# Export all names
# exportPattern(".")

# S3 methods
S3method(plot, clustered_phylo)

# exported functions
export(BrownianMotionModel,drawPhylProcess,estimate.evolutionary.model,fitch.mvsl,generate.model.setups,mvslouchModel,ouchModel,parametric.bootstrap,phyltree_paths,plot.clustered_phylo,simulate_clustered_phylogeny,simulBMProcPhylTree,simulMVSLOUCHProcPhylTree,simulOUCHProcPhylTree,SummarizeBM,SummarizeMVSLOUCH,SummarizeOUCH)

# exported classes
exportClasses("clustered_phylo")

# Import all packages listed as Imports or Depends
importFrom(mvtnorm, rmvnorm)
importFrom(ape, rtree, node.depth.edgelength, drop.tip, plot.phylo)
importFrom(ouch, ape2ouch)
importFrom(stats, cov, cov2cor, lm, nlminb, optim, qnorm, qt, rexp, rnorm, runif)
importFrom(graphics, abline, legend, mtext, par, plot, points)
importFrom(PCMBase, PCM, PCMParamCount ,PCMCreateLikelihood, PCMLik, PCMParamLoadOrStore, PCMOptions)
importFrom("methods", "as")
importFrom(matrixcalc, is.diagonal.matrix, is.positive.semi.definite, is.singular.matrix, is.symmetric.matrix)
importFrom(Matrix,nearPD)
importFrom(abind, abind)
importFrom(TreeSim, sim.bd.taxa)






