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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Ok,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">So got it working now by omitting the D <- as.matrix(X) step and running the hclust only from the D <- dist(X)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">M<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Thibaut Jombart [mailto:thibautjombart@gmail.com]
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<b>Sent:</b> 05 August 2016 10:41<br>
<b>To:</b> Mark Coulson <Mark.Coulson.ic@uhi.ac.uk><br>
<b>Cc:</b> adegenet-forum@lists.r-forge.r-project.org<br>
<b>Subject:</b> Re: [adegenet-forum] error in hclust<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Odd indeed. Are there any NAs in 'X'?<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Cheers<o:p></o:p></p>
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<p class="MsoNormal">Thibaut<o:p></o:p></p>
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--<br>
Dr Thibaut Jombart<br>
Lecturer, Department of Infectious Disease Epidemiology<o:p></o:p></p>
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<p class="MsoNormal">Imperial College London<br>
<a href="https://sites.google.com/site/thibautjombart/" target="_blank">https://sites.google.com/site/thibautjombart/</a><o:p></o:p></p>
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<p class="MsoNormal"><a href="https://github.com/thibautjombart" target="_blank">https://github.com/thibautjombart<br>
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<p class="MsoNormal">Twitter: <a href="https://twitter.com/TeebzR" target="_blank">
@TeebzR</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On 5 August 2016 at 10:34, Mark Coulson <<a href="mailto:Mark.Coulson.ic@uhi.ac.uk" target="_blank">Mark.Coulson.ic@uhi.ac.uk</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hello,<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">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<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">laidon <- import2genind("laidon_project_data_no_sibs.str")<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">X <- tab(laidon, freq=TRUE, NA.method="mean")
<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">D <- dist(X)<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">D <- as.matrix(D)<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">h1 <- hclust(D, method="complete")<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<span style="font-size:10.0pt;font-family:"Lucida Console";color:#C5060B">Error in if (<a href="http://is.na" target="_blank">is.na</a>(n) || n > 65536L) stop("size cannot be NA nor exceed 65536") :
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;line-height:11.25pt;background:white;word-break:break-all">
<span style="font-size:10.0pt;font-family:"Lucida Console";color:#C5060B"> missing value where TRUE/FALSE needed</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Not sure what this error means but more confused as to why suddenly it isn’t working. Nothing else has changed<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Mark<o:p></o:p></p>
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<p class="MsoNormal">Inverness College UHI, a partner in the University of the Highlands and Islands
<a href="http://www.inverness.uhi.ac.uk" target="_blank">www.inverness.uhi.ac.uk</a> Board of Management of Inverness College (known as Inverness College UHI), Scottish Charity No SC021197.
<o:p></o:p></p>
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_______________________________________________<br>
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<p class="MsoNormal"><o:p> </o:p></p>
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Inverness College UHI, a partner in the University of the Highlands and Islands www.inverness.uhi.ac.uk Board of Management of Inverness College (known as Inverness College UHI), Scottish Charity No SC021197.
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