Hello, I loaded RAxML trees via ape::read.tree and when I run steac.sptree, I end up with error:
install.packages("http://faculty.franklin.uga.edu/lliu/sites/faculty.franklin.uga.edu.lliu/files/phybase_1.5.tar.gz", repos=NULL)
library(phybase)
raxml_best_trees <- read.tree(file="raxml_best_trees.nwk")
raxml_best_trees.speciesname <- raxml_best_trees[[1]]$tip.label
raxml_best_trees.taxaname <- raxml_best_trees.speciesname
raxml_best_trees.species.structure <- matrix(data=0, ncol=length(raxml_best_trees), nrow=length(raxml_best_trees))
diag(raxml_best_trees.species.structure) <- 1
raxml_best_trees.steac <- steac.sptree(trees=raxml_best_trees, speciesname=raxml_best_trees.speciesname, taxaname=raxml_best_trees.taxaname, outgroup="Oxalis-acetosella_S96", method="nj")
Error in read.tree.nodes(trees[i]) :
The number of comma in the tree string is wrong!
sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-suse-linux-gnu (64-bit)
Running under: openSUSE Tumbleweed
locale:
[1] LC_CTYPE=cs_CZ.UTF-8 LC_NUMERIC=C LC_TIME=cs_CZ.UTF-8
[4] LC_COLLATE=cs_CZ.UTF-8 LC_MONETARY=cs_CZ.UTF-8 LC_MESSAGES=cs_CZ.UTF-8
[7] LC_PAPER=cs_CZ.UTF-8 LC_NAME=cs_CZ.UTF-8 LC_ADDRESS=cs_CZ.UTF-8
[10] LC_TELEPHONE=cs_CZ.UTF-8 LC_MEASUREMENT=cs_CZ.UTF-8 LC_IDENTIFICATION=cs_CZ.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] phybase_1.5 Matrix_1.2-9 ape_4.1 rkward_0.6.5
loaded via a namespace (and not attached):
[1] parallel_3.3.2 tools_3.3.2 nlme_3.1-131 grid_3.3.2 lattice_0.20-35
The input file seems to be fine as I can use it in another analysis, plot it, etc. I tried also with APE 3.5, but with same result.
Hello, I loaded RAxML trees via ape::read.tree and when I run steac.sptree, I end up with error:
The input file seems to be fine as I can use it in another analysis, plot it, etc. I tried also with APE 3.5, but with same result.