<div dir="ltr">Dear Michael, <div><br></div><div>good point. I'll fix this tomorrow. I have posted an issue from your post:</div><div><br></div><div><a href="https://github.com/thibautjombart/adegenet/issues/143">https://github.com/thibautjombart/adegenet/issues/143</a><br></div><div><br></div><div>Follow it to track progress.</div><div><br></div><div>Best</div><div>Thibaut</div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div><div><br>--<br>Dr Thibaut Jombart<br>Lecturer, Department of Infectious Disease Epidemiology<br></div></div>Imperial College London<br><a href="https://sites.google.com/site/thibautjombart/" target="_blank">https://sites.google.com/site/thibautjombart/</a><br></div><div><a href="https://github.com/thibautjombart" target="_blank">https://github.com/thibautjombart<br></a></div>Twitter: <a href="https://twitter.com/TeebzR" target="_blank">@TeebzR</a><br></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On 3 June 2016 at 15:44, michael fontaine <span dir="ltr"><<a href="mailto:mikafontaine@gmail.com" target="_blank">mikafontaine@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Dear all,<div><br></div><div>The function na.replace seems to have disappear from the last version of ADEGENET 2.0.1.</div><div><br></div><div>Now, one can use scaleGen()  or tab() to replace missing data by the “mean”, for example. However the returned object is a frequency table. It seems that the spca() function does not accept frequencies since adegenet 2.0.0.  What is the recommended procedure to replace missing data by the mean and conduct a sPCA? </div><div><br></div><div>Furthermore, I am using the jitter function to put some noise around my coordinates. It worked very well in the former version. In this new version, the sPCA tells me that it has found duplicates. I have checked the coordinates with noise, and there are none. Not sure what’s going on.</div><div><br></div><div>Is there any similar report from other user?</div><div><br></div><div>I am looking forward you advices.</div><div><br></div><div>Thanks in advance </div><div><br></div><div>Michael</div><div><div>
<span style="border-collapse:separate;text-align:-webkit-auto;text-indent:0px;border-spacing:0px"><span style="border-collapse:separate;text-align:-webkit-auto;text-indent:0px;border-spacing:0px"><span style="border-collapse:separate;text-align:-webkit-auto;text-indent:0px;border-spacing:0px"><span style="border-collapse:separate;text-align:-webkit-auto;text-indent:0px;border-spacing:0px"><span style="border-collapse:separate;text-align:-webkit-auto;text-indent:0px;border-spacing:0px"><span style="border-collapse:separate;text-align:-webkit-auto;text-indent:0px;border-spacing:0px"><span style="border-collapse:separate;text-align:-webkit-auto;text-indent:0px;border-spacing:0px"><span style="border-collapse:separate;text-align:-webkit-auto;text-indent:0px;border-spacing:0px"><span style="border-collapse:separate;text-align:-webkit-auto;text-indent:0px;border-spacing:0px"><span style="border-collapse:separate;text-align:-webkit-auto;text-indent:0px;border-spacing:0px"><span style="border-collapse:separate;text-align:-webkit-auto;text-indent:0px;border-spacing:0px"><font face="'Lucida Grande'"><span style="background-color:transparent"><span style="text-align:-webkit-auto;text-indent:0px"><div style="word-wrap:break-word"><span style="text-indent:0px"><div style="word-wrap:break-word"><span style="text-indent:0px"><div style="word-wrap:break-word"><span style="text-indent:0px"><div style="word-wrap:break-word"><span style="text-indent:0px"><div style="word-wrap:break-word"><span style="text-indent:0px"><div style="word-wrap:break-word"><span style="text-indent:0px"><div style="word-wrap:break-word"><span style="text-indent:0px"><div style="word-wrap:break-word"><span style="text-indent:0px"><div style="word-wrap:break-word"><span style="text-indent:0px"><div style="word-wrap:break-word"><span style="text-indent:0px"><div style="word-wrap:break-word"><span style="text-indent:0px"><div style="word-wrap:break-word"><span style="text-indent:0px"><div style="word-wrap:break-word"><font><span style="text-indent:0px"><span style="text-indent:0px"><div style="word-wrap:break-word"><span style="text-indent:0px"><div style="word-wrap:break-word"><span style="text-indent:0px"><div style="word-wrap:break-word"><span style="text-indent:0px"><div style="word-wrap:break-word"><span style="text-indent:0px"><div style="word-wrap:break-word"><span style="text-indent:0px"><div style="word-wrap:break-word"><span style="text-indent:0px"><div style="word-wrap:break-word"><span style="text-indent:0px"><div style="word-wrap:break-word"><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:13px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-transform:none;white-space:normal;word-spacing:0px;border-collapse:separate;border-spacing:0px"><span style="text-align:-webkit-auto">--</span></div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:13px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-transform:none;white-space:normal;word-spacing:0px;border-collapse:separate;border-spacing:0px"><br></div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:13px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-transform:none;white-space:normal;word-spacing:0px;border-collapse:separate;border-spacing:0px"><font color="#1e39f6">><((((º>`·.¸¸.·´¯`·.¸.·´¯`·...¸><((((º>¸.<br>`·.¸¸.·´¯`·.¸¸·´¯`·.. ><((((º>`·.¸¸.·´¯`·.¸.·´¯`·...¸><((((º></font></div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:13px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-transform:none;white-space:normal;word-spacing:0px;border-collapse:separate;border-spacing:0px"><br></div><div style="border-collapse:separate;border-spacing:0px"><font color="#1e39f6" size="2">Groningen Institute for Evolutionary Life Sciences (GELIFES)<br>University of Groningen<br>Nijenborgh 7<br>9747 AG Groningen<br>The Netherlands</font></div><div style="border-collapse:separate;border-spacing:0px"><font color="#1e39f6" size="2"><br></font></div><div style="border-collapse:separate;border-spacing:0px"><font color="#1e39f6" size="2">Office phone: <a href="tel:%28%2B31%29%20%280%2950%20363%202146" value="+31503632146" target="_blank">(+31) (0)50 363 2146</a><br></font><span style="color:rgb(30,57,246);font-size:small;text-align:-webkit-auto">Email: <a href="mailto:m.c.fontaine@rug.nl" target="_blank">m.c.fontaine@rug.nl</a></span><br></div><div style="border-collapse:separate;border-spacing:0px"><a href="http://scholar.google.com/citations?hl=en&user=rvFE0t4AAAAJ&sortby=pubdate&view_op=list_works&pagesize=100" target="_blank">Google scholar profile</a><font color="#1e39f6" size="2"><br>Researcher-ID (G-5350-2011)</font></div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:13px;font-style:normal;font-variant:normal;font-weight:normal;letter-sp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