Hi all,
I have been hitting intermittent problems using trees generated by
ape::rphylo. Here is a reproducible example.
############################
library(ape)
sessionInfo()
# Simulate a tree with e.g. 5 species
nspecies = 5
set.seed(123465)
tr_wFossils = rphylo(n=nspecies, birth=0.3, death=0.25, T0=50,
fossils=TRUE, eps=1e-06)
# Ladderize tree with fossils
ltr = ladderize(tr_wFossils, right=FALSE)
ltr$edge
round(ltr$edge.length, 4)
write.tree(phy=ltr, file="")
tr_wFossils = read.tree(file="", text=write.tree(phy=ltr, file="") )
tr_wFossils$tip.label = paste0("sp", 1:length(tr_wFossils$tip.label))
plot(tr_wFossils); axisPhylo(); title("Sim Tree w Fossils")
############################
Output:
############################
> library(ape)
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ape_3.3
loaded via a namespace (and not attached):
[1] nlme_3.1-121 grid_3.2.2 lattice_0.20-33
>
> # Simulate a tree with e.g. 5 species
> nspecies = 5
> set.seed(123465)
> tr_wFossils = rphylo(n=nspecies, birth=0.3, death=0.25, T0=50,
fossils=TRUE, eps=1e-06)
>
> # Ladderize tree with fossils
> ltr = ladderize(tr_wFossils, right=FALSE)
> ltr$edge
[,1] [,2]
[1,] 7 11
[2,] 11 2
[3,] 8 5
[4,] 8 9
[5,] 9 6
[6,] 9 10
[7,] 10 4
[8,] 10 3
> round(ltr$edge.length, 4)
[1] 2.6862 0.0670 1.2078 0.1028 0.4985 0.0915 1.0135 1.0135
> write.tree(phy=ltr, file="")
[1] "((t2:0.06701971429):2.686176768);"
>
> tr_wFossils = read.tree(file="", text=write.tree(phy=ltr, file="") )
Warning message:
In FUN(X[[i]], ...) : NAs introduced by coercion
> tr_wFossils$tip.label = paste0("sp", 1:length(tr_wFossils$tip.label))
> plot(tr_wFossils); axisPhylo(); title("Sim Tree w Fossils")
NULL
Warning message:
In plot.phylo(tr_wFossils) : found less than 2 tips in the tree
Error in get("last_plot.phylo", envir = .PlotPhyloEnv) :
object 'last_plot.phylo' not found
############################
It looks like a problem with the edge matrix generated by rphylo - perhaps
older simulation code. The workaround is Yea Olde Writeth To And Readeth
>From Newick trick:
###########################
# Simulate a tree with e.g. 5 species
nspecies = 5
set.seed(123465)
tr_wFossils = rphylo(n=nspecies, birth=0.3, death=0.25, T0=50,
fossils=TRUE, eps=1e-06)
tr_wFossils = read.tree(file="", text=write.tree(phy=tr_wFossils, file="") )
# Ladderize tree with fossils
ltr = ladderize(tr_wFossils, right=FALSE)
ltr$edge
round(ltr$edge.length, 4)
write.tree(phy=ltr, file="")
tr_wFossils = read.tree(file="", text=write.tree(phy=ltr, file="") )
tr_wFossils$tip.label = paste0("sp", 1:length(tr_wFossils$tip.label))
plot(tr_wFossils); axisPhylo(); title("Sim Tree w Fossils")
###########################
Now there are no issues:
###########################
> # Simulate a tree with e.g. 5 species
> nspecies = 5
> set.seed(123465)
> tr_wFossils = rphylo(n=nspecies, birth=0.3, death=0.25, T0=50,
fossils=TRUE, eps=1e-06)
> tr_wFossils = read.tree(file="", text=write.tree(phy=tr_wFossils,
file="") )
> # Ladderize tree with fossils
> ltr = ladderize(tr_wFossils, right=FALSE)
> ltr$edge
[,1] [,2]
[1,] 7 8
[2,] 8 1
[3,] 8 2
[4,] 7 9
[5,] 9 6
[6,] 9 10
[7,] 10 3
[8,] 10 11
[9,] 11 4
[10,] 11 5
> round(ltr$edge.length, 4)
[1] 2.6862 0.0670 0.0670 1.5454 1.2078 0.1028 0.4985 0.0915 1.0135 1.0135
> write.tree(phy=ltr, file="")
[1]
"((t2:0.06701971429,t1:0.06701971429):2.686176768,(t5:1.207768321,(t6:0.4984853178,(t4:1.013489985,t3:1.013489985):0.09146602338):0.1028123128):1.545428161);"
>
> tr_wFossils = read.tree(file="", text=write.tree(phy=ltr, file="") )
> tr_wFossils$tip.label = paste0("sp", 1:length(tr_wFossils$tip.label))
> plot(tr_wFossils); axisPhylo(); title("Sim Tree w Fossils")
###########################
Cheers,
Nick
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