Last data update: 2014.03.03
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bayou
Package: bayou
Type: Package
Title: Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies
Version: 1.1.0
Date: 2015-10-16
Author: Josef C. Uyeda, Jon Eastman and Luke Harmon
Maintainer: Josef C. Uyeda <josef.uyeda@gmail.com>
Description: Tools for fitting and simulating multi-optima Ornstein-Uhlenbeck
models to phylogenetic comparative data using Bayesian reversible-jump
methods.
License: GPL (>= 2)
Depends: ape (>= 3.0-6), geiger (>= 2.0), R (>= 2.15.0), phytools, coda
Imports: Rcpp (>= 0.10.3), MASS, mnormt, fitdistrplus, denstrip,
foreach, stats, grDevices, graphics
Suggests: doParallel
LinkingTo: Rcpp, RcppArmadillo
Collate: 'RcppExports.R' 'bayou-utilities.R' 'probability.R'
'bayou-weight_matrix.R' 'bayou-moves.R' 'bayou-likelihood.R'
'bayou-prior.R' 'conversion-utilities.R'
'bayou-mcmc-utilities.R' 'bayou-mcmc.R' 'bayou-plotting.R'
'bayou-simulation.r' 'bayou-steppingstone.R' 'bayou-package.R'
NeedsCompilation: yes
Packaged: 2015-10-17 14:40:06 UTC; josef
Repository: CRAN
Date/Publication: 2015-10-25 08:55:52
Install log
* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'bayou' ...
** package 'bayou' successfully unpacked and MD5 sums checked
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppArmadillo/include" -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppArmadillo/include" -fpic -g -O2 -c branches.cpp -o branches.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppArmadillo/include" -fpic -g -O2 -c threepoint.cpp -o threepoint.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppArmadillo/include" -fpic -g -O2 -c weightmatrix.cpp -o weightmatrix.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o bayou.so RcppExports.o branches.o threepoint.o weightmatrix.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/bayou/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'bayou'
finding HTML links ... done
Lposterior html
OU.lik html
OU.repar html
OUphenogram html
OUwie2bayou html
QG.alpha html
QG.sig2 html
bayou-package html
bayou.lik html
bayou.mcmc html
bayou2OUwie html
cdpois html
combine.chains html
dataSim html
dhalfcauchy html
dloc html
dsb html
gelman.R html
identifyBranches html
load.bayou html
make.powerposteriorFn html
make.prior html
make.refFn html
makeTransparent html
overparameterize.startingPoint html
parmap.W html
pars2simmap html
phenogram.density html
plot.bayouMCMC html
plot.ssMCMC html
plotBayoupars html
plotRegimes html
plotSimmap.mcmc html
print.bayouFit html
print.priorFn html
print.refFn html
print.ssMCMC html
priorSim html
pull.pars html
regime.plot html
set.burnin html
simmap.W html
steppingstone html
summary.bayouMCMC html
** building package indices
** testing if installed package can be loaded
* DONE (bayou)
Making 'packages.html' ... done
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