DESCRIPTION

Package: phyloGLM
Type: Package
Title: Tests for signals of variable rates of evolution between gene classes and lineages for probabalistic alleles
Version: 0.93.1
Date: 2018-08-16
Author: Noah Dukler
Maintainer: Noah Dukler <ndukler@cshl.edu>
Description: One paragraph description of what the package does as one or more full sentences.
License: GPL (>= 2)
biocViews:
Remotes: bioc::release/ggtree
Imports: Rcpp (>= 1.0.0),
         RcppArmadillo,
         rlang,
         data.table,
         ape,
         methods,
         numDeriv,
         cowplot,
         ggplot2
LinkingTo: Rcpp,
           RcppArmadillo
RcppModules: paramIndex,
             phylogeny
Suggests: 
    testthat,
    knitr,
    rmarkdown,
    randomcoloR
Encoding: UTF-8
RoxygenNote: 6.1.1
Collate: 
    'RcppExports.R'
    'stlMatrix-class.R'
    'alleleDataValidityCheck.R'
    'alleleData-class.R'
    'rateModelValidityCheck.R'
    'rateModel-class.R'
    'bic.R'
    'copy.R'
    'disCharToProb.R'
    'fit.R'
    'forceParameterZero.R'
    'getAlleleData.R'
    'getEdgeTable.R'
    'getParams.R'
    'getSiblings.R'
    'getSiteInfo.R'
    'getTree.R'
    'lrt.R'
    'marginal.R'
    'pack.R'
    'package.R'
    'phyloGrad.R'
    'phyloHess.R'
    'pi.R'
    'plotElementTransitions.R'
    'plotParams.R'
    'plotTree.R'
    'predict.R'
    'rateBounds.R'
    'rates.R'
    'rcppModules.R'
    'readPAF.R'
    'scaledLL.R'
    'se.R'
    'setFixed.R'
    'setParams.R'
    'show.R'
    'simulateSites.R'
    'siteLL.R'
    'updateFormula.R'
VignetteBuilder: knitr