newick.eg {ade4}R Documentation

Phylogenetic trees in Newick format

Description

This data set contains various exemples of phylogenetic trees in Newick format.

Usage

data(newick.eg)

Format

newick.eg is a list containing 14 character strings in Newick format.

Source

Trees 1 to 7 were obtained from the URL
http://evolution.genetics.washington.edu/phylip/newicktree.html.

Trees 8 and 9 were obtained by Clémentine Carpentier-Gimaret gimaret@biomserv.univ-lyon1.fr.

Tree 10 was obtained from Treezilla Data Sets starting from
http://www.cis.upenn.edu/~krice/treezilla/.

Trees 11 and 12 are taken from Bauwens and D\'iaz-Uriarte (1997).

Tree 13 is taken from Cheverud and Dow (1985).

Tree 13 is taken from Martins and Hansen (1997).

References

Bauwens, D. and D\'iaz-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)

Worked out examples


> library(ade4)
> ### Name: newick.eg
> ### Title: Phylogenetic trees in Newick format
> ### Aliases: newick.eg
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(newick.eg)
> newick2phylog(newick.eg[[11]])
Phylogenetic tree with 18 leaves and 17 nodes
$class: phylog
$call: newick2phylog(x.tre = newick.eg[[11]])
$tre: ((Sa,Sh)I1,((((Tl,(Mc,My)...Ls,Lv)I13)I14)I15)I16)Root; 

        class   length content                                     
$leaves numeric 18     length of the first preceeding adjacent edge
$nodes  numeric 17     length of the first preceeding adjacent edge
$parts  list    17     subsets of descendant nodes                 
$paths  list    35     path from root to node or leave             
$droot  numeric 35     distance to root                            

         class      dim   content                                   
$Wmat    matrix     18-18 W matrix : root to the closest ancestor   
$Wdist   dist       153   Nodal distances                           
$Wvalues numeric    17    Eigen values of QWQ/sum(Q)                
$Wscores data.frame 18-17 Eigen vectors of QWQ '1/n' normed         
$Amat    matrix     18-18 Topological proximity matrix A            
$Avalues numeric    17    Eigen values of QAQ matrix                
$Adim    integer    1     number of positive eigen values of QAQ    
$Ascores data.frame 18-17 Eigen vectors of QAQ '1/n' normed         
$Aparam  data.frame 17-3  Topological indices for nodes             
$Bindica data.frame 18-17 class indicator from nodes                
$Bscores data.frame 18-17 Topological orthonormal basis '1/n' normed
$Blabels character  17    Nodes labelling from orthonormal basis    
> radial.phylog(newick2phylog(newick.eg[[7]]), circ = 1,
+  clabel.l = 0.75)
> 
> 
> 
> 

[Package ade4 Index]