<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=us-ascii"><meta name=Generator content="Microsoft Word 14 (filtered medium)"><style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
@font-face
{font-family:"Antique Olive";
panose-1:0 0 0 0 0 0 0 0 0 0;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri","sans-serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal;
font-family:"Calibri","sans-serif";
color:windowtext;}
span.EmailStyle18
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='color:#1F497D'>Dear,<o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='color:#1F497D'>The problem does not seem to be related to my commands, since I do get results for subsets of my data (1000 individuals takes 40 seconds), but it does not seem to work for my entire dataset of >25000 individuals (should theoretically take 16.6 minutes, but after 4 hours still no result) … any suggestions? <o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'><br>many thanks in advance<o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='color:#1F497D'>evert<o:p></o:p></span></p><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> adegenet-forum-bounces@r-forge.wu-wien.ac.at [mailto:adegenet-forum-bounces@r-forge.wu-wien.ac.at] <b>On Behalf Of </b>Thomas, Evert (Bioversity-Colombia)<br><b>Sent:</b> Friday, July 01, 2011 1:56 PM<br><b>To:</b> adegenet-forum@r-forge.wu-wien.ac.at<br><b>Subject:</b> [adegenet-forum] dataset too large?<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><span style='color:black'>Dear colleagues,<o:p></o:p></span></p><p class=MsoNormal><span style='color:black'><o:p> </o:p></span></p><p class=MsoNormal><span style='color:black'>I am new to R so apologies for my ignorance, but I have a couple of questions: <o:p></o:p></span></p><p class=MsoNormal><span style='color:black'><o:p> </o:p></span></p><p class=MsoNormal><span style='color:black'>I am trying to use adegenet (on a 64bit system, windows7) for analyzing a SSR dataset. It consists 96 loci and I have >25000 individuals (after resampling). I have loaded the database as a dataframe in R, but am not able to convert to genind format (PC physical memory becomes saturated, while only 10% of CPU is used) . Could this be related to the size of my dataset? Any suggestions?<o:p></o:p></span></p><p class=MsoNormal><span style='color:black'> <o:p></o:p></span></p><p class=MsoNormal><span style='color:black'>On another note: Alternatively, I tried importing my data to genind object from the corresponding file in Structure format. However, my version of Structure (2.3.3.) does not seem to generate .stru or .str files, any solution there?<o:p></o:p></span></p><p class=MsoNormal><span style='color:black'> <o:p></o:p></span></p><p class=MsoNormal><span style='color:black'>And a last point: I am unable to install/load the R application multicore because it is not among the packages list…<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>This is what I have done:<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>I did a read.csv with “header=T”, and then rownames<-cacaoCSV[,1]<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>The problems occurs with the following command<o:p></o:p></p><p class=MsoNormal>cacao<-df2genind(cacaoCSV, sep="/",ind.names=NULL, loc.names=NULL, pop=cacaoCSV[,2], missing=NA, ploidy=2, type="codom")<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Many thanks in advance for any advice or suggestion you might have!<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal style='margin-bottom:12.0pt'>Enjoy the weekend<o:p></o:p></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Antique Olive","serif";color:black'>Evert Thomas,</span><i><span style='font-family:"Antique Olive","serif";color:black'> PhD<o:p></o:p></span></i></p><p class=MsoNormal><i><span style='font-size:10.0pt;font-family:"Antique Olive","serif";color:#0070C0'>Associate Expert, Conservation and Use of </span></i><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'><o:p></o:p></span></p><p class=MsoNormal><i><span style='font-size:10.0pt;font-family:"Antique Olive","serif";color:#0070C0'>Forest Genetic Resources in Latin America</span></i><span style='font-size:10.0pt;font-family:"Antique Olive","serif";color:black'><o:p></o:p></span></p><p class=MsoNormal style='text-align:justify'><span style='font-size:10.0pt;color:black'> </span><span style='font-size:10.0pt;font-family:"Times New Roman","serif";color:black'><o:p></o:p></span></p><p class=MsoNormal style='text-align:justify'><b><span lang=EN-GB style='font-size:10.0pt;font-family:"Antique Olive","serif";color:#009900'>Bioversity International<o:p></o:p></span></b></p><p class=MsoNormal style='text-align:justify'><span lang=EN-GB style='font-size:10.0pt;font-family:"Antique Olive","serif";color:black'>Regional Office for the Americas<o:p></o:p></span></p><p class=MsoNormal style='text-align:justify'><span lang=IT style='font-size:10.0pt;font-family:"Antique Olive","serif";color:black'>Recta Cali-Palmira Km 17 – CIAT<o:p></o:p></span></p><p class=MsoNormal style='text-align:justify'><span lang=IT style='font-size:10.0pt;font-family:"Antique Olive","serif";color:black'>Cali, Colombia<o:p></o:p></span></p><p class=MsoNormal style='text-align:justify'><span style='font-size:10.0pt;font-family:"Antique Olive","serif";color:black'>P.O. Box 6713<o:p></o:p></span></p><p class=MsoNormal style='text-align:justify'><span lang=EN-GB style='font-size:10.0pt;font-family:"Antique Olive","serif";color:black'><o:p> </o:p></span></p><p class=MsoNormal style='text-align:justify'><b><span lang=EN-GB style='font-size:10.0pt;font-family:"Antique Olive","serif";color:black'>Tel</span></b><span lang=EN-GB style='font-size:10.0pt;font-family:"Antique Olive","serif";color:black'>. 57 2 4450048 / 49 Ext 113</span><span style='font-size:10.0pt;font-family:"Antique Olive","serif";color:black'><o:p></o:p></span></p><p class=MsoNormal style='text-align:justify'><b><span lang=FR style='font-size:10.0pt;font-family:"Antique Olive","serif";color:black'>Fax</span></b><span lang=FR style='font-size:10.0pt;font-family:"Antique Olive","serif";color:black'> 57 2 4450096<o:p></o:p></span></p><p class=MsoNormal><b><span lang=FR style='font-size:10.0pt;font-family:"Antique Olive","serif";color:black'>Email</span></b><span lang=FR style='font-size:10.0pt;font-family:"Antique Olive","serif";color:black'>: <a href="mailto:e.thomas@cgiar.org" title="mailto:e.thomas@cgiar.org">e.thomas@cgiar.org</a></span><u><span lang=FR style='font-size:10.0pt;font-family:"Antique Olive","serif";color:green'><o:p></o:p></span></u></p><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Antique Olive","serif";color:black'>Skype</span></b><span style='font-size:10.0pt;font-family:"Antique Olive","serif";color:black'>: evertthomas</span><span lang=FR style='font-size:10.0pt;font-family:"Antique Olive","serif";color:black'><o:p></o:p></span></p><p class=MsoNormal><u><span lang=EN-GB style='font-size:10.0pt;font-family:"Antique Olive","serif";color:green'><a href="blocked::http://www.bioversityinternational.org/" title="blocked::http://www.bioversityinternational.org/ http://www.bioversityinternational.org/">www.bioversityinternational.org</a><o:p></o:p></span></u></p><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'><o:p> </o:p></span></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>