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 <[email protected]> Pour : <[email protected]> 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: [email protected] [mailto:[email protected]] On Behalf Of Ivan Calandra Sent: 09 August 2010 10:40 To: [email protected] 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]] > > ______________________________________________ > [email protected] 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 [email protected] ********** http://www.for771.uni-bonn.de http://webapp5.rrz.uni-hamburg.de/mammals/eng/mitarbeiter.php [[alternative HTML version deleted]] [[alternative HTML version deleted]]
______________________________________________ [email protected] 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.
