vec, type="n", xlab="", ylab="")
    > attr(PA, "Size")
    [1] 67
    > text(vec, rownames(vec), cex=0.5)
    > attr(PA, "Size")
    [1] 67
    >
    > vec8 <- MDS(PA, 8)
    > attr(PA, "Size")
    [1] 67
    > d2 <- dist(vec)
    > attr(PA, "Size"); attr(d2, "Size")
    [1] 67
    [1] 67
    > d8 <- dist(vec8)
    > attr(PA, "Size"); attr(d2, "Size"); attr(d8, "Size")
    [1] 67
    [1] 67
    [1] 67
    > cor(PA, d2)
    [1] 0.9370243
    > attr(PA, "Size"); attr(d2, "Size"); attr(d8, "Size")
    [1] 67
    [1] 67
    [1] 67
    > cor(PA, d8)
    [1] 0.9773668
    > attr(PA, "Size"); attr(d2, "Size"); attr(d8, "Size")
    [1] 67
    [1] 67
    [1] 67
    >
    > plot(c(min(PA), max(PA)), c(min(d2, d8), max(d2, d8)),
    +      type="n", xlab="PA", ylab="dist( cmdscale( PA ) )")
    > attr(PA, "Size"); attr(d2, "Size"); attr(d8, "Size")
    [1] 67
    [1] 67
    [1] 67
    > points(PA, d2, pch=20, cex=0.5, col="black")
# here is when it changes
    > attr(PA, "Size"); attr(d2, "Size"); attr(d8, "Size")
    [1] 67.00000
    [1] 67
    [1] 67
    > points(PA, d8, pch=20, cex=0.5, col="blue")
    > attr(PA, "Size"); attr(d2, "Size"); attr(d8, "Size")
    [1] 67.00000
    [1] 67
    [1] 67
    > legend(min(PA),max(c(d2,d8)),c("dim = 2", "dim = 8"), fill=c("black", "blue"))
    > attr(PA, "Size"); attr(d2, "Size"); attr(d8, "Size")
    [1] 67.00000
    [1] 67
    [1] 67

It gets weirder...

    > rm(PA)
    > data(PA)
    > attr(PA, "Size")
    [1] 67.00000

If I do the following, the 'Size' attributes becomes an integer,
and seems to stay an integer:

    > PA <- as.dist(PA)

...however, running cmdscale on it produces nonsense

--please do not edit the information below--

Version:
 platform = i386-pc-mingw32
 arch = x86
 os = Win32
 system = x86, Win32
 status =
 major = 1
 minor = 4.0
 year = 2001
 month = 12
 day = 19
 language = R

Windows 95 4.0 (build 1111)  B

Search Path:
 .GlobalEnv, package:ctest, Autoloads, package:base


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[Rd] Size of type double in object type dist (PR#1255)
kleiweg@let.rug.nl