BAMMtools

Package: BAMMtools
Type: Package
Title: Analysis and Visualization of Macroevolutionary Dynamics on
Phylogenetic Trees
Version: 2.1.4
Date: 2016-06-10
Author: Dan Rabosky, Mike Grundler, Pascal Title, Carlos Anderson, Jeff Shi,
Joseph Brown, Huateng Huang, Jon Mitchell
Maintainer: Pascal Title <ptitle@umich.edu>
Imports: Rcpp (>= 0.11.0), gplots, methods
Depends: ape, R (>= 2.10)
Description: Provides functions for analyzing and visualizing complex
macroevolutionary dynamics on phylogenetic trees. It is a companion
package to the command line program BAMM (Bayesian Analysis of
Macroevolutionary Mixtures) and is entirely oriented towards the analysis,
interpretation, and visualization of evolutionary rates. Functionality
includes visualization of rate shifts on phylogenies, estimating
evolutionary rates through time, comparing posterior distributions of
evolutionary rates across clades, comparing diversification models using
Bayes factors, and more.
License: GPL (>= 2)
URL: http://www.bamm-project.org
NeedsCompilation: yes
Suggests: parallel
RoxygenNote: 5.0.1
Packaged: 2016-06-10 11:30:24 UTC; pascaltitle
Repository: CRAN
Date/Publication: 2016-06-10 14:00:18

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'BAMMtools' ...
** package 'BAMMtools' successfully unpacked and MD5 sums checked
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c cohort_matrix.c -o cohort_matrix.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c dtrates.c -o dtrates.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c jenksBrks.c -o jenksBrks.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c treetraverse.c -o treetraverse.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o BAMMtools.so cohort_matrix.o dtrates.o jenksBrks.o treetraverse.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/BAMMtools/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'BAMMtools'
    finding HTML links ... done
    BAMMlikelihood                          html  
    BAMMtools-data                          html  
    BAMMtools                               html  
    ShiftProbsTree                          html  
    addBAMMlegend                           html  
    addBAMMshifts                           html  
    assignColorBreaks                       html  
    cohorts                                 html  
    finding level-2 HTML links ... done

    computeBayesFactors                     html  
    credibleShiftSet                        html  
    distinctShiftConfigurations             html  
    dtRates                                 html  
    generateControlFile                     html  
    getBestShiftConfiguration               html  
    getBranchShiftPriors                    html  
    getCladeRates                           html  
    getCohortMatrix                         html  
    getEventData                            html  
    getJenksBreaks                          html  
    getMarginalBranchRateMatrix             html  
    getMeanBranchLengthTree                 html  
    getRateThroughTimeMatrix                html  
    getShiftNodesFromIndex                  html  
    getTipRates                             html  
    getmrca                                 html  
    marginalOddsRatioBranches               html  
    maximumShiftCredibility                 html  
    plot.bammdata                           html  
    plot.bammshifts                         html  
    plot.credibleshiftset                   html  
    plotPrior                               html  
    plotRateThroughTime                     html  
    ratesHistogram                          html  
    richColors                              html  
    samplingProbs                           html  
    setBAMMpriors                           html  
    speciesByRatesMatrix                    html  
    subsetEventData                         html  
    subtreeBAMM                             html  
    summary.bammdata                        html  
    summary.credibleshiftset                html  
    testTimeVariableBranches                html  
    traitDependentBAMM                      html  
    transparentColor                        html  
    writeEventData                          html  
** building package indices
** testing if installed package can be loaded
* DONE (BAMMtools)
Making 'packages.html' ... done