Creates a variance-covariance matrix for a network and parameters.
ComputeVCV(phy.graph, sigma.sq = 1, mu = 0, bt = 1, vh = 0, SE = 0, measurement.error = 0, gamma = 0.5)
| phy.graph | An ape::evonet object (a phylogeny stored in phylo format that also includes a reticulation matrix) |
|---|---|
| sigma.sq | Value for sigma squared |
| mu | Value for state at the root |
| bt | Value for beta parameter |
| vh | Value for Vh, the variance that comes from a hybridization event |
| SE | Standard error |
| measurement.error | How much uncertainty there is in tip values; a single number is applied to all taxa, a vector is applied to the corresponding taxa |
| gamma | In a hybridization event, what proportion of the trait comes from the donating parent. 0.5 means half comes from each parent |
Returns the variance-covariance matrix