<div dir="ltr">On closer inspection, it appears the new version stores missing data as alleles (i.e. *.00 in @tab). So using tab to replace the allele counts doesn't work. For example, x@tab <- tab(x, NA.method="mean") does nothing because missing data is stored as normal data. Here's a workaround I created, although probably not the most clever method, it fixed my problem. Hopefully this helps someone!<div>Paul<br><br><div><div><font face="monospace, monospace"># Fix missing values to reflect depracated option, missing = "mean"</font></div><div><font face="monospace, monospace">x@tab <- x@tab[,-grep("\\.00",colnames(x@tab))] #remove "00" alleles</font></div><div><font face="monospace, monospace">rep <- gsub("([^\\.]+)\\.\\d+","\\1",colnames(x@tab)) #locus names</font></div><div><font face="monospace, monospace">loci <- unique(x@loc.fac) #unique locus names</font></div><div><font face="monospace, monospace">x@loc.fac <- as.factor(rep)</font></div><div><font face="monospace, monospace">for (i in 1:length(x@all.names))</font></div><div><font face="monospace, monospace"> if ("00" %in% x@all.names[[i]]) #remove "00" from allele names</font></div><div><font face="monospace, monospace"> x@all.names[[i]] <- x@all.names[[i]][-which(x@all.names[[i]]=="00")]</font></div><div><font face="monospace, monospace">for (i in 1:length(x@loc.n.all)) #remove "00" from allele counts</font></div><div><font face="monospace, monospace"> x@loc.n.all[[i]] <- length(x@all.names[[i]])</font></div><div><font face="monospace, monospace">for (i in 1:length(loci)) { #replace missing data with mean allele counts</font></div><div><font face="monospace, monospace"> df <- data.frame(x@tab[,which(loci[i] == rep)]) #df, alleles for one locus</font></div><div><font face="monospace, monospace"> for (j in 1:nrow(df)) {</font></div><div><font face="monospace, monospace"> if (sum(df[j,]) == 0) {</font></div><div><font face="monospace, monospace"> for (k in 1:length(df[j,])) { #mean allele counts from rows with data</font></div><div><font face="monospace, monospace"> df[j,k] <- round(mean( df[which(apply(df,1,sum) != 0),k] ))</font></div><div><font face="monospace, monospace"> }</font></div><div><font face="monospace, monospace"> x@tab[j,which(loci[i] == rep)] <- as.numeric(df[j,])</font></div><div><font face="monospace, monospace"> }</font></div><div><font face="monospace, monospace"> }</font></div><div><font face="monospace, monospace">}</font></div></div></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature"><div dir="ltr"><div><br></div><div>----------------------------------------------</div><div>Paul Maier</div><div><br></div><div>San Diego State, PhD Student</div><div>US Geological Survey, Biologist</div><div>The Biodiversity Group, Science Advisor</div><div><br></div></div></div></div>
<br><div class="gmail_quote">On Tue, Jul 14, 2015 at 2:30 PM, Paul Maier <span dir="ltr"><<a href="mailto:maierpa@gmail.com" target="_blank">maierpa@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 dir="ltr">Thanks, Thibaut, for clearing that up.<span class="HOEnZb"><font color="#888888"><br>Paul<br></font></span></div><div class="gmail_extra"><span class=""><br clear="all"><div><div><div dir="ltr"><div><br></div><div>----------------------------------------------</div><div>Paul Maier</div><div><br></div><div>San Diego State, PhD Student</div><div>US Geological Survey, Biologist</div><div>The Biodiversity Group, Science Advisor</div><div><br></div></div></div></div>
<br></span><div><div class="h5"><div class="gmail_quote">On Tue, Jul 14, 2015 at 1:01 PM, Jombart, Thibaut <span dir="ltr"><<a href="mailto:t.jombart@imperial.ac.uk" target="_blank">t.jombart@imperial.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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Hello, <br>
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yes, this change is on purpose. adegenet 2.0.0 includes a lot of reforms of the code, with some breaking backward compatibility.
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Here is a good example: storing replacement of missing values inside a genind object was bad practice - one ends up not knowing if all values are genuine, or if some are merely NAs that have been replaced. In the new version, missing data are stored as missing,
but they can be easily replaced when extracting a table of allele counts or frequencies (see ?tab).
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Cheers<br>
Thibaut<br>
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==============================<br>
Dr Thibaut Jombart<br>
MRC Centre for Outbreak Analysis and Modelling<br>
Department of Infectious Disease Epidemiology<br>
Imperial College - School of Public Health<br>
Norfolk Place, London W2 1PG, UK<br>
Tel. : 0044 (0)20 7594 3658<br>
<a href="http://sites.google.com/site/thibautjombart/" target="_blank">http://sites.google.com/site/thibautjombart/</a><br>
<a href="http://sites.google.com/site/therepiproject/" target="_blank">http://sites.google.com/site/therepiproject/</a><br>
<a href="http://adegenet.r-forge.r-project.org/" target="_blank">http://adegenet.r-forge.r-project.org/</a><br>
Twitter: @thibautjombart<br>
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<div style="direction:ltr"><font face="Tahoma" size="2" color="#000000"><b>From:</b> <a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org" target="_blank">adegenet-forum-bounces@lists.r-forge.r-project.org</a> [<a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org" target="_blank">adegenet-forum-bounces@lists.r-forge.r-project.org</a>] on behalf of Paul Maier [<a href="mailto:maierpa@gmail.com" target="_blank">maierpa@gmail.com</a>]<br>
<b>Sent:</b> 14 July 2015 20:50<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] read.genepop (adegenet 2.0.0 with R v. 3.2.1)<br>
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<div dir="ltr">Hi all,
<div>It appears the new version of this function (read.genepop) doesn't have the 'missing' option. Can someone either post an older version of adegenet compatible with R 3.2.1, or post R code for the earlier version of the read.genepop function? I hadn't anticipated
trying to figure this out manually.</div>
<div>Thanks!</div>
<div>Paul</div>
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<div>----------------------------------------------</div>
<div>Paul Maier</div>
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<div>San Diego State, PhD Student</div>
<div>US Geological Survey, Biologist</div>
<div>The Biodiversity Group, Science Advisor</div>
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