bomeara / phybase

Fork for Liang Liu's 1.4 version; used for teaching phylometh

This is a fork of Liang Liu's phybase package, just to make it easier for students in my course to install and use (it's not on CRAN). For the canonical version, go to https://faculty.franklin.uga.edu/lliu/content/phybase?.

You can install Liang's version by doing

install.packages("https://faculty.franklin.uga.edu/lliu/sites/faculty.franklin.uga.edu.lliu/files/phybase_1.4.tar.gz", repos=NULL)

And I would advise that for any real work. This version, you can do:

install.packages("devtools")
devtools::install_github("bomeara/phybase")

In either case, then do library(phybase).

The citation for phybase is

Liu L. and Yu L. 2010. Phybase: an R package for species tree analysis. Bioinformatics 26: 962-963.

phybase's Issues

Error in steac.sptree

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.