Re: [R-sig-phylo] Triploid microsatellites?
Yes, it was easy, thank You for pointing me in the good direction. ssrs3n.table - read.table(ssrs3n.txt, header=TRUE, sep=\t, quote= , dec=., row.names=1) ssrs3n.populations - read.table(populations.txt, header=TRUE) ssrs3n.pops - ssrs3n.populations[,1] ssrs3n.genind - df2genind(ssrs3n.table, sep=/, ncode=3, pop=ssrs3n.pops, missing=NA, ploidy=3, type=“codom“) That trick with populations is not probably the most elegant one, but it is easy and working fine. :-) Sincerely, Vojtěch Dne Pá 30. května 2014 10:13:27 jste napsal(a): Hi there, yes, the formats you mention are not designed for triploid data, but reading your data in should be easy. Just use read.table or read.csv to read your file in, then use df2genind to convert your data into a genind object, with sep=/ and ploidy=3. Cheers Thibaut From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] on behalf of Vojtěch Zeisek [vo...@trapa.cz] Sent: 30 May 2014 10:17 To: mailinglist R Subject: Re: [R-sig-phylo] Triploid microsatellites? Hello, thank You both. poppr looks interesting, I need to explore it more. Adegenet is famous package. I didn't know it can also handle triploid data. I found problem when importing data to it. Functions of import2genind group (read.genetix, read.structure, read.fstat and read.genepop) are only for diploid data. So I used read.loci. The input file was easy: first line with names of markers etc, first row with names of samples, second row with populations and from third row alleles. I coded alleles in this way 123/234/345, so that each individual has 3 alleles. Missing alleles are just NA. ssrs3n.loci - read.loci(ssrs3n.txt, header=TRUE, loci.sep=\t, allele.sep=/, col.pop=2, col.loci=3:10, row.names=1) ssrs3n.loci Allelic data frame: 130 individuals 8 loci 1 additional variable ssrs3n.genind - loci2genind(ssrs3n.loci) ssrs3n.genind # ### Genind object ### # - genotypes of individuals - S4 class: genind @call: df2genind(X = as.matrix(x[, attr(x, locicol)]), sep = /, pop = pop) @tab: 130 x 115 matrix of genotypes @ind.names: vector of 130 individual names @loc.names: vector of 8 locus names @loc.nall: number of alleles per locus @loc.fac: locus factor for the 115 columns of @tab @all.names: list of 8 components yielding allele names for each locus @ploidy: 2 @type: codom Optional contents: @pop: factor giving the population of each individual @pop.names: factor giving the population of each individual @other: - empty - As You can see, it was imported as diploid and I haven't found way how import it as triploid data. Imported data matrix seems to be wrong. When I used input file formatted in the same way for diploids, it works perfectly... Any ideas how to fix that? Thank You in advance, Vojtěch Zeisek Dne Pá 30. května 2014 03:34:49 jste napsal(a): Hi there, yes, adegenet handles any (constant) ploidy for most purposes. For input formats etc. please see the tutorial on basics, section 'documents' on: http://adegenet.r-forge.r-project.org/ Please feel free to use the adegenet forum for adegenet-related questions. Cheers Thibaut From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] on behalf of Gilles Benjamin Leduc [g...@hi.is] Sent: 29 May 2014 17:12 To: Vojtěch Zeisek Cc: mailinglist R Subject: Re: [R-sig-phylo] Triploid microsatellites? 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 vo...@trapa.cz 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 signature.asc Description: This is a digitally signed message part. ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] Early burst branch rescale
Hi Jon, So there are are a few ways I can imagine doing this. One thing you should probably not do though is rescale the branches of the tree directly, at least in the case of OU, as this leads to incorrect covariances for pairs of taxa where one or either does not survive to the present day (see this in press note: http://onlinelibrary.wiley.com/doi/10./2041-210X.12201/abstract), as I suspect you have in your tree. Probably the most appropriate way is therefore to 1) split the VCV into one or more matrices describing the variances and covariances over the intervals that youre interested in; 2) transform the matrices according the model and associated parameters you want over that interval, 3) stick them back together, and 4) draw your data directly from a multivariate normal distribution using the transformed covariance matrix. Ill send you some code off list to do that (its also in the corrected dryad pack accompanying the note above) Graham Graham Slater Peter Buck Post-Doctoral Fellow Department of Paleobiology National Museum of Natural History The Smithsonian Institution [NHB, MRC 121] P.O. Box 37012 (202) 633-1316 slat...@si.edumailto:slat...@si.edu www.fourdimensionalbiology.comhttp://www.fourdimensionalbiology.com On Jun 2, 2014, at 3:55 PM, Jonathan Mitchell mitchel...@uchicago.edumailto:mitchel...@uchicago.edu wrote: Hello all, I'm trying to figure out how to rescale certain branches of a tree according to an early burst model. First I've generated a tree using TreeSim N - 100 Nn - N*2 -1 test - sim.bd.taxa(N, 1, 1, 0.8, complete=FALSE) Then I 'paint' the branches depending on whether or not they occur in the first or second half of the clade's history: Root -max(nodeHeights(test2)) Age - 0.5*Root test2 - make.era.map(test[[1]][[1]], c(0, Age)) Using rescale() from geiger, I can reformat the whole tree, and using sim.rates() from phytools, it's easy to simulate different sigmas. But what I'd like to do is also simulate different evolutionary modes (OU and EB) in the different regimes (like Graham's MEE paper). Is there a way to rescale the branches in one portion of the tree according to the OU alpha or EB r parameters? Thanks! -- Jon _ Jonathan S. Mitchell http://home.uchicago.edu/~mitchelljs/ PhD Student Committee on Evolutionary Biology The University of Chicago 1025 57th Str, Culver Hall 402 Chicago, IL 60637 Geology Department The Field Museum of Natural History 1400 S. Lake Shore Dr. Chicago, IL 60605 [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] Early burst branch rescale
Hi Jon, Take a look at the mvSHIFT function in mvMORPH. This is typically what you are looking for and you can use it with non-ultrametric trees (it's maybe faster than classic functions). Best, Julien Date: Mon, 2 Jun 2014 14:55:06 -0500 From: mitchel...@uchicago.edu To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] Early burst branch rescale Hello all, I'm trying to figure out how to rescale certain branches of a tree according to an early burst model. First I've generated a tree using TreeSim N - 100 Nn - N*2 -1 test - sim.bd.taxa(N, 1, 1, 0.8, complete=FALSE) Then I 'paint' the branches depending on whether or not they occur in the first or second half of the clade's history: Root -max(nodeHeights(test2)) Age - 0.5*Root test2 - make.era.map(test[[1]][[1]], c(0, Age)) Using rescale() from geiger, I can reformat the whole tree, and using sim.rates() from phytools, it's easy to simulate different sigmas. But what I'd like to do is also simulate different evolutionary modes (OU and EB) in the different regimes (like Graham's MEE paper). Is there a way to rescale the branches in one portion of the tree according to the OU alpha or EB r parameters? Thanks! -- Jon _ Jonathan S. Mitchell http://home.uchicago.edu/~mitchelljs/ PhD Student Committee on Evolutionary Biology The University of Chicago 1025 57th Str, Culver Hall 402 Chicago, IL 60637 Geology Department The Field Museum of Natural History 1400 S. Lake Shore Dr. Chicago, IL 60605 [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] Early burst branch rescale
Julien- Does mvSHIFT account for the OU rescaling issue on non-ultrametric trees that Graham mentions? If so, how? Cheers, -Dave On Mon, Jun 2, 2014 at 5:26 PM, Julien Clavel julien.cla...@hotmail.fr wrote: Hi Jon, Take a look at the mvSHIFT function in mvMORPH. This is typically what you are looking for and you can use it with non-ultrametric trees (it's maybe faster than classic functions). Best, Julien Date: Mon, 2 Jun 2014 14:55:06 -0500 From: mitchel...@uchicago.edu To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] Early burst branch rescale Hello all, I'm trying to figure out how to rescale certain branches of a tree according to an early burst model. First I've generated a tree using TreeSim N - 100 Nn - N*2 -1 test - sim.bd.taxa(N, 1, 1, 0.8, complete=FALSE) Then I 'paint' the branches depending on whether or not they occur in the first or second half of the clade's history: Root -max(nodeHeights(test2)) Age - 0.5*Root test2 - make.era.map(test[[1]][[1]], c(0, Age)) Using rescale() from geiger, I can reformat the whole tree, and using sim.rates() from phytools, it's easy to simulate different sigmas. But what I'd like to do is also simulate different evolutionary modes (OU and EB) in the different regimes (like Graham's MEE paper). Is there a way to rescale the branches in one portion of the tree according to the OU alpha or EB r parameters? Thanks! -- Jon _ Jonathan S. Mitchell http://home.uchicago.edu/~mitchelljs/ PhD Student Committee on Evolutionary Biology The University of Chicago 1025 57th Str, Culver Hall 402 Chicago, IL 60637 Geology Department The Field Museum of Natural History 1400 S. Lake Shore Dr. Chicago, IL 60605 [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ -- David W. Bapst, PhD Adjunct Asst. Professor, Geology and Geol. Eng. South Dakota School of Mines and Technology 501 E. St. Joseph Rapid City, SD 57701 http://webpages.sdsmt.edu/~dbapst/ http://cran.r-project.org/web/packages/paleotree/index.html ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
