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

[Martin van der Meer]

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
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