I'm trying to use the iNextPD R package to estimate phylogenetic diversity and one of the required input is a phylogenetic tree as a
phylog object, which can be generated with the
newick2phylog() function from ade4 package.
However, when I try this function with my Newick tree (generated by QIIME), R just process the command for hours and occupies all available RAM without proceeding.
I'm not sure if the problem is with my tree file or the function itself, but it does import properly as a
phylo object with
read.tree() function from ape package, so if there's a way to convert an
ape::phylo object to
ade4::phylog object it would be helpful as well.
This is the code that I'm using and the tree file can be downloaded here:
library(ade4) library(ape) # importing the tree as a 'phylo' object tree.phylo <- read.tree("rep_set.tre") # this works # read the tree as a character string tree.nw <- scan("rep_set.tre", what="character") # import the tree as a 'phylog' object bact.phy <- newick2phylog(tree.nw) # does not finish and leaks memory
Many thanks for your help, Ido