Suggests: covr, knitr, rmarkdown, testthat,

Title: Hybrid Trait Evolution under Brownian Motion
Author: Dwueng-Chwuan Jhwueng <djhwueng@umail.iu.edu> and Brian O'Meara
Imports: corpcor, numDeriv, geiger, ape, TreeSim, phytools, phylobase,
mvtnorm, grDevices, graphics, methods, stats, lhs, viridis,
Description: Analyzes the phenotypic evolution of species
of hybrid origin on a phylogenetic network. This package can detect the hybrid
vigor effect, a burst of variation at formation, and the relative portion of
heritability from its parents. Parameters are estimated by maximum likelihood.
Users need to enter a comparative data set, a phylogeny, and information on gene
flow leading to hybrids. See Jhwueng and O'Meara (2017)

Title: Comparative Methods for Phylogenetic Networks
Authors@R: c(person("Dwueng-Chwuan", "Jhwueng", role = c("aut", "cre"),
person("Brian C.", "O'Meara", role = c("aut"),
Imports: corpcor, numDeriv, geiger, ape, TreeSim, mvtnorm, methods,
lhs, viridis, Matrix, DEoptim, igraph, MASS, grDevices,
ggplot2, cowplot, graphics, stats, metR, parallel, phytools,
Description: Analyze the phenotypic evolution of species
of hybrid origin on a phylogenetic network. This can detect a burst of variation
at the formation of a hybrid as well as an increase or decrease in trait
value at a hybridization event. Parameters are estimated by maximum
likelihood, and model averaging can be done automatically. Users need to
enter a comparative data set and a phylogenetic network.
Author: Dwueng-Chwuan Jhwueng [aut, cre],

Description: The BMhyd package analyzes the phenotypic evolution of species of hybrid origin on a phylogenetic network. This package can detect the hybrid vigor effect, a burst of variation at formation, and the relative portion of heritability from its parents. Parameters are estimated by maximum likelihood technique. Users need to enter comparative data set and phylogenetic networks in eNewick format. The full model contains five parameters: the overall mean, the overall variance, the hybrid vigor, the hybrid variation and the proportion of heritability. We report four different models. All fix the heritability to equal contributions from each parent. Model 1 fixes the hybrid vigor and burst of variation at formation at 1 and 0; respectively. Model 2 fixes the hybrid vigor at 1 but allow the burst of variation at formation to vary; model 3 allows hybrid vigor to vary but fixes burst of variation at origin; and model 4 allows both to vary. Those models are compared under sample size correction Akaike Information Criterion (AICc). The model averaged parameter estimates are reported.