[adegenet-forum] Error in `row.names<-.data.frame`

Tue Sep 20 06:09:14 CEST 2011

Hi Thibaut

Thanks, that sorted out the probelm straight away.

cheers
Martin

On 20 September 2011 09:15, Jombart, Thibaut <t.jombart at imperial.ac.uk>wrote:

> Hello,
>
> if "m.pca" is a dudi.pca object (that is, a list), this instruction should
> not work. I assume "M" is your genind object with a relevant clustering
> information returned by "pop(M)". Can you try:
>
> ####
> m.dapc <- dapc(M, grp=pop(M))
> ####
> ?
>
> Cheers
>
> Thibaut
> ________________________________________
> From: adegenet-forum-bounces at r-forge.wu-wien.ac.at [
> adegenet-forum-bounces at r-forge.wu-wien.ac.at] on behalf of Martin van der
> Meer [martinhvandermeer at gmail.com]
> Sent: 19 September 2011 23:44
> To: adegenet-forum at r-forge.wu-wien.ac.at
> Subject: Re: [adegenet-forum] Error in `row.names<-.data.frame`
>
> Hi All
>
> Further to this post, i tried giving all the individuals in the dataset a
> unique value before
> importing as a geniod object in R, i then used the same code as below.
>  This still had the same effect at the end:
>
> > m.dapc <- dapc(m.pca, grp=pop(M))
> Choose the number PCs to retain (>=1): 23
> Error in `row.names<-.data.frame`(`*tmp*`, value = c("Axis1", "Axis2", :
> invalid 'row.names' length
> I tired on a friends Mac OS computer last night with the latest version of
> all packages
> installed from CRAN and it still didnt work? This code worked in the past
> on older versions
> of R and adegenet, im wondering if this is where the issue might lie?
>
> Has anyone tried running an (unedited)  Genpop file with the below commands
> in the new versions, im
> interested to see if they can reproduce the errors i have.
>
> cheers
> Martin
>
>
> Martin van der Meer
> PhD candidate
> Molecular Ecology and Evolutionary Laboratory
> Australian Tropical Sciences and Innovation Precinct
> School of Marine and Tropical Biology
> James Cook University
> Townsville
> Australia
>
>
> On 19 September 2011 13:25, Martin van der Meer <
> martinhvandermeer at gmail.com<mailto:martinhvandermeer at gmail.com>> wrote:
> Hi All
>
> Ive had to switch to a PC (Windows Vista) since the Mac OS system crashed.
> Ive installed R with all
> the packages for running DAPC (ade4, Adegenet, MASS). I use the same
> command codes that i
> used for R in the Mac OS. I have not changed the directories from where R
> was loaded and
> all packages and R are the latest version. My file format is in Genepop. I
> have tried a vraiety of
> methods including importing as a table and using read.table, giving
> individual numbers in the genepop file,
>  i have run R as an administrator, etc all to no avail. This is incredibely
> frustrating as it works without flaw
> in the Mac OS. Any help would be appreciated. Here is the code im using for
> R:
>
>
>
> > read.genepop("Aa.gen") -> M
>  Converting data from a Genepop .gen file to a genind object...
>
> File description:  Title line:"Aa"
> ...done.
> > M1 <- scaleGen(M, missing="mean")
> Pop1 Pop2 Pop3 Pop4 Pop5
>  14   20   24   28   33
> Warning message:
> In validityMethod(object) :
> duplicate names in ind.names:
> > m.pca <- dudi.pca(M1, center=FALSE, scale=FALSE, scannf=FALSE, nf=100)
> Error in `row.names<-.data.frame`(`*tmp*`, value = c("Pop1", "Pop1",
> "Pop1",  :
>  duplicate 'row.names' are not allowed
> In addition: Warning message:
> non-unique values when setting 'row.names': ‘Pop1’, ‘Pop2’, ‘Pop3’, ‘Pop4’,
> ‘Pop5’
> > uniquewt.df(M1)-> M2
> Warning message:
> In data.row.names(row.names, rowsi, i) :
>  some row.names duplicated:
> 2,3,4,5,6,7,8,9,10,11,12,13,14,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119
> --> row.names NOT used
> > m.pca <- dudi.pca(M2, center=FALSE, scale=FALSE, scannf=FALSE, nf=100)
> > barplot(m.pca$eig, main="eigen")
> > temp <- cumsum(m.pca$eig)/sum(m.pca$eig)
> > plot(temp, xlab="addedpc", ylab="totgenet")
> > min(which(temp > 0.95))
> [1] 92
> > axis(1, at = 92, lab = 92)
> > segments(92, 0, 92, temp[92], col = "red")
> > segments(-5, 0.95, 92, 0.95, col = "red")
> > s.class(m.pca$li, M$pop, lab= M$pop.names, sub="PCA 1-2", csub= 2)
> > add.scatter.eig(m.pca$eig[1:20], nf = 3, xax = 1, yax = 2, posi =
> "bottom")
> > m.lda <- lda(m.pca$li[, 1:92], grouping=pop(M))
> > names(m.lda)
> [1] "prior"   "counts"  "means"   "scaling" "lev"     "svd"     "N"
> "call"
> > m.pred <- predict(m.lda)
> > m.pred$class
>  [1] Pop1 Pop1 Pop1 Pop1 Pop1 Pop1 Pop1 Pop1 Pop1 Pop1 Pop1 Pop1 Pop1 Pop1
> Pop2 Pop2 Pop2 Pop2 Pop2
>  [20] Pop2 Pop2 Pop2 Pop2 Pop2 Pop2 Pop2 Pop2 Pop2 Pop2 Pop2 Pop2 Pop2 Pop2
> Pop2 Pop3 Pop3 Pop3 Pop3
>  [39] Pop3 Pop3 Pop3 Pop3 Pop3 Pop3 Pop3 Pop3 Pop3 Pop3 Pop3 Pop3 Pop3 Pop3
> Pop3 Pop3 Pop3 Pop3 Pop3
>  [58] Pop3 Pop4 Pop4 Pop4 Pop4 Pop4 Pop4 Pop4 Pop4 Pop4 Pop4 Pop4 Pop4 Pop4
> Pop4 Pop4 Pop4 Pop4 Pop4
>  [77] Pop4 Pop4 Pop4 Pop4 Pop4 Pop4 Pop4 Pop4 Pop4 Pop4 Pop5 Pop5 Pop5 Pop5
> Pop5 Pop5 Pop5 Pop5 Pop5
>  [96] Pop5 Pop5 Pop5 Pop5 Pop5 Pop5 Pop5 Pop5 Pop5 Pop5 Pop5 Pop5 Pop5 Pop5
> Pop5 Pop5 Pop5 Pop5 Pop5
> [115] Pop5 Pop5 Pop5 Pop5 Pop5
> Levels: Pop1 Pop2 Pop3 Pop4 Pop5
> > head(m.pred$posterior[, 1:5])
>  Pop1         Pop2         Pop3         Pop4         Pop5
> 1    1 4.177827e-31 1.917492e-27 1.506373e-34 7.272060e-35
> 2    1 4.848692e-28 9.903303e-25 2.649258e-33 4.010207e-35
> 3    1 4.937353e-20 5.195535e-16 1.195006e-19 2.183740e-24
> 4    1 4.608358e-19 1.503307e-15 7.937646e-22 5.661887e-24
> 5    1 1.225733e-27 2.661842e-20 6.963585e-34 2.458251e-36
> 6    1 3.344632e-15 2.383149e-18 1.608183e-26 7.585079e-31
> > mean(m.pred$class==pop(M))
> [1] 1
> > misAs <-tapply(m.pred$class !=pop(M), pop(M), mean)
> > barplot(misAs, xlab="populations", ylab= "% of missassignments per pop",
> col="orange", las=3)
> > table.paint(head(m.pred$posterior, 119, col.lab= paste("population", 1:5,
> sep=".")))
> > m.dapc <- dapc(m.pca, grp=pop(M))
> Choose the number PCs to retain (>=1): 23
> Error in `row.names<-.data.frame`(`*tmp*`, value = c("Axis1", "Axis2",  :
>  invalid 'row.names' length
>
>
> --
> Martin van der Meer
> PhD candidate
> Molecular Ecology and Evolutionary Laboratory
> Australian Tropical Sciences and Innovation Precinct
> School of Marine and Tropical Biology
> James Cook University
> Townsville
> Australia
>
>
>
>
> --
> Martin van der Meer
> PhD candidate
> Molecular Ecology and Evolutionary Laboratory
> Australian Tropical Sciences and Innovation Precinct
> School of Marine and Tropical Biology
> James Cook University
> Townsville
> Australia
>
>

-- 
Martin van der Meer
PhD candidate
Molecular Ecology and Evolutionary Laboratory
Australian Tropical Sciences and Innovation Precinct
School of Marine and Tropical Biology
James Cook University
Townsville
Australia
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