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<p>Thank you for your help, Roman,</p>
<p><br>
</p>
<p>By asking me to provide an example you made me realize something. I tried again this morning, with exactly the same commands, and could not reproduce the issue. This is weird. It is not the first time it happens though, i.e. getting unexpected behavior in
R which I could not replicate after rebooting. I have no idea what the cause could be. Some of the packages I had loaded yesterday (apart from Adegenet) were not loaded today. I guess I'll have to be even more paranoid and check that each step of my analysis
does what is supposed to be doing. <br>
</p>
<p><br>
</p>
<p>Cheers,</p>
<p>Max<br>
</p>
<p><br>
</p>
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<div style="font-family:Tahoma; font-size:13px">Massimiliano S. Tagliamonte</div>
<div style="font-family:Tahoma; font-size:13px">Graduate Student</div>
<div style="font-family:Tahoma; font-size:13px">University of Florida<br>
College of Veterinary Medicine</div>
<div style="font-family:Tahoma; font-size:13px">Department of Infectious Diseases and Pathology<br>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" color="#000000" face="Calibri, sans-serif"><b>From:</b> Roman Luštrik <roman.lustrik@biolitika.si><br>
<b>Sent:</b> Tuesday, January 3, 2017 5:44 PM<br>
<b>To:</b> Tagliamonte,Massimiliano S<br>
<b>Cc:</b> adegenet-forum@lists.r-forge.r-project.org<br>
<b>Subject:</b> Re: [adegenet-forum] df2genind function unexpected behavior</font>
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<div>Can you provide a reproducible example?</div>
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<div>FWIW, you can use accessor functions like `tab(genind_obj)` or access the other slot through `other(genind_obj)`, e.g.</div>
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</div>
<div>library(adegenet)<br>
<br>
data(nancycats)<br>
<br>
other(nancycats)$xy</div>
<div><br>
</div>
<div>or assigning things </div>
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<div><span style="color:#000000; font-family:'trebuchet ms',sans-serif; font-size:16px; font-style:normal; font-weight:normal; letter-spacing:normal; orphans:2; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:2; word-spacing:0px; background-color:#ffffff; display:inline!important; float:none">other(nancycats)$xy
<- xy_object</span></div>
<div><br>
</div>
<div>To access genotypes, you can use </div>
<div><br>
tab(nancycats)</div>
<div><br>
</div>
<div><br>
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<div>Cheers,</div>
<div>Roman</div>
<div><br>
</div>
<div>----<br>
In god we trust, all others bring data.</div>
<br>
<hr id="zwchr">
<div><b>From: </b>"Tagliamonte,Massimiliano S" <mstagliamonte@ufl.edu><br>
<b>To: </b>"adegenet-forum@lists.r-forge.r-project.org" <adegenet-forum@r-forge.wu-wien.ac.at><br>
<b>Sent: </b>Tuesday, January 3, 2017 10:36:20 PM<br>
<b>Subject: </b>Re: [adegenet-forum] df2genind function unexpected behavior<br>
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<p>Update:</p>
<p>OK, I have replaced the dots (".") in the names with "_", now the order of the isolates is maintained. I'll have to keep in mind this behavior. I guess it's a bad idea to introduce special characters in my data in R.</p>
<p><br>
</p>
<p>Sincerely,</p>
<p><br>
</p>
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<div style="font-family:Tahoma; font-size:13px">
<div style="font-family:Tahoma; font-size:13px">
<div style="font-family:Tahoma; font-size:13px">Massimiliano S. Tagliamonte</div>
<div style="font-family:Tahoma; font-size:13px">Graduate Student</div>
<div style="font-family:Tahoma; font-size:13px">University of Florida<br>
College of Veterinary Medicine</div>
<div style="font-family:Tahoma; font-size:13px">Department of Infectious Diseases and Pathology<br>
<br>
</div>
</div>
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