compare.evol.rates: Error in C[rownames(x), rownames(x)] : subscript out of bounds

[juanmac17]

I am trying to use compare.evol.rates function but i keep getting this error message. I check the input data type with the one provided as examples and see no difference.

[EmSherratt]

Juan, It sounds like there may be an issue with your specimen names in your input array. Without further information on the data objects your are running the function with, I can't be sure. Please provide this.

[juanmac17]

Hi Emma, thx for replying so fast. I have a twelve taxa phylogenetic tree (I used read.tree and drop.tip functions) and a tps file with twelve configurations of 25 landmark. The ID of the tps match with the tip.labels of the tree.

I´ll send you information of the input data:

The tree call prunned

> prunned

Phylogenetic tree with 12 tips and 11 internal nodes.

Tip labels:
	uru1, uru2, neu6, neu2, sin1, sin2, ...

Rooted; includes branch lengths.

Procrustes coordinates:

> gpa$coords
, , uru1

              [,1]         [,2]
 [1,] -0.014883788  0.302994270
 [2,] -0.042942243  0.198536940
 [3,] -0.095284883  0.241169024
 [4,] -0.120021961  0.161931023
 [5,] -0.152289381  0.052026499
 [6,] -0.180429888  0.026058193
 [7,] -0.205598521 -0.116457242
 [8,] -0.182587635 -0.256411508
 [9,] -0.057261179 -0.215244021
[10,]  0.008027162 -0.200048510
[11,]  0.064287982 -0.214952529
[12,]  0.188964218 -0.244111250
[13,]  0.204993802 -0.102330702
[14,]  0.175152658  0.029744124
[15,]  0.148053432  0.053877861
[16,]  0.117864055  0.158628035
[17,]  0.092489501  0.238908449
[18,]  0.043144302  0.198408406
[19,] -0.056968347  0.007038989
[20,] -0.099200053 -0.048875534
[21,] -0.048095034 -0.099068849
[22,]  0.052766325 -0.096113602
[23,]  0.100335240 -0.047957450
[24,]  0.057070481  0.010093991
[25,]  0.002413753 -0.037844607

, , uru2

Group designation:

> land.gp
 uru1  uru2  neu6  neu2  sin1  sin2  sin4  sca5  sca4  sca7 sca13 sca14 
    1     1     1     2     1     1     2     1     1     1     1     1 
Levels: 1 2

[EmSherratt]

The issue is coming from the internal function phylo.mat, that is calculating the phylogenetic covariance matrix from the tree. Specifically:

  C<-ape::vcv.phylo(phy,anc.nodes=FALSE) # phy is your tree (prunned)
  C<-C[rownames(x),rownames(x)] # x is a 2D array of the data (gpa$coords)

You can run that yourself, and you'll get the same error. Thus the issue is clearly a disconnect between the row names of x and the names in the tree. Double check those are the same using the function match

[mlcollyer]

In my experience, this issue often arrises from an extra space somewhere, which cloaks the misspecified name. For example, if in the data one row has the name, “taxon1” and in the tree, it is a tip label, “taxon1 “, printing to the screen that removes quotes will not reveal the extra space at the end of the tip label. Nevertheless, this extra character means the names are not the same. Using the match function Emma suggested is a great way to pinpoint where mismatches occur, but if it appears names still match, using the as.character function might elucidate if there are extra spaces somewhere. Mike

…

On Mar 17, 2017, at 12:58 AM, Emma Sherratt ***@***.***> wrote: The issue is coming from the internal function phylo.mat, that is calculating the phylogenetic covariance matrix from the tree. Specifically: C<-ape::vcv.phylo(phy,anc.nodes=FALSE) # phy is your tree (prunned) C<-C[rownames(x),rownames(x)] # x is a 2D array of the data (gpa$coords) You can run that yourself, and you'll get the same error. Thus the issue is clearly a disconnect between the row names of x and the names in the tree. Double check those are the same using the function match — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#10 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AGjacvEjgX20mmVY_KRdgPQbHr2O0X6Mks5rmhMIgaJpZM4MeVj5>.

[juanmac17]

Thank you very much Emma and Mike. I have spaces everywhere!!

[mlcollyer]

A little tip for quickly omitting spaces, use the gsub function. An example: tipnames <- dimnames(mydata)[[3]] # if using an array, can change to rownames for a matrix tipnames <- gsub(“ “, “”, tipnames) # first argument is what to replace, second what to replace it with, third the values dimnames(mydata)[[3]] <- tipnames Hope that helps! -Mike

…

On Mar 17, 2017, at 9:06 AM, juanmac17 ***@***.***> wrote: Thank you very much Emma and Mike. I have spaces everywhere!! — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#10 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AGjacrlRHaiOACUjinBi608knSDIDelkks5rmoVogaJpZM4MeVj5>.