You should reply to the list, not just me, and even more because I
cannot really help you!!
My guess (but I don't know this package, and even less this function) is
that pvclust() is expecting a matrix as the first argument. However,
"cluster" is no data, it is a function. Why, I don't know. Take a
closer
look at ?pvclust, especially the "usage", "arguments" and
"examples" parts.
HTH,
Ivan
-------- Message original --------
Sujet: RE: pvclust function
Date : Mon, 9 Aug 2010 10:52:30 +0100
De : Holt, Hannah Rebecca <hholt@rvc.ac.uk>
Pour : <ivan.calandra@uni-hamburg.de>
Sorry Ivan,
Thanks for your tips the output from str(cluster) is;
function (file, header = FALSE, sep = "", quote =
"\"'", dec = ".",
row.names, col.names, as.is = !stringsAsFactors, na.strings =
"NA",
colClasses = NA, nrows = -1, skip = 0, check.names = TRUE,
fill = !blank.lines.skip, strip.white = FALSE, blank.lines.skip = TRUE,
comment.char = "#", allowEscapes = FALSE, flush = FALSE,
stringsAsFactors = default.stringsAsFactors(), fileEncoding = "",
encoding = "unknown")
I am not sure how to interpret this!
Kind Regards,
Hannah
-----Original Message-----
From: r-help-bounces@r-project.org [mailto:r-help-bounces@r-project.org] On
Behalf Of Ivan Calandra
Sent: 09 August 2010 10:40
To: r-help@r-project.org
Subject: Re: [R] (no subject)
Hi Hannah,
First, don't forget to add a subject to your email!
Second, the best way to share data is to copy/paste the output from the
dput() function into the email.
I have never used pvclust, but the error tells you that your object
"cluster" is not a matrix.
What does str(cluster) return?
You may think it's a matrix, but depending on how you've created it, it
might be a data.frame or something else.
str() is a very useful function.
HTH,
Ivan
Le 8/9/2010 11:22, Holt, Hannah Rebecca a écrit :> Hi there,
>
>
>
> I have been trying to use the "pvclust" package but have been
having
> some difficulties. This is the first time I have used R so I am sure
> the mistake I am making is a basic one. The data I have is a distance
> matrix and I have been using the command; fit<- pvclust(cluster,
> nboot=1000,
> method.dist="euclidean") to try and perform hierarchical
clustering
> with bootstrapped p-values, but I get the error message; Error in
> t.default(x) : argument is not a matrix. I guess there is a problem
> with the way the data is laid out, do you know how the data should be
> displayed in order to get the command to work (the data I am using I
> have pasted below), I have tried various methods of organising it!
>
>
>
> V1 V2 V3 V4
>
> 1 0.00000000 0.03162278 0.05830952 0.1315295
>
> 2 0.03162278 0.00000000 0.06000000 0.1627882
>
> 3 0.05830952 0.06000000 0.00000000 0.1627882
>
> 4 0.13152946 0.16278821 0.16278821 0.0000000
>
>
>
> Any help you could give me would be greatly appreciated.
>
>
>
> Kind Regards,
>
>
>
> Hannah
>
>
>
>
>
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help@r-project.org 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.
>
--
Ivan CALANDRA
PhD Student
University of Hamburg
Biozentrum Grindel und Zoologisches Museum Abt. Säugetiere
Martin-Luther-King-Platz 3
D-20146 Hamburg, GERMANY
+49(0)40 42838 6231
ivan.calandra@uni-hamburg.de
**********
http://www.for771.uni-bonn.de
http://webapp5.rrz.uni-hamburg.de/mammals/eng/mitarbeiter.php
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