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<div>Hello, </div>
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<div>it looks like your object contains only one population:</div>
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<div><font face="Courier New" color="#808080">> cnt75_cl94_all <- read.structure("Excelformat_cnt75_cl94_2-16_ml80_maf0.10_missing0.8_hwe0.05.stru", n.ind=98, n.loc=735, onerowperind=TRUE, col.lab=1, col.pop=2, row.marknames=1, NA.char="0")</font></div>
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<div><font face="Courier New" color="#808080"> Which other optional columns should be read (press 'return' when done)? 1: </font></div>
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<div><font face="Courier New" color="#808080"> Converting data from a STRUCTURE .stru file to a genind object... </font></div>
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<div><font face="Courier New" color="#808080">> cnt75_cl94_all</font></div>
<div><font face="Courier New" color="#808080">/// GENIND OBJECT /////////</font></div>
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<div><font face="Courier New" color="#808080"> // 98 individuals; 735 loci; 1,470 alleles; size: 932.8 Kb</font></div>
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<div><font face="Courier New" color="#808080"> // Basic content</font></div>
<div><font face="Courier New" color="#808080"> @tab: 98 x 1470 matrix of allele counts</font></div>
<div><font face="Courier New" color="#808080"> @loc.n.all: number of alleles per locus (range: 2-2)</font></div>
<div><font face="Courier New" color="#808080"> @loc.fac: locus factor for the 1470 columns of @tab</font></div>
<div><font face="Courier New" color="#808080"> @all.names: list of allele names for each locus</font></div>
<div><font face="Courier New" color="#808080"> @ploidy: ploidy of each individual (range: 2-2)</font></div>
<div><font face="Courier New" color="#808080"> @type: codom</font></div>
<div><font face="Courier New" color="#808080"> @call: read.structure(file = "Excelformat_cnt75_cl94_2-16_ml80_maf0.10_missing0.8_hwe0.05.stru", </font></div>
<div><font face="Courier New" color="#808080"> n.ind = 98, n.loc = 735, onerowperind = TRUE, col.lab = 1, </font></div>
<div><font face="Courier New" color="#808080"> col.pop = 2, row.marknames = 1, NA.char = "0")</font></div>
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</font></div>
<div><font face="Courier New" color="#808080"> // Optional content</font></div>
<div><font face="Courier New" color="#808080"> @pop: population of each individual (group size range: 98-98)</font></div>
<div><font face="Courier New" color="#808080">> pop(cnt75_cl94_all)</font></div>
<div><font face="Courier New" color="#808080"> 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 </font></div>
<div><font face="Courier New" color="#808080"> 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 </font></div>
<div><font face="Courier New" color="#808080">53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 </font></div>
<div><font face="Courier New" color="#808080"> 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 </font></div>
<div><font face="Courier New" color="#808080">Levels: 1</font></div>
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<div>Cheers</div>
<div>Thibaut</div>
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<div id="divRpF758518" style="direction: ltr;"><font face="Tahoma" size="2" color="#000000"><b>From:</b> adegenet-forum-bounces@lists.r-forge.r-project.org [adegenet-forum-bounces@lists.r-forge.r-project.org] on behalf of LAURA NICOLE WOODINGS [17869067@students.latrobe.edu.au]<br>
<b>Sent:</b> 05 October 2015 04:43<br>
<b>To:</b> adegenet-forum@lists.r-forge.r-project.org<br>
<b>Subject:</b> [adegenet-forum] DAPC error<br>
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<div style="color:rgb(0,0,0); font-family:Calibri,sans-serif; font-size:14px">Hi,</div>
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<div style="color:rgb(0,0,0); font-family:Calibri,sans-serif; font-size:14px">I am using adegenet to perform a DAPC on some SNP data. When I run the DAPC using the following command:</div>
<div style="color:rgb(0,0,0); font-family:Calibri,sans-serif; font-size:14px">Dapc_cnt75_cl94_all <- dapc(cnt75_cl94_all, grp=Cluster_cnt75_cl94_k15$grp</div>
<div style="color:rgb(0,0,0); font-family:Calibri,sans-serif; font-size:14px">I get this error: Error in svd(X, nu = 0L) : infinite or missing values in ‘x’</div>
<div>I have checked that all the group memberships are in the input file using “pop(cnt75_cl94<span style="font-style:italic">_</span>all)” and all group memberships are present.</div>
<div>The code I use to read in the original structure input file is:</div>
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<div>cnt75_cl94_all <- read.structure("../Excelformat_cnt75_cl94_2-16_ml80_maf0.10_missing0.8_hwe0.05.stru", n.ind=98, n.loc=735, onerowperind=TRUE, col.lab=1, col.pop=2, row.marknames=1, NA.char="0", missing=0)</div>
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<div>I am not sure why I am getting this error. I have attached my input file. Any help would be much appreciated.</div>
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<div>Thanks,</div>
<div style="color:rgb(0,0,0); font-family:Calibri,sans-serif; font-size:14px"><span style="font-family:Calibri">Laura</span></div>
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<div><font class="Apple-style-span" color="#000000"><font class="Apple-style-span" face="Calibri">PhD Candidate</font></font></div>
<div><font class="Apple-style-span" color="#000000"><font class="Apple-style-span" face="Calibri">Department of Ecology, Environment and Evolution| La Trobe University | Bundoora 3086 | Australia</font></font></div>
<div><font class="Apple-style-span" color="#000000"><font class="Apple-style-span" face="Calibri"><br>
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<div><font class="Apple-style-span" color="#000000"><font class="Apple-style-span" face="Calibri">m: +61 408 642 006 | e: 17869067@students.latrobe.edu.au</font></font></div>
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