[adegenet-forum] error in hclust

[Roman Luštrik]

Hi, 

it would be great if you could whip up a small reproducible example (you could consider creating a gist at e.g. gist.github.com) which demonstrates this problem. Without the data and code in hand, it's really all just speculation. 

Cheers, 
Roman 

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


From: "Mark Coulson" <Mark.Coulson.ic at uhi.ac.uk> 
To: "Roman Luštrik" <roman.lustrik at biolitika.si> 
Cc: "Thibaut Jombart" <thibautjombart at gmail.com>, adegenet-forum at lists.r-forge.r-project.org 
Sent: Friday, August 5, 2016 11:54:30 AM 
Subject: RE: [adegenet-forum] error in hclust 



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 > 
To: "Thibaut Jombart" < thibautjombart at gmail.com > 
Cc: 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 > 
Cc: 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 





On 5 August 2016 at 10:34, Mark Coulson < 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 (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 Board of Management of Inverness College (known as Inverness College UHI), Scottish Charity No SC021197. 



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