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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi,<br>
<br>
Thanks. I have corrected readFLindicesVPA, and tested it with 3 different files. Could you please reinstall FLCore from the repository and confirm it is working fine?<br>
<br>
Thanks,<br>
<br>
<br>
Iago<br>
<div><br>
<div style="font-family:Tahoma; font-size:13px">
<div style="font-family:Tahoma; font-size:13px"><font face="Courier New"><br>
-- <br>
Dr Iago Mosqueira<br>
<br>
European Commission<br>
DG Joint Research Centre<br>
Directorate D - Sustainable Resources <br>
Unit D.02 Water and Marine Resources<br>
<br>
TP 051, Via Enrico Fermi 2749<br>
I-21027 Ispra (VA), Italy<br>
<br>
Phone : +39 0332 785413<br>
<br>
iago.mosqueira@ec.europa.eu</font></div>
</div>
</div>
<div style="font-family: Times New Roman; color: #000000; font-size: 16px">
<hr tabindex="-1">
<div id="divRpF474464" style="direction: ltr;"><font size="2" face="Tahoma" color="#000000"><b>From:</b> flr-list-bounces@lists.r-forge.r-project.org [flr-list-bounces@lists.r-forge.r-project.org] on behalf of Alessandro Orio [alessandro.orio@slu.se]<br>
<b>Sent:</b> 21 February 2018 08:36<br>
<b>To:</b> flr-list@flr-project.org<br>
<b>Subject:</b> Re: [FLR-list] help with bubble plot<br>
</font><br>
</div>
<div></div>
<div>
<div class="WordSection1">
<p class="MsoNormal"><span style="font-size:11.0pt; font-family:"Arial",sans-serif; color:#44546A">Hi,</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt; font-family:"Arial",sans-serif; color:#44546A"> </span></p>
<p class="MsoNormal"><span style="font-size:11.0pt; font-family:"Arial",sans-serif; color:#44546A" lang="EN-GB">Here are two files.</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt; font-family:"Arial",sans-serif; color:#44546A" lang="EN-GB"> </span></p>
<p class="MsoNormal"><span style="font-size:11.0pt; font-family:"Arial",sans-serif; color:#44546A" lang="EN-GB">Cheers,</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt; font-family:"Arial",sans-serif; color:#44546A" lang="EN-GB"> </span></p>
<p class="MsoNormal"><span style="font-size:11.0pt; font-family:"Arial",sans-serif; color:#44546A">Ale</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt; font-family:"Arial",sans-serif; color:#44546A"> </span></p>
<div>
<div style="border:none; border-top:solid #E1E1E1 1.0pt; padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span style="font-size:11.0pt; font-family:"Calibri",sans-serif" lang="EN-US">From:</span></b><span style="font-size:11.0pt; font-family:"Calibri",sans-serif" lang="EN-US"> flr-list-bounces@lists.r-forge.r-project.org [mailto:flr-list-bounces@lists.r-forge.r-project.org]
<b>On Behalf Of </b>Iago Mosqueira<br>
<b>Sent:</b> 20 February 2018 18:06<br>
<b>To:</b> flr-list@flr-project.org<br>
<b>Subject:</b> Re: [FLR-list] help with bubble plot</span></p>
</div>
</div>
<p class="MsoNormal"> </p>
<div>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Verdana",sans-serif">Weird, apologies. Could you please send me the files you are using?<br>
<br>
<br>
Iago<br>
---<br>
Sent from mobile</span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"> </span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"><br>
---- On Tue, 20 Feb 2018 16:58:18 +0100 <b><a href="mailto:alessandro.orio@slu.se" target="_blank">alessandro.orio@slu.se</a>
</b>wrote ----<br>
<br>
<br>
</span></p>
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<p class="MsoNormal" style=""><span style="font-size:11.0pt; font-family:"Arial",sans-serif; color:#44546A">Hi Iago,</span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
<p class="MsoNormal" style=""><span style="font-size:11.0pt; font-family:"Arial",sans-serif; color:#44546A"> </span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
<p class="MsoNormal" style=""><span style="font-size:11.0pt; font-family:"Arial",sans-serif; color:#44546A">Sorry to bother you again. It seems the plots are now working but now readFLIndex and readFLIndices are not working anymore. I have tried with different
tuning files. With and without NAs and I always get this error.</span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
<p class="MsoNormal" style=""><span style="font-size:11.0pt; font-family:"Arial",sans-serif; color:#44546A"> </span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt; font-family:"Lucida Console"; color:#C5060B">Error in
<a href="mailto:x@.Data[[match(i" target="_blank">x@.Data[[match(i</a>, names(x))]] <- value :
</span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt; font-family:"Lucida Console"; color:#C5060B"> attempt to select less than one element in integerOneIndex</span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
<p class="MsoNormal" style=""><span style="font-size:11.0pt; font-family:"Arial",sans-serif; color:#44546A"> </span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
<p class="MsoNormal" style=""><span style="font-size:11.0pt; font-family:"Arial",sans-serif; color:#44546A">Sorry,</span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
<p class="MsoNormal" style=""><span style="font-size:11.0pt; font-family:"Arial",sans-serif; color:#44546A"> </span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
<p class="MsoNormal" style=""><span style="font-size:11.0pt; font-family:"Arial",sans-serif; color:#44546A">Ale</span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
<p class="MsoNormal" style=""><span style="font-size:11.0pt; font-family:"Arial",sans-serif; color:#44546A"> </span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
<div>
<div style="border:none; border-top:solid #E1E1E1 1.0pt; padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal" style=""><b><span style="font-size:11.0pt; font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt; font-family:"Calibri",sans-serif">
<a href="mailto:flr-list-bounces@lists.r-forge.r-project.org" target="_blank">flr-list-bounces@lists.r-forge.r-project.org</a> [mailto:<a href="mailto:flr-list-bounces@lists.r-forge.r-project.org" target="_blank">flr-list-bounces@lists.r-forge.r-project.org</a>]
<b>On Behalf Of </b>Iago Mosqueira<br>
<b>Sent:</b> 20 February 2018 15:25<br>
<b>To:</b> flr-list <<a href="mailto:flr-list@flr-project.org" target="_blank">flr-list@flr-project.org</a>><br>
<b>Subject:</b> Re: [FLR-list] help with bubble plot</span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
</div>
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<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"> </span></p>
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<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Verdana",sans-serif">Hi,</span></p>
</div>
<div>
<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"> </span></p>
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<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Verdana",sans-serif">FLCore 2.6.6 is now in the repository, and bubbles appears to work again. Only available in Windows for R 3.4</span></p>
</div>
<div>
<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"> </span></p>
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<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Verdana",sans-serif">Best,</span></p>
</div>
<div>
<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"> </span></p>
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<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"> </span></p>
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<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Verdana",sans-serif">Iago</span></p>
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<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"> </span></p>
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<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Verdana",sans-serif">---- On Mon, 19 Feb 2018 17:23:03 +0100 <b>Mikaela Bergenius <<a href="mailto:mikaela.bergenius@slu.se" target="_blank">mikaela.bergenius@slu.se</a>></b> wrote ----</span></p>
</div>
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<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"> </span></p>
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<p class="MsoNormal" style=""><span style="font-size:11.0pt; font-family:"Arial",sans-serif; color:#44546A">Thanks heaps!!</span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
<p class="MsoNormal" style=""><span style="font-size:11.0pt; font-family:"Arial",sans-serif; color:#44546A"> </span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
<p class="MsoNormal" style=""><span style="font-size:11.0pt; font-family:"Arial",sans-serif; color:#44546A">Best, Mikaela</span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
<p class="MsoNormal" style=""><span style="font-size:11.0pt; font-family:"Arial",sans-serif; color:#44546A"> </span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
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<p class="MsoNormal" style=""><b><span style="font-size:11.0pt; font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt; font-family:"Calibri",sans-serif">
<a href="mailto:flr-list-bounces@lists.r-forge.r-project.org" target="_blank">flr-list-bounces@lists.r-forge.r-project.org</a> [mailto:<a href="mailto:flr-list-bounces@lists.r-forge.r-project.org" target="_blank">flr-list-bounces@lists.r-forge.r-project.org</a>]
<b>On Behalf Of </b>Alessandro Orio<br>
<b>Sent:</b> den 19 februari 2018 14:24<br>
<b>To:</b> <a href="mailto:flr-list@flr-project.org" target="_blank">flr-list@flr-project.org</a><br>
<b>Subject:</b> Re: [FLR-list] help with bubble plot</span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
</div>
</div>
<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"> </span></p>
<p class="MsoNormal" style=""><span style="font-size:11.0pt; font-family:"Arial",sans-serif; color:#44546A">Thanks to you!!</span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
<p class="MsoNormal" style=""><span style="font-size:11.0pt; font-family:"Arial",sans-serif; color:#44546A"> </span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
<p class="MsoNormal" style=""><span style="font-size:11.0pt; font-family:"Arial",sans-serif; color:#44546A">Cheers,</span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
<p class="MsoNormal" style=""><span style="font-size:11.0pt; font-family:"Arial",sans-serif; color:#44546A"> </span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
<p class="MsoNormal" style=""><span style="font-size:11.0pt; font-family:"Arial",sans-serif; color:#44546A">Ale</span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
<p class="MsoNormal" style=""><span style="font-size:11.0pt; font-family:"Arial",sans-serif; color:#44546A"> </span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
<div>
<div style="border:none; border-top:solid #E1E1E1 1.0pt; padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal" style=""><b><span style="font-size:11.0pt; font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt; font-family:"Calibri",sans-serif">
<a href="mailto:flr-list-bounces@lists.r-forge.r-project.org" target="_blank">flr-list-bounces@lists.r-forge.r-project.org</a> [<a href="mailto:flr-list-bounces@lists.r-forge.r-project.org" target="_blank">mailto:flr-list-bounces@lists.r-forge.r-project.org</a>]
<b>On Behalf Of </b>Iago Mosqueira<br>
<b>Sent:</b> 19 February 2018 13:22<br>
<b>To:</b> flr-list <<a href="mailto:flr-list@flr-project.org" target="_blank">flr-list@flr-project.org</a>><br>
<b>Subject:</b> Re: [FLR-list] help with bubble plot</span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
</div>
</div>
<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"> </span></p>
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<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Verdana",sans-serif">Hi,</span></p>
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<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"> </span></p>
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<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Verdana",sans-serif">I can replicate the problem now. The code in the development version of FLCore does not have this problem, although I cannot see why the changes lead to this.</span></p>
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<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"> </span></p>
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<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Verdana",sans-serif">I will update FLCore in the repository tomorrow to version 2.6.6.</span></p>
</div>
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<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"> </span></p>
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<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Verdana",sans-serif">Thanks,</span></p>
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<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"> </span></p>
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<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Verdana",sans-serif">Iago</span></p>
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<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Verdana",sans-serif">---- On Mon, 19 Feb 2018 10:27:06 +0100 <b>Alessandro Orio <<a href="mailto:alessandro.orio@slu.se" target="_blank">alessandro.orio@slu.se</a>></b> wrote ----</span></p>
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<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"> </span></p>
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<p class="MsoNormal" style=""><span style="font-size:11.0pt; font-family:"Arial",sans-serif; color:#44546A">Hi Iago,</span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
<p class="MsoNormal" style=""><span style="font-size:11.0pt; font-family:"Arial",sans-serif; color:#44546A"> </span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
<p class="MsoNormal" style=""><span style="font-size:11.0pt; font-family:"Arial",sans-serif; color:#44546A">I’m having the same exact problem and I’m working on the latest version of the package and on R 3.4.</span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
<p class="MsoNormal" style=""><span style="font-size:11.0pt; font-family:"Arial",sans-serif; color:#44546A"> </span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
<p class="MsoNormal" style=""><span style="font-size:11.0pt; font-family:"Arial",sans-serif; color:#44546A">This is the plot of the residuals of ple4…</span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
<p class="MsoNormal" style=""><span style="font-size:11.0pt; font-family:"Arial",sans-serif; color:#44546A"> </span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
<p class="MsoNormal" style=""><span style="font-size:11.0pt; font-family:"Arial",sans-serif; color:#44546A">Best,</span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
<p class="MsoNormal" style=""><span style="font-size:11.0pt; font-family:"Arial",sans-serif; color:#44546A"> </span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
<p class="MsoNormal" style=""><span style="font-size:11.0pt; font-family:"Arial",sans-serif; color:#44546A">Ale</span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
<p class="MsoNormal" style=""><span style="font-size:11.0pt; font-family:"Arial",sans-serif; color:#44546A"> </span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
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<p class="MsoNormal" style=""><b><span style="font-size:11.0pt; font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt; font-family:"Calibri",sans-serif">
<a href="mailto:flr-list-bounces@lists.r-forge.r-project.org" target="_blank">flr-list-bounces@lists.r-forge.r-project.org</a> [<a href="mailto:flr-list-bounces@lists.r-forge.r-project.org" target="_blank">mailto:flr-list-bounces@lists.r-forge.r-project.org</a>]
<b>On Behalf Of </b>Iago Mosqueira<br>
<b>Sent:</b> 17 February 2018 16:26<br>
<b>To:</b> flr-list <<a href="mailto:flr-list@flr-project.org" target="_blank">flr-list@flr-project.org</a>><br>
<b>Subject:</b> Re: [FLR-list] help with bubble plot</span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
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<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Verdana",sans-serif">Hi,</span></p>
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<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Verdana",sans-serif">I am testing it with the index.res obtained from running FLXSA on ple4 and ple4.indices, which also has some NAs, and I am getting no error</span></p>
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<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Verdana",sans-serif">library(FLXSA)</span></p>
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<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Verdana",sans-serif">data(ple4)</span></p>
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<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Verdana",sans-serif">data(ple4.indices)</span></p>
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<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Verdana",sans-serif">res <- FLXSA(ple4, ple4.indices)</span></p>
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<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Verdana",sans-serif">bubbles(age ~ year|qname, data = index.res(res))</span></p>
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<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Verdana",sans-serif">Are you on the latest versions of the package and on R 3.4?</span></p>
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<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Verdana",sans-serif">Best,</span></p>
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<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Verdana",sans-serif">Iago</span></p>
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<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Verdana",sans-serif">---- On Tue, 13 Feb 2018 16:36:43 +0100 <b>Mikaela Bergenius <<a href="mailto:mikaela.bergenius@slu.se" target="_blank">mikaela.bergenius@slu.se</a>></b> wrote ----</span></p>
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<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Arial",sans-serif">Hi,</span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Arial",sans-serif">Im trying to plot the standardized residuals of my XSA using the function bubbles</span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Arial",sans-serif">bubbles(age ~ year|qname, data = index.res(xsa.results7)).</span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Arial",sans-serif">In an earlier version of R I had no problems with this plot. Now I get this error message in the plot:</span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Arial",sans-serif"> </span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
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<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Arial",sans-serif">The problem is that in this newest version of FL core if I have NAs in some years of my index I will not get the plot. While before I was getting only an empty column
in the years with NAs. Ca you please advice me on what to do?</span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Arial",sans-serif">Thank you!</span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
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<p class="MsoNormal" style=""><span style="font-size:10.0pt; font-family:"Arial",sans-serif">Mikaela</span><span style="font-size:10.0pt; font-family:"Verdana",sans-serif"></span></p>
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