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</o:shapelayout></xml><![endif]--></head><body lang=EN-GB link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='color:#1F497D'>This work well. Thank you. <o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> Jombart, Thibaut [mailto:t.jombart@imperial.ac.uk] <br><b>Sent:</b> 15 July 2015 16:33<br><b>To:</b> LAWAL RAMAN; adegenet-forum@lists.r-forge.r-project.org<br><b>Subject:</b> RE: NA.REPLACE<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'><o:p> </o:p></span></p><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'>Hi there, <br><br>yes, na.replace has been removed in adegenet 2.0.0. <br><br>Instead, you can use:<br>tab(x, NA.method="mean")<br><br>where 'x' is your genind. If you want frequencies, you will need to add 'freq=TRUE'. See ?tab, and the basics tutorial for more info on data handling:<br><a href="https://github.com/thibautjombart/adegenet/wiki/Tutorials" target="_blank">https://github.com/thibautjombart/adegenet/wiki/Tutorials</a><br><br>Cheers<br>Thibaut<o:p></o:p></span></p><div><div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'><o:p> </o:p></span></p></div></div></div></div><div><div class=MsoNormal align=center style='text-align:center'><span style='font-size:12.0pt;font-family:"Times New Roman","serif";color:black'><hr size=2 width="100%" align=center></span></div><div id=divRpF376537><p class=MsoNormal style='margin-bottom:12.0pt'><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'> <a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a> [adegenet-forum-bounces@lists.r-forge.r-project.org] on behalf of Raman Lawal [plxral@nottingham.ac.uk]<br><b>Sent:</b> 15 July 2015 15:08<br><b>To:</b> <a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a><br><b>Subject:</b> [adegenet-forum] NA.REPLACE</span><span style='font-size:12.0pt;font-family:"Times New Roman","serif";color:black'><o:p></o:p></span></p></div><div><div><p class=MsoNormal><span class=apple-converted-space><span style='font-size:10.5pt;font-family:"Helvetica","sans-serif";color:black;background:white'>I have tried to prepare all necessary files but wanted to remove the NA using the na.replace option of the ade4 as seen in command below. When I ran </span></span><span style='color:black'>test<- na.replace(genind_ABCDEFGH,"mean", quiet=FALSE), I get “Error: could not find function "na.replace". I am not certainly sure what I was doing wrong. Could you please advise me on what to do.<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'>library(adegenet)<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'>datan<- as.numeric(data4)<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'>pop<-data4@phdata$pop<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'>genind_ABCDEFGH<-as.genind(datan,pop)<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'>rm(data4)<o:p></o:p></span></p><p class=MsoNormal><span style='color:black'>rm(datan)<o:p></o:p></span></p><p class=MsoNormal><span style='color:black'>#rm(pop)<o:p></o:p></span></p><p class=MsoNormal><span style='color:black'>library(ade4)<o:p></o:p></span></p><p class=MsoNormal><span style='color:black'>## Replacing NAs<o:p></o:p></span></p><p class=MsoNormal><span style='color:black'>test<- na.replace(genind_ABCDEFGH,"mean", quiet=FALSE)<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'> LAWAL<o:p></o:p></span></p></div><pre><span style='color:black'>This message and any attachment are intended solely for the addressee<o:p></o:p></span></pre><pre><span style='color:black'>and may contain confidential information. If you have received this<o:p></o:p></span></pre><pre><span style='color:black'>message in error, please send it back to me, and immediately delete it. <o:p></o:p></span></pre><pre><span style='color:black'><o:p> </o:p></span></pre><pre><span style='color:black'>Please do not use, copy or disclose the information contained in this<o:p></o:p></span></pre><pre><span style='color:black'>message or in any attachment. Any views or opinions expressed by the<o:p></o:p></span></pre><pre><span style='color:black'>author of this email do not necessarily reflect the views of the<o:p></o:p></span></pre><pre><span style='color:black'>University of Nottingham.<o:p></o:p></span></pre><pre><span style='color:black'><o:p> </o:p></span></pre><pre><span style='color:black'>This message has been checked for viruses but the contents of an<o:p></o:p></span></pre><pre><span style='color:black'>attachment may still contain software viruses which could damage your<o:p></o:p></span></pre><pre><span style='color:black'>computer system, you are advised to perform your own checks. Email<o:p></o:p></span></pre><pre><span style='color:black'>communications with the University of Nottingham may be monitored as<o:p></o:p></span></pre><pre><span style='color:black'>permitted by UK legislation.<o:p></o:p></span></pre></div></div></div></div><PRE>
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