Hello Dne Po 10. června 2013 14:26:41 jste napsal(a): > Hello, > > dist.genpop is a re-implementation of dist.genet - all material for genetics > in ade4 should be deprecated by now, as it has been transfered into > adegenet or adephylo a few years ago already.
OK, I see. So can I use dist.genpop() also for genind objects? > I do not know about a package implementing Goldstein's distance. > > As for your question, you are right: adding a constant to a set of distances > to make them Euclidean alters the geometry of the cloud of points, and is > thus not very satisfying. This said, especially when it comes to individual > microsatellite data, I have yet to see a fancy distance do more than the > basic Euclidean distance in a PCoA, which in this case is also a PCA. The > advantage of PCA is that it will also give you allele loadings which can be > biologically meaningful. Not to say you should stick to it, but it is > probably a good start to look at your data. PCA and PCoA using distance generated by dist() give me more or less same results. I really wonder how this problem was solved in old Syntax (Podani, 2000), which was calculating PCA/PCoA from any distance. ;-) For now I don't see any enough good solution, but I at least understand it more. :-) > Cheers > Thibaut Have a nice day, Vojtěch > ________________________________________ > From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] > on behalf of Vojtěch Zeisek [vojtech.zei...@opensuse.org] > Sent: 10 June > 2013 14:59 > To: r-sig-phylo@r-project.org > Subject: Re: [R-sig-phylo] PCoA with custom distance matrix > > Hello, > thank You very much for Your reply. I'm sftill little confused. > > Dne Pá 7. června 2013 16:03:13 jste napsal(a): > > > Hello there, > > > > > > > > you could have done the PCoA on Chord's distance using adegenet, it would > > have probably been simpler (see the vignette adegenet-basics, section 6 > > "Multivariate Analysis“). > > > Function dist.genpop() contains Nei's distance, but man pages says it is > only for genpop objects (I wish to analyse individuals, not populations). > I imported the data using read.loci() and converted it to genind using > loci2genind(). I found also function dist.genet() from ade4 package, but it > requires genet object. So far I didn't find straightforward way to convert > my data to it. And I haven't find any function providing the Goldstein's > distance. > > > 'dist' is the canonical Euclidean distance, but dudi.pco will accept any > > Euclidean distance. You can use "cailliez" in ade4 to make your distance > > Euclidean before the PCoA. > > > I'm not mathematician, so I don't understand one point. Let's say I have > non-Euclidean distance matrix and some individuals (e.g. from same > population) have zero distance (they are identical). When I use cailliez(), > I have two possibilities (parameter cor.zero): > 1) to add the constant also to zero-length distances, so that the shift is > everywhere same. But as the result, the distance between originally > identical objects is positive, so they will be treated as different in > ongoing analysis, right?; or > 2) keep zero-length distances, so that those objects stay identical, but > their distances from another objects change, so the further analysis are > biased again, right? > Is there any solution? Or am I wrong? > > > > Cheers > > Thibaut > > > Sincerely, > Vojtěch > > > > -- > > ###################################### > > Dr Thibaut JOMBART > > MRC Centre for Outbreak Analysis and Modelling > > Department of Infectious Disease Epidemiology > > Imperial College - School of Public Health > > St Mary’s Campus > > Norfolk Place > > London W2 1PG > > United Kingdom > > Tel. : 0044 (0)20 7594 3658 > > t.jomb...@imperial.ac.uk > > http://sites.google.com/site/thibautjombart/ > > http://adegenet.r-forge.r-project.org/ > > ________________________________________ > > From: r-sig-phylo-boun...@r-project.org > > [r-sig-phylo-boun...@r-project.org] > > on behalf of Vojtěch Zeisek > > [vojtech.zei...@opensuse.org] > > Sent: 07 June > > 2013 15:46 > > To: mailinglist R > > Subject: [R-sig-phylo] PCoA with custom distance matrix > > > > > > > > Hello, > > I have microsatellite data and I would like to analyze them using PCoA in > > R. I would like to use following genetic distance: Goldstein's (1995) > > (dμ)2 and Nei's chord distance (1983). I calculated those distances in > > MSA (Dieringer and Schlötterer 2003), because I didn't find any > > possibility to calculate them in R. I imported the distances like that: > > dist.dms <- read.csv("dms_ind.txt", header=TRUE, sep="\t", dec=".", > > row.names=1) > > dioszegia.dist.dms <- as.dist(dioszegia.dist.dms) > > class(dioszegia.dist.dms) > > [1] "dist“ > > dms_ind.txt is ordinary square matrix with diagonal. > > But using of dudi.pco() from ade4 package fails: > > pcoa <- dudi.pco(dist.dms, scannf=FALSE, nf=3) > > Warning message: > > In dudi.pco(dioszegia.dist.dms, scannf = FALSE, nf = 3) : > > > > Non euclidean distance > > > > When using Euclidean distance (function dist()), it works fine. It > > produces some results despite the above error, but the results are very > > far from those I get using dist() function. And the results don't look > > realistic. What do I do wrong? :-) > > Have a nice day! > > Vojtěch -- Vojtěch Zeisek Komunita openSUSE GNU/Linuxu Community of the openSUSE GNU/Linux http://www.opensuse.org/ http://trapa.cz/
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