Hi Agus,
The problem is that spaces are ignored in Newick and NEXUS files. Maybe
you do not need to replace "_" for " " ?
Best,
Emmanuel
Le 29/06/2013 15:15, Agus Camacho a écrit :
Dear all,
After correcting the names of a otherwise perfectly functional tree using
gsub,
tree$tip.label=gsub("_", " ", tree$tip.label
the new tree looks nice, but when i save it using write.nexus and reopen
it, i get:
wtree=read.nexus("tree_corrected_names.nexus")Warning message:In matrix(x, ncol
= 2, byrow = TRUE) :
data length [105] is not a sub-multiple or multiple of the number of rows
[53]
wtree$tip.label [1] "Tupinambis" "2" "ocellifer"
"Kentropyx"
[5] "4" "atriventris" "Anotosaura" "6"
[9] "percarinatum" "Arthrosaura" "8" "reticulata"
[13] "Bachia" "10" "panoplia" "Bachia"
[17] "12" "bicarinatus" "Placosoma" "14"
[21] "glabellum" "Neusticurus" "16" "quadrilineata"
[25] "Cercosaura" "18" "ocelatta" "Cercosaura"
[29] "20" "brachylepis" "Heterodactylus" "22"
[33] "modesta" "Iphisa" "24" "paeminosus"
[37] "Gymnophthalmus" "26" "ablephara" "Calyptommatus"
[41] "28" "leiolepis" "Calyptommatus" "30"
[45] "atticolus" "Micrablepharus" "32" "agilis"
[49] "Vanzosaura" "34" "erythrocercus" "Procellosaurinus"
[53] "1"
thanks in advance
Agus
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