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Good Afternoon,
<div class=""> I cannot get results from “xialdapc”. I apologize for the long list of attempts.</div>
<div class="">In general, I have followed the advice in the "A tutorial for Discriminant Analysis of Principal Components (DAPC) using adegenet 2.0.0”, "<a href="https://grunwaldlab.github.io/Population_Genetics_in_R/DAPC.html" class="">https://grunwaldlab.github.io/Population_Genetics_in_R/DAPC.html</a>”
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<div class="">thibautjombart commented on May 9 • edited about Replace NA in genlight file for xvalDapc #168</div>
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<div class="">Mydata;</div>
<div class="">Using penlight object:</div>
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<div class="">/// GENLIGHT OBJECT /////////</div>
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<div class=""> // 69 genotypes, 3,243 binary SNPs, size: 487.6 Kb</div>
<div class=""> 32430 (14.49 %) missing data</div>
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<div class=""> // Basic content</div>
<div class=""> @gen: list of 69 SNPbin</div>
<div class=""> @ploidy: ploidy of each individual (range: 2-2)</div>
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<div class=""> // Optional content</div>
<div class=""> @ind.names: 69 individual labels</div>
<div class=""> @loc.names: 3243 locus labels</div>
<div class=""> @pop: population of each individual (group size range: 4-22)</div>
<div class=""> @other: a list containing: sex phenotype pat mat</div>
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<div class="">COMMANDS & ERRORS:</div>
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<div class="">cmd:</div>
<div class="">xval1 <- xvalDapc(CR_grp, grp, n.pca.max = 65, training.set = 0.9, result = "groupMean", center = TRUE, scale = FALSE, n.pca = NULL, n.rep = 30, xval.plot = TRUE)</div>
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<div class="">#error</div>
<div class="">Error in sort.list(y) : 'x' must be atomic for 'sort.list'</div>
<div class="">Have you called 'sort' on a list</div>
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</div>
<div class="">cmd:</div>
<div class="">grp <- pop(CR_grp)</div>
<div class="">cmd:</div>
<div class="">xval1 <- xvalDapc(dapcCRg, grp, n.pca.max = 65, training.set = 0.9, result = "groupMean", center = TRUE, scale = FALSE, n.pca = NULL, n.rep = 30, xval.plot = TRUE)</div>
<div class="">#error </div>
<div class="">Error in as.data.frame.default(df) : cannot coerce class ""dapc"" to a data.frame</div>
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<div class="">
<div class=""><b class="">Following DAPC tutorial 2.0.0</b></div>
<div class="">Cmd:</div>
<div class="">mat <- as.matrix(na.replace(CR_grp, method="mean"))</div>
<div class=""># error </div>
<div class="">Error in as.matrix(na.replace(CR_grp, method = "mean")) : </div>
<div class=""> error in evaluating the argument 'x' in selecting a method for function 'as.matrix': Error: could not find function "na.replace"</div>
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<div class=""><b class="">Following thibautjombart commented on May 9</b></div>
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<div class="">Cmd:</div>
<div class="">mat <- as.matrix(CR_grp, NA.method = "mean")</div>
<div class="">#ok</div>
<div class="">Cmd:</div>
<div class="">grp <- pop(CR_grp)</div>
<div class="">#ok</div>
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<div class="">Cmd:</div>
<div class="">xvalg <- xvalDapc(mat, grp, n.pca.max = 300, training.set = 0.9,</div>
<div class=""> result = "groupMean", center = TRUE, scale = FALSE,</div>
<div class=""> n.pca = NULL, n.rep = 30, xval.plot = TRUE)</div>
<div class="">error:</div>
<div class="">Error in dudi.pca(x, nf = n.pca.max, scannf = FALSE, center = center, : </div>
<div class=""> na entries in table</div>
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<div class="">
<div class=""><b class="">Following https</b>://<a href="http://grunwaldlab.github.io/Population_Genetics_in_R/DAPC.html" class="">grunwaldlab.github.io/Population_Genetics_in_R/DAPC.html</a></div>
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<div class="">CRgrpx <- xvalDapc(tab(CR_grp, NA.method = "mean"), pop(CR_grp))</div>
<div class="">#Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘tab’ for signature ‘"genlight"’</div>
<div class="">CRgrpx <- xvalDapc(CR_grp, pop(CR_grp))</div>
<div class="">#Error in dudi.pca(x, nf = n.pca.max, scannf = FALSE, center = center,: na entries in table</div>
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<div class="">Any suggestions would be appreciated.</div>
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<div class="">Douglas</div>
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Douglas L. Crawford<br class="">
Professor, Marine Biology & Ecology<br class="">
Rosenstiel School of Marine & Atmospheric Science<br class="">
University of Miami<br class="">
4600 Rickenbacker Causeway<br class="">
Mami, FL 33149<br class="">
305-421-4121<br class="">
<br class="">
<a href="mailto:dcrawford@miami.edu" class="">dcrawford@miami.edu</a><br class="">
http://www.funhe-evol.org/<br class="">
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