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

[Jombart, Thibaut]

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