[adegenet-forum] error in hclust

[Mark Coulson]

I ran exactly that same script.

From: Roman Luštrik [mailto:roman.lustrik at biolitika.si]
Sent: 05 August 2016 10:52
To: Mark Coulson <Mark.Coulson.ic at uhi.ac.uk>
Cc: Thibaut Jombart <thibautjombart at gmail.com>; adegenet-forum at lists.r-forge.r-project.org
Subject: Re: [adegenet-forum] error in hclust

It's not entirely clear what you've done yesterday. Can you provide a reproducible example?

Cheers,
Roman

----
In god we trust, all others bring data.

________________________________
From: "Mark Coulson" <Mark.Coulson.ic at uhi.ac.uk<mailto:Mark.Coulson.ic at uhi.ac.uk>>
To: "Thibaut Jombart" <thibautjombart at gmail.com<mailto:thibautjombart at gmail.com>>
Cc: adegenet-forum at lists.r-forge.r-project.org<mailto:adegenet-forum at lists.r-forge.r-project.org>
Sent: Friday, August 5, 2016 11:42:48 AM
Subject: Re: [adegenet-forum] error in hclust

There are but this should be taken care of by NA.method and again worked just fine yesterday!

Mark

From: Thibaut Jombart [mailto:thibautjombart at gmail.com]
Sent: 05 August 2016 10:41
To: Mark Coulson <Mark.Coulson.ic at uhi.ac.uk<mailto:Mark.Coulson.ic at uhi.ac.uk>>
Cc: adegenet-forum at lists.r-forge.r-project.org<mailto:adegenet-forum at lists.r-forge.r-project.org>
Subject: Re: [adegenet-forum] error in hclust

Odd indeed. Are there any NAs in 'X'?

Cheers
Thibaut


--
Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology
Imperial College London
https://sites.google.com/site/thibautjombart/
https://github.com/thibautjombart
Twitter: @TeebzR<https://twitter.com/TeebzR>

On 5 August 2016 at 10:34, Mark Coulson <Mark.Coulson.ic at uhi.ac.uk<mailto:Mark.Coulson.ic at uhi.ac.uk>> wrote:
Hello,

Yesterday I ran  the following code and everything worked just fine. Today I simply opened up my script and re-ran it and got the following

laidon <- import2genind("laidon_project_data_no_sibs.str")
X <- tab(laidon, freq=TRUE, NA.method="mean")

D <- dist(X)
D <- as.matrix(D)

h1 <- hclust(D, method="complete")

Error in if (is.na<http://is.na>(n) || n > 65536L) stop("size cannot be NA nor exceed 65536") :
  missing value where TRUE/FALSE needed

Not sure what this error means but more confused as to why suddenly it isn’t working. Nothing else has changed

Mark
Inverness College UHI, a partner in the University of the Highlands and Islands www.inverness.uhi.ac.uk<http://www.inverness.uhi.ac.uk> Board of Management of Inverness College (known as Inverness College UHI), Scottish Charity No SC021197.

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Inverness College UHI, a partner in the University of the Highlands and Islands www.inverness.uhi.ac.uk<http://www.inverness.uhi.ac.uk> Board of Management of Inverness College (known as Inverness College UHI), Scottish Charity No SC021197.
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