SigTree

Package: SigTree
Type: Package
Title: Identify and Visualize Significantly Responsive Branches in a
Phylogenetic Tree
Version: 1.10.3
Date: 2016-02-05
Author: John R. Stevens and Todd R. Jones
Maintainer: John R. Stevens <john.r.stevens@usu.edu>
Description: Takes a phylogenetic tree (of class phylo) and a data frame (or matrix) of corresponding tip labels and p-values, and determines the significance of the branches (families of p-values) and plots the tree with colored branches (corresponding to families) according to their levels of significance. Also produces a CSV file with the p-values of all of the branches as well as which tips belong to which branches. Finally, it exports a file that can be opened in FigTree that produces a colored plot (colored branches according to their significance of corresponding groups of p-values) with p-value annotations.
Imports: ape, phylobase, phyext2, RColorBrewer, phyloseq, graphics,
utils, stats
Repository: CRAN
License: GPL-3
NeedsCompilation: yes
Packaged: 2016-02-05 22:28:45 UTC; John
Date/Publication: 2016-02-06 11:07:46

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'SigTree' ...
** package 'SigTree' successfully unpacked and MD5 sums checked
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c SigTree.c -o SigTree.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o SigTree.so SigTree.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/SigTree/libs
** R
** inst
** preparing package for lazy loading
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
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** help
*** installing help indices
  converting help for package 'SigTree'
    finding HTML links ... done
    SigTree-package                         html  
    SigTree.other                           html  
    export.figtree                          html  
    export.inherit                          html  
    plotSigTree                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
* DONE (SigTree)
Making 'packages.html' ... done