Hi, I like the poppr package very much. And I like microstallites and don't like AFLP. ;-) I found a problem with some tree constructing. When I run bruvo.boot, it crashes at some random point:
ssrs3n.nj.bruvo <- bruvo.boot(pop=ssrs3n.missingno, replen=rep(2, 8), sample=100, tree="upgma", showtree=TRUE, cutoff=33, quiet=FALSE) Bootstrapping... (note: calculation of node labels can take a while even after the progress bar is full) |========================== | 37%Error in hclust(DD, method = method, ...) : NA/NaN/Inf in foreign function call (arg 11) Calls: bruvo.boot -> poppr.boot.phylo -> FUN -> newfunk -> hclust If I choose NJ, it crashes very quickly: ssrs3n.nj.bruvo <- bruvo.boot(pop=ssrs3n.missingno, replen=rep(2, 8), sample=100, tree="nj", showtree=TRUE, cutoff=33, quiet=FALSE) Warning in bruvo.boot(pop = ssrs3n.missingno, replen = rep(2, 8), sample = 100, : Some branch lengths of the tree are negative. Normalizing branches according to Kuhner and Felsenstein (1994) Bootstrapping... (note: calculation of node labels can take a while even after the progress bar is full) |= | 1%Error in newfunk(bruvos_distance(x)) : missing values are not allowed in the distance matrix Consider using njs() Calls: bruvo.boot -> poppr.boot.phylo -> FUN -> newfunk The genind object doesn't contain missing data. I checked all point and I don't see any problem... :-( Any idea how to fix it? BTW, poppr's manual speak about parameter B for number of bootstraps for bruvo.boot() function, but its manual speaks about parameter sample, which is the correct one. ;-) Sincerely, Vojtěch Zeisek Dne Čt 29. května 2014 16:12:31 jste napsal(a): > Hi, > > Yes it is possible in R, there is a package created for related purposes: > poppr or something like that… The dev version on github should be > preferred. I have seen several R work with polyploids and microsatelites, > unfortunately… I work with ALFP :p Benjamin > > Le Jeudi 29 Mai 2014 13:40 GMT, Vojtěch Zeisek <[email protected]> a écrit: > > Hello, > > I wonder if it is possible to handle triploid microsatellite (yes, all > > individuals are regular 3n) data in adegenet and another R packages. And > > if so, how to enter the data. Any experiences and/or Ideas are very > > welcomed. :-) Structure and BAPS are working well. > > Yours sincerely, > > Vojtěch Zeisek -- Vojtěch Zeisek http://trapa.cz/en/ Department of Botany, Faculty of Science Charles University in Prague Benátská 2, Prague, 12801, CZ http://botany.natur.cuni.cz/en/ Institute of Botany, Academy of Science Zámek 1, Průhonice, 25243, CZ http://www.ibot.cas.cz/en/ Czech Republic
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