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<div><font size="2">Hi Robert, <br>
<br>
thanks for sharing this!<br>
<br>
Best<br>
Thibaut<br>
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<div style="direction: ltr;" id="divRpF108956"><font color="#000000" face="Tahoma" size="2"><b>From:</b> adegenet-forum-bounces@lists.r-forge.r-project.org [adegenet-forum-bounces@lists.r-forge.r-project.org] on behalf of Robert Fairweather [osue37@bangor.ac.uk]<br>
<b>Sent:</b> 09 October 2015 16:32<br>
<b>To:</b> adegenet-forum@lists.r-forge.r-project.org<br>
<b>Subject:</b> Re: [adegenet-forum] Converting between adegenet and genetics<br>
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<p class="MsoNormal"><span style="color:#2E74B5">Hi Thibaut, and for future users,</span></p>
<p class="MsoNormal"><span style="color:#2E74B5">I have found that the package poppr, which is highly compatable with adegenet, has a useful function for saving genind objects as csv files in genalex format. Genalex format can be converted to genepop and structure
format at the flick of a swtich with the free GenAlex add on in Excel, and this add on has several handy features of it’s own.</span></p>
<p class="MsoNormal"><span style="color:#2E74B5">Of course Thibaut is right, and R is a highly universal and wonderfully flexible program, but hopefully this info will help others to move outside of R if they need or prefer to.
</span></p>
<p class="MsoNormal"><span style="color:#2E74B5">Many thanks again for your help,</span></p>
<p class="MsoNormal"><span style="color:#2E74B5">Robert</span></p>
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<p class="MsoNormal"><b><span lang="EN-US">From:</span></b><span lang="EN-US"> Jombart, Thibaut [mailto:t.jombart@imperial.ac.uk]
<br>
<b>Sent:</b> 09 October 2015 16:24<br>
<b>To:</b> Robert Fairweather <osue37@bangor.ac.uk>; adegenet-forum@lists.r-forge.r-project.org<br>
<b>Subject:</b> RE: Converting between adegenet and genetics</span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Tahoma",sans-serif; color:black">Hi there, </span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Courier New"; color:black">genind2df
</span><span style="font-size:10.0pt; font-family:"Tahoma",sans-serif; color:black">will be helpful for recoding the data as allele, but then there will still be a way to go to export data for Genepop. As our purpose deveioping packages in R is to make R a
single (free) platform for data analysis, I'd expect exporting data to other software is not going to be a priority for most developers.<br>
<br>
Cheers</span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:10.0pt; font-family:"Tahoma",sans-serif; color:black">Thibaut</span></p>
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<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"> Robert Fairweather [osue37@bangor.ac.uk]<br>
<b>Sent:</b> 09 October 2015 15:02<br>
<b>To:</b> Jombart, Thibaut<br>
<b>Subject:</b> RE: Converting between adegenet and genetics</span><span style="font-size:12.0pt; font-family:"Times New Roman",serif; color:black"></span></p>
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<p class="MsoNormal"><span style="color:#1F497D">Dear Thibaut,</span><span style="color:black"></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Many thanks for your response. Specifically I am trying to convert my genind object into genepop format so that I can use genetics to export it as a .gen file in said format. I have been getting the impression
that support for genetics is waning across the board, and so am looking into alternative packages that may be able to save genepops and which adegenet can export to. Please do let me know if you know any. My data is co-dominant SNP data, originally imported
into adegenet as a .gen file.</span><span style="color:black"></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Cheers,</span><span style="color:black"></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Robert</span><span style="color:black"></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> </span><span style="color:black"></span></p>
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<p class="MsoNormal"><b><span style="color:black" lang="EN-US">From:</span></b><span style="color:black" lang="EN-US"> Jombart, Thibaut [<a href="mailto:t.jombart@imperial.ac.uk" target="_blank">mailto:t.jombart@imperial.ac.uk</a>]
<br>
<b>Sent:</b> 09 October 2015 14:56<br>
<b>To:</b> Robert Fairweather <<a href="mailto:osue37@bangor.ac.uk" target="_blank">osue37@bangor.ac.uk</a>>;
<a href="mailto:adegenet-forum@lists.r-forge.r-project.org" target="_blank">adegenet-forum@lists.r-forge.r-project.org</a><br>
<b>Subject:</b> RE: Converting between adegenet and genetics</span><span style="color:black"></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Tahoma",sans-serif; color:black">Dear Robert,
</span><span style="color:black"></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Tahoma",sans-serif; color:black">as of version 2.0.0, adegenet is no longer interfaced with the package genetics, but is meant to work with a number of others: hierfstat, pegas, poppr, ape, etc.
I believe most functionalities implemented in genetics are implemented elsewhere, but please let me know if something is missing.</span><span style="color:black"></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Tahoma",sans-serif; color:black">Cheers</span><span style="color:black"></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Tahoma",sans-serif; color:black">Thibaut</span><span style="color:black"></span></p>
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<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" target="_blank">
adegenet-forum-bounces@lists.r-forge.r-project.org</a> [adegenet-forum-bounces@lists.r-forge.r-project.org] on behalf of Robert Fairweather [osue37@bangor.ac.uk]<br>
<b>Sent:</b> 09 October 2015 14:46<br>
<b>To:</b> <a href="mailto:adegenet-forum@lists.r-forge.r-project.org" target="_blank">
adegenet-forum@lists.r-forge.r-project.org</a><br>
<b>Subject:</b> [adegenet-forum] Converting between adegenet and genetics</span><span style="color:black"></span></p>
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<p class="MsoNormal"><span style="color:black">Dear Thibaut,</span></p>
<p class="MsoNormal"><span style="color:black">I am trying to export a genind object from adegenet to genetics package format so that I can use functions in that package not available in adegenet. The adegenet homepage suggests that this is possible, but I
cannot find anything in the instruction pdf detailing the appropriate function(s). An earlier post suggests the function genind2genotype, but this does not exist in the manual and cannot be found in the version of adegenet that I am using (2.0.0).</span></p>
<p class="MsoNormal"><span style="color:black">How can I export my genind object into genetics?</span></p>
<p class="MsoNormal"><span style="color:black">Best wishes,</span></p>
<p class="MsoNormal"><span style="color:black">Robert</span></p>
<p class="MsoNormal"><span style="color:black"> </span></p>
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