The ade4 Package - NexTag Supports Open Source Initiatives

newick2phylog 175
References
Bauwens, D. and Díaz-Uriarte, R. (1997) Covariation of life-history traits in lacertid lizards: a
comparative study. American Naturalist, 149, 91–111.
Cheverud, J. and Dow, M.M. (1985) An autocorrelation analysis of genetic variation due to lineal
fission in social groups of rhesus macaques. American Journal of Physical Anthropology, 67, 113–
122.
Martins, E. P. and Hansen, T.F. (1997) Phylogenies and the comparative method: a general approach
to incorporating phylogenetic information into the analysis of interspecific data. American
Naturalist, 149, 646–667.
Examples
data(newick.eg)
newick2phylog(newick.eg[[11]])
radial.phylog(newick2phylog(newick.eg[[7]]), circ = 1,
clabel.l = 0.75)
newick2phylog
Create phylogeny
Description
Usage
The first three functions ensure to create object of class phylog from either a character string in
Newick format (newick2phylog) or an object of class ’hclust’ (hclust2phylog) or a
taxonomy (taxo2phylog). The function newick2phylog.addtools is an internal function
called by newick2phylog, hclust2phylog and taxo2phylog when newick2phylog.addtools
= TRUE. It adds some items in ’phylog’ objects.
newick2phylog(x.tre, add.tools = TRUE, call = match.call())
hclust2phylog(hc, add.tools = TRUE)
taxo2phylog(taxo, add.tools = FALSE, root="Root", abbrev=TRUE)
newick2phylog.addtools(res, tol = 1e-07)
Arguments
x.tre
add.tools
call
hc
taxo
res
a character string corresponding to a phylogenetic tree in Newick format
(http://evolution.genetics.washington.edu/phylip/newicktree.
html)
if TRUE, executes the function newick2phylog.addtools
call
an object of class hclust
an object of class taxo
an object of class phylog (an internal argument of the function newick2phylog)